diff --git a/.Rbuildignore b/.Rbuildignore
index 5c7dbad65f33379850f6c86bc7b0c8cde6549c57..708610f47beec04f16f9dfe7f49791ded3b7bfb9 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@
^index\.md$
^_pkgdown\.yml$
^pkgdown$
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
index c141603ff53809e900bb7dc49ab0e47884c6838f..c0399849fba9b381c6fbd18b712e68c9df48ee87 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,3 +26,5 @@ vignettes/*.pdf
*.knit.md
.Rproj.user
inst/doc
+doc
+Meta
diff --git a/DESCRIPTION b/DESCRIPTION
index badf1f30e9ff77e3fd2b90ed65fd966ff7efb2cb..05b3a97a59b9cbd433fb08be1a05c1edd25a7574 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,9 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.7.2
-Date: 2018-12-06
-Author: Luke Zappia
+Version: 1.9.8
+Date: 2019-10-11
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
email = "luke.zappia@mcri.edu.au",
@@ -14,7 +13,6 @@ Authors@R:
person("Alicia", "Oshlack", role = c("aut"),
email = "alicia.oshlack@mcri.edu.au",
comment = c(ORCID = "0000-0001-9788-5690")))
-Maintainer: Luke Zappia <luke.zappia@mcri.edu.au>
Description: Splatter is a package for the simulation of single-cell RNA
sequencing count data. It provides a simple interface for creating complex
simulations that are reproducible and well-documented. Parameters can be
@@ -23,7 +21,7 @@ Description: Splatter is a package for the simulation of single-cell RNA
License: GPL-3 + file LICENSE
LazyData: TRUE
Depends:
- R (>= 3.4),
+ R (>= 3.6),
SingleCellExperiment
Imports:
akima,
@@ -37,11 +35,13 @@ Imports:
matrixStats,
methods,
scales,
- scater (>= 1.7.4),
+ scater (>= 1.13.11),
stats,
SummarizedExperiment,
utils,
- crayon
+ crayon,
+ S4Vectors,
+ rlang
Suggests:
BiocStyle,
covr,
@@ -53,15 +53,17 @@ Suggests:
pscl,
testthat,
rmarkdown,
- S4Vectors,
scDD,
scran,
mfa,
phenopath,
- BASiCS,
+ BASiCS (>= 1.7.10),
zinbwave,
SparseDC,
- BiocManager
+ BiocManager,
+ spelling,
+ igraph,
+ DropletUtils
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
@@ -69,3 +71,4 @@ BugReports: https://github.com/Oshlack/splatter/issues
RoxygenNote: 6.1.1
Encoding: UTF-8
VignetteBuilder: knitr
+Language: en-GB
diff --git a/NAMESPACE b/NAMESPACE
index b0706b9b162d1b10ebd0e493b7b0c82ca2fc3bdb..b598fdb63acf174b7ea7e6db3bd7b8c835306d7c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,8 @@
S3method(BASiCSEstimate,SingleCellExperiment)
S3method(BASiCSEstimate,matrix)
+S3method(kersplatEstimate,SingleCellExperiment)
+S3method(kersplatEstimate,matrix)
S3method(lun2Estimate,SingleCellExperiment)
S3method(lun2Estimate,matrix)
S3method(lunEstimate,SingleCellExperiment)
@@ -28,6 +30,10 @@ export(compareSCEs)
export(diffSCEs)
export(getParam)
export(getParams)
+export(kersplatEstimate)
+export(kersplatSample)
+export(kersplatSetup)
+export(kersplatSimulate)
export(listSims)
export(lun2Estimate)
export(lun2Simulate)
@@ -39,6 +45,7 @@ export(makeOverallPanel)
export(mfaEstimate)
export(mfaSimulate)
export(newBASiCSParams)
+export(newKersplatParams)
export(newLun2Params)
export(newLunParams)
export(newMFAParams)
@@ -67,6 +74,7 @@ export(summariseDiff)
export(zinbEstimate)
export(zinbSimulate)
exportClasses(BASiCSParams)
+exportClasses(KersplatParams)
exportClasses(Lun2Params)
exportClasses(LunParams)
exportClasses(MFAParams)
@@ -78,8 +86,11 @@ exportClasses(SplatParams)
exportClasses(ZINBParams)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
+importFrom(S4Vectors,"metadata<-")
+importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"cpm<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SingleCellExperiment,cpm)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
@@ -96,15 +107,20 @@ importFrom(checkmate,checkIntegerish)
importFrom(checkmate,checkNumber)
importFrom(checkmate,checkNumeric)
importFrom(ggplot2,aes_string)
+importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
+importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_fill_distiller)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
@@ -117,11 +133,19 @@ importFrom(locfit,locfit)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
+importFrom(methods,is)
importFrom(methods,new)
+importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
+importFrom(stats,aggregate)
+importFrom(stats,approxfun)
+importFrom(stats,cor)
+importFrom(stats,dbeta)
+importFrom(stats,density)
importFrom(stats,dnbinom)
+importFrom(stats,ks.test)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
diff --git a/NEWS.md b/NEWS.md
index 7d08f770935a5ddca6747a6efd1c58316b6199a6..3984e30823bd40bab2fd90189eb66e635899c978 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,164 @@
+# DEVELOPMENT VERSION
+
+## Version 1.9.8 (2019-10-11)
+
+* Add Kersplat simulation! Still experimental but is useable.
+* Check for counts assay when estimating from SingleCellExperiment objects
+ (Fixes #82)
+* Fix where simpleSimulate stores parameters (Fixes #72)
+
+### Version 1.9.7.9019 (2019-10-11)
+
+* Run checks
+
+### Version 1.9.7.9018 (2019-10-10)
+
+* Document Splotch estimation functions
+* Add Splotch to listSims
+* Rename Splotch to Kersplat
+
+### Version 1.9.7.9017 (2019-10-09)
+
+* Document Splotch simulation functions
+
+### Version 1.9.7.9016 (2019-10-01)
+
+* Change the default SplotchParams cell design to place cells at end of path
+* Add one time warning for Splotch simulation
+* Avoid unnecessarily resetting cells.design in SplotchParams
+
+### Version 1.9.7.9015 (2019-09-26)
+
+* Add doublets to splotchSimulate
+
+### Version 1.9.7.9014 (2019-09-24)
+
+* Add ambient expression and empty cells to splotchSimulate
+
+### Version 1.9.7.9013 (2019-09-19)
+
+* Merge master into splotch branch
+
+## Version 1.9.7 (2019-09-19)
+
+* Rescale when sampling Phi in BASiCSSimulate
+
+## Version 1.9.6 (2019-09-17)
+
+* Adjust BASiCSSimulate to match development version of BASiCS
+
+### Version 1.9.5.9012 (2019-09-09)
+
+* Merge master into splotch branch
+
+## Version 1.9.5 (2019-09-09)
+
+* Fix bug in NAMESPACE
+
+### Version 1.9.4.9011 (2019-08-29)
+
+* Add BCV adjustment to Splotch simulation
+* Use new exponential correction for bcv.common
+
+### Version 1.9.4.9010 (2019-08-22)
+
+* Add density sampling options for means and library sizes
+
+### Version 1.9.4.9009 (2019-08-21)
+
+* Replace library size log-normal with density and rejection sampling
+* Add violins to comparison plots
+
+### Version 1.9.4.9008 (2019-08-20)
+
+* Merge master into splotch branch
+* Fix dataset in splotchEstimate example
+
+## Version 1.9.4 (2019-08-20)
+
+* Fix deprecated column name in diffSCEs QQ plots
+* Fix bugs where parameters were not being passed correctly in BASiCSEstimate
+ and sparseDCEstimate
+* Replace the sc_example_counts dataset from scater with the mockSCE function
+* Tidy and improve estimation function examples
+
+### Version 1.9.3.9008 (2019-08-20)
+
+* Add expression outliers to Splotch
+
+### Version 1.9.3.9007 (2019-08-14)
+
+* Fix bug in selectFit
+
+### Version 1.9.3.9006 (2019-08-13)
+
+* Add splotchEstimate function
+
+### Version 1.9.3.9005 (2019-08-08)
+
+* Simulate counts in splotchSimulate
+* Split splotchSimulate into separate functions for each stage
+
+### Version 1.9.3.9004 (2019-08-08)
+
+* Merge master into splotch branch
+
+## Version 1.9.3 (2019-08-08)
+
+* Remove deprecated scater functions
+
+### Version 1.9.2.9003 (2019-07-17)
+
+* Topologically sort Splotch paths
+* Add library size parameters to SplotchParams
+* Simulate cell means in splotchSimulate
+
+### Version 1.9.2.9002 (2019-07-16)
+
+* Add paths parameters to SplotchParams
+
+### Version 1.9.2.9001 (2019-07-16)
+
+* Add mean parameters to SplotchParams
+
+### Version 1.9.2.9000 (2019-07-11)
+
+* Add SplotchParams object
+
+## Version 1.9.2 (2019-06-13)
+
+* Add variable gene correlation plot to compareSCEs
+
+## Version 1.9.1 (2019-06-05)
+
+* Refactor the summariseDiff function
+* Add the KS statistic to summariseDiff
+* Set gam method for fitted lines in comparison plots
+* Add checks for suggested packages in examples
+
+## Version 1.9.0 (2019-05-03)
+
+* Bioconductor 3.10 devel
+
+# Version 1.8.0 (2019-05-03)
+
+* Bioconductor 3.9 release
+
+## Version 1.7.5 (2018-04-18)
+
+* Add Splat parameters vignette
+* Fix spelling
+
+## Version 1.7.4 (2018-04-17)
+
+* Allow SplatParams parameters to be set in any order
+
+## Version 1.7.3 (2018-04-15)
+
+* Minor changes to documentation
+* Protect against integer overflow in simulation functions
+* Fix order of groups in splatSimulate
+
## Version 1.7.2 (2018-12-06)
* Add ImmunoOncology biocViews tag at request of Bioconductor team
@@ -8,7 +169,7 @@
## Version 1.7.0 (2018-11-01)
- * Bioconductor 3.9 devel
+* Bioconductor 3.9 devel
## Version 1.6.1 (2018-12-06)
@@ -43,7 +204,7 @@
* Fix bug in getLNormFactors when reversing factors less than one
* Update documentation to new Roxygen version (6.1.0)
-* Change varible name in vignette for compatibility with scater
+* Change variable name in vignette for compatibility with scater
* Add suggested package checks to tests
## Version 1.5.1 (2018-06-12)
@@ -216,7 +377,7 @@
## Version 0.99.13 (2017-03-25)
-* Modify how Lun2Params stores gene paramters to use data.frame
+* Modify how Lun2Params stores gene parameters to use data.frame
* Move sampling of genes/cells to lun2Simulate
* Return to old Lun2 nGenes estimate
@@ -226,7 +387,7 @@
* Update compareSCESets plots
* Modify Lun2 nGenes estimate
* Modify how addFeatureStats names columns
-* Add infinte bcv.df warning to splatSimulate
+* Add infinite bcv.df warning to splatSimulate
## Version 0.99.11 (2017-03-20)
@@ -328,7 +489,7 @@
* Redesign how parameters are stored
* Each simulation now has it's own S4 Params class
-* Modify exisiting simulations to use new parameter objects
+* Modify existing simulations to use new parameter objects
## Version 0.6.0 (2016-10-12)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index dff138aced34f648538eb44a98320cf5714bb1de..bc1ce616d0d6b50cebd6e7947bac2be5721df7d1 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -23,7 +23,7 @@ setClass("Params",
nCells = "numeric",
seed = "numeric"),
prototype = prototype(nGenes = 10000, nCells = 100,
- seed = sample(1:1e6, 1)))
+ seed = sample(seq_len(1e6), 1)))
#' The SimpleParams class
#'
@@ -63,11 +63,11 @@ setClass("SimpleParams",
#' The SplatParams class
#'
-#' S4 class that holds parameters for the Splatter simulation.
+#' S4 class that holds parameters for the Splat simulation.
#'
#' @section Parameters:
#'
-#' The Splatter simulation requires the following parameters:
+#' The Splat simulation requires the following parameters:
#'
#' \describe{
#' \item{\code{nGenes}}{The number of genes to simulate.}
@@ -126,7 +126,7 @@ setClass("SimpleParams",
#' \describe{
#' \item{\code{[de.prob]}}{Probability that a gene is differentially
#' expressed in a group. Can be a vector.}
-#' \item{\code{[de.loProb]}}{Probability that a differentially
+#' \item{\code{[de.downProb]}}{Probability that a differentially
#' expressed gene is down-regulated. Can be a vector.}
#' \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
#' differential expression factor log-normal distribution. Can be a
@@ -167,9 +167,10 @@ setClass("SimpleParams",
#' this form would have a "from" parameter of c(0, 1, 1) (where 0 is
#' the origin). If no vector is given all paths will start at the
#' origin.}
-#' \item{\code{[path.length]}}{Vector giving the number of steps to
+#' \item{\code{[path.nSteps]}}{Vector giving the number of steps to
#' simulate along each path. If a single value is given it will be
-#' applied to all paths.}
+#' applied to all paths. This parameter was previously called
+#' \code{path.length}.}
#' \item{\code{[path.skew]}}{Vector giving the skew of each path.
#' Values closer to 1 will give more cells towards the starting
#' population, values closer to 0 will give more cells towards the
@@ -188,7 +189,7 @@ setClass("SimpleParams",
#' }
#'
#' The parameters not shown in brackets can be estimated from real data using
-#' \code{\link{splatEstimate}}. For details of the Splatter simulation
+#' \code{\link{splatEstimate}}. For details of the Splat simulation
#' see \code{\link{splatSimulate}}.
#'
#' @name SplatParams
@@ -221,7 +222,7 @@ setClass("SplatParams",
dropout.mid = "numeric",
dropout.shape = "numeric",
path.from = "numeric",
- path.length = "numeric",
+ path.nSteps = "numeric",
path.skew = "numeric",
path.nonlinearProb = "numeric",
path.sigmaFac = "numeric"),
@@ -249,11 +250,173 @@ setClass("SplatParams",
dropout.mid = 0,
dropout.shape = -1,
path.from = 0,
- path.length = 100,
+ path.nSteps = 100,
path.skew = 0.5,
path.nonlinearProb = 0.1,
path.sigmaFac = 0.8))
+#' The KersplatParams class
+#'
+#' S4 class that holds parameters for the Kersplat simulation.
+#'
+#' @section Parameters:
+#'
+#' The Kersplat simulation uses the following parameters:
+#'
+#' \describe{
+#' \item{\code{nGenes}}{The number of genes to simulate.}
+#' \item{\code{nCells}}{The number of cells to simulate.}
+#' \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#' \item{\emph{Mean parameters}}{
+#' \describe{
+#' \item{\code{mean.shape}}{Shape parameter for the mean gamma
+#' distribution.}
+#' \item{\code{mean.rate}}{Rate parameter for the mean gamma
+#' distribution.}
+#' \item{\code{mean.outProb}}{Probability that a gene is an
+#' expression outlier.}
+#' \item{\code{mean.outFacLoc}}{Location (meanlog) parameter for
+#' the expression outlier factor log-normal distribution.}
+#' \item{\code{mean.outFacScale}}{Scale (sdlog) parameter for the
+#' expression outlier factor log-normal distribution.}
+#' \item{\code{mean.dens}}{\code{\link{density}} object describing
+#' the log gene mean density.}
+#' \item{\code{[mean.method]}}{Method to use for simulating gene
+#' means. Either "fit" to sample from a gamma distribution (with
+#' expression outliers) or "density" to sample from the provided
+#' density object.}
+#' \item{\code{[mean.values]}}{Vector of means for each gene.}
+#' }
+#' }
+#' \item{\emph{Biological Coefficient of Variation parameters}}{
+#' \describe{
+#' \item{\code{bcv.common}}{Underlying common dispersion across all
+#' genes.}
+#' \item{\code{[bcv.df]}}{Degrees of Freedom for the BCV inverse
+#' chi-squared distribution.}
+#' }
+#' }
+#' \item{\emph{Network parameters}}{
+#' \describe{
+#' \item{\code{[network.graph]}}{Graph containing the gene network.}
+#' \item{\code{[network.nRegs]}}{Number of regulators in the
+#' network.}
+#' }
+#' }
+#' \item{\emph{Paths parameters}}{
+#' \describe{
+#' \item{\code{[paths.programs]}}{Number of expression programs.}
+#' \item{\code{[paths.design]}}{data.frame describing path
+#' structure. See \code{\link{kersplatSimPaths}} for details.}
+#' }
+#' }
+#' \item{\emph{Library size parameters}}{
+#' \describe{
+#' \item{\code{lib.loc}}{Location (meanlog) parameter for the
+#' library size log-normal distribution, or mean parameter if a
+#' normal distribution is used.}
+#' \item{\code{lib.scale}}{Scale (sdlog) parameter for the library
+#' size log-normal distribution, or sd parameter if a normal
+#' distribution is used.}
+#' \item{\code{lib.dens}}{\code{\link{density}} object describing
+#' the library size density.}
+#' \item{\code{[lib.method]}}{Method to use for simulating library
+#' sizes. Either "fit" to sample from a log-normal distribution or
+#' "density" to sample from the provided density object.}
+#' }
+#' }
+#' \item{\emph{Design parameters}}{
+#' \describe{
+#' \item{\code{[cells.design]}}{data.frame describing cell
+#' structure. See \code{\link{kersplatSimCellMeans}} for details.}
+#' }
+#' }
+#' \item{\emph{Doublet parameters}}{
+#' \describe{
+#' \item{\code{[doublet.prop]}}{Proportion of cells that are
+#' doublets.}
+#' }
+#' }
+#' \item{\emph{Ambient parameters}}{
+#' \describe{
+#' \item{\code{[ambient.scale]}}{Scaling factor for the library
+#' size log-normal distribution when generating ambient library
+#' sizes.}
+#' \item{\code{[ambient.nEmpty]}}{Number of empty cells to
+#' simulate.}
+#' }
+#' }
+#' }
+#'
+#' The parameters not shown in brackets can be estimated from real data using
+#' \code{\link{kersplatEstimate}}. For details of the Kersplat simulation
+#' see \code{\link{kersplatSimulate}}.
+#'
+#' @name KersplatParams
+#' @rdname KersplatParams
+#' @aliases KersplatParams-class
+#' @exportClass KersplatParams
+setClass("KersplatParams",
+ contains = "Params",
+ slots = c(mean.shape = "numeric",
+ mean.rate = "numeric",
+ mean.outProb = "numeric",
+ mean.outLoc = "numeric",
+ mean.outScale = "numeric",
+ mean.dens = "density",
+ mean.method = "character",
+ mean.values = "numeric",
+ bcv.common = "numeric",
+ bcv.df = "numeric",
+ network.graph = "ANY",
+ network.nRegs = "numeric",
+ network.regsSet = "logical",
+ paths.nPrograms = "numeric",
+ paths.design = "data.frame",
+ paths.means = "list",
+ lib.loc = "numeric",
+ lib.scale = "numeric",
+ lib.dens = "density",
+ lib.method = "character",
+ cells.design = "data.frame",
+ doublet.prop = "numeric",
+ ambient.scale = "numeric",
+ ambient.nEmpty = "numeric"),
+ prototype = prototype(mean.rate = 0.3,
+ mean.shape = 0.6,
+ mean.outProb = 0.05,
+ mean.outLoc = 4,
+ mean.outScale = 0.5,
+ mean.dens = density(rgamma(10000, rate = 0.3,
+ shape = 0.6)),
+ mean.method = "fit",
+ mean.values = numeric(),
+ bcv.common = 0.1,
+ bcv.df = 60,
+ network.graph = NULL,
+ network.nRegs = 100,
+ network.regsSet = FALSE,
+ paths.nPrograms = 10,
+ paths.design = data.frame(
+ Path = 1,
+ From = 0,
+ Steps = 100
+ ),
+ paths.means = list(),
+ lib.loc = 11,
+ lib.scale = 0.2,
+ lib.dens = density(rlnorm(10000, 11, 0.2)),
+ lib.method = "fit",
+ cells.design = data.frame(
+ Path = 1,
+ Probability = 1,
+ Alpha = 1,
+ Beta = 0
+ ),
+ doublet.prop = 0,
+ ambient.scale = 0.05,
+ ambient.nEmpty = 0))
+
#' The LunParams class
#'
#' S4 class that holds parameters for the Lun simulation.
@@ -331,10 +494,10 @@ setClass("LunParams",
#' \item{\emph{Gene parameters}}{
#' \describe{
#' \item{\code{gene.params}}{A \code{data.frame} containing gene
-#' parameters with two coloumns: \code{Mean} (mean expression for
+#' parameters with two columns: \code{Mean} (mean expression for
#' each gene) and \code{Disp} (dispersion for each gene).}
#' \item{\code{zi.params}}{A \code{data.frame} containing
-#' zero-inflated gene parameters with three coloumns: \code{Mean}
+#' zero-inflated gene parameters with three columns: \code{Mean}
#' (mean expression for each gene), \code{Disp} (dispersion for
#' each, gene), and \code{Prop} (zero proportion for each gene).}
#' }
@@ -342,7 +505,7 @@ setClass("LunParams",
#' \item{\code{[nPlates]}}{The number of plates to simulate.}
#' \item{\emph{Plate parameters}}{
#' \describe{
-#' \item{\code{plate.ingroup}}{Character vecotor giving the plates
+#' \item{\code{plate.ingroup}}{Character vector giving the plates
#' considered to be part of the "ingroup".}
#' \item{\code{plate.mod}}{Plate effect modifier factor. The plate
#' effect variance is divided by this value.}
@@ -491,7 +654,7 @@ setClass("SCDDParams",
#' \item{\emph{Gene parameters}}{
#' \describe{
#' \item{\code{gene.params}}{A \code{data.frame} containing gene
-#' parameters with two coloumns: \code{Mean} (mean expression for
+#' parameters with two columns: \code{Mean} (mean expression for
#' each biological gene) and \code{Delta} (cell-to-cell
#' heterogeneity for each biological gene).}
#' }
@@ -505,7 +668,7 @@ setClass("SCDDParams",
#' \item{\emph{Cell parameters}}{
#' \describe{
#' \item{\code{cell.params}}{A \code{data.frame} containing gene
-#' parameters with two coloumns: \code{Phi} (mRNA content factor for
+#' parameters with two columns: \code{Phi} (mRNA content factor for
#' each cell, scaled to sum to the number of cells in each batch)
#' and \code{S} (capture efficient for each cell).}
#' }
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 10444230061b6c27e36f9ae1b67b0756a3e61e0b..4c8d46c004c713bdb19beca478df29bf01f832ed 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -36,7 +36,7 @@ setGeneric("getParam", function(object, name) {standardGeneric("getParam")})
#'
#' @param object object to set parameter in.
#' @param name name of the parameter to set.
-#' @param value value to set the paramter to.
+#' @param value value to set the parameter to.
#'
#' @return Object with new parameter value.
#'
@@ -46,9 +46,8 @@ setGeneric("getParam", function(object, name) {standardGeneric("getParam")})
#'
#' @rdname setParam
#' @export
-setGeneric("setParam",
- function(object, name, value) {
- standardGeneric("setParam")
+setGeneric("setParam", function(object, name, value) {
+ standardGeneric("setParam")
})
#' Set a parameter UNCHECKED
@@ -58,15 +57,49 @@ setGeneric("setParam",
#'
#' @param object object to set parameter in.
#' @param name name of the parameter to set.
-#' @param value value to set the paramter to.
+#' @param value value to set the parameter to.
#'
#' @return Object with new parameter value.
#'
#' @rdname setParamUnchecked
-setGeneric("setParamUnchecked",
- function(object, name, value) {
- standardGeneric("setParamUnchecked")
- })
+setGeneric("setParamUnchecked", function(object, name, value) {
+ standardGeneric("setParamUnchecked")
+})
+
+#' Set parameters
+#'
+#' Set multiple parameters in a Params object.
+#'
+#' @param object Params object to set parameters in.
+#' @param update list of parameters to set where \code{names(update)} are the
+#' names of the parameters to set and the items in the list are values.
+#' @param ... additional parameters to set. These are combined with any
+#' parameters specified in \code{update}.
+#'
+#' @details
+#' Each parameter is set by a call to \code{\link{setParam}}. If the same
+#' parameter is specified multiple times it will be set multiple times.
+#' Parameters can be specified using a list via \code{update} (useful when
+#' collecting parameter values in some way) or individually (useful when setting
+#' them manually), see examples.
+#'
+#' @return Params object with updated values.
+#'
+#' @examples
+#' params <- newSimpleParams()
+#' params
+#' # Set individually
+#' params <- setParams(params, nGenes = 1000, nCells = 50)
+#' params
+#' # Set via update list
+#' params <- setParams(params, list(mean.rate = 0.2, mean.shape = 0.8))
+#' params
+#'
+#' @rdname setParams
+#' @export
+setGeneric("setParams", function(object, update = NULL, ...) {
+ standardGeneric("setParams")
+})
#' Expand parameters
#'
@@ -81,4 +114,4 @@ setGeneric("setParamUnchecked",
#' @rdname expandParams
setGeneric("expandParams", function(object, ...) {
standardGeneric("expandParams")
-})
\ No newline at end of file
+})
diff --git a/R/BASiCS-estimate.R b/R/BASiCS-estimate.R
index f3148eda55932c2113611772f2a272329bfc5449..4375d64731cbc731fdacc29b1c2b4a7b57e227b8 100644
--- a/R/BASiCS-estimate.R
+++ b/R/BASiCS-estimate.R
@@ -35,13 +35,13 @@
#' \dontrun{
#' # Load example data
#' library(scater)
-#' data("sc_example_counts")
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
+#' spike.info <- data.frame(Name = rownames(sce)[1:10],
#' Input = rnorm(10, 500, 200),
#' stringsAsFactors = FALSE)
-#' params <- BASiCSEstimate(sc_example_counts[1:100, 1:30],
-#' spike.info)
+#' params <- BASiCSEstimate(sce[1:100, 1:30], spike.info)
#' params
#' }
#' @export
@@ -62,8 +62,9 @@ BASiCSEstimate.SingleCellExperiment <- function(counts, spike.info = NULL,
params = newBASiCSParams(),
verbose = TRUE, progress = TRUE,
...) {
- counts <- BiocGenerics::counts(counts)
- BASiCSEstimate(counts, params)
+ counts <- getCounts(counts)
+ BASiCSEstimate(counts, spike.info, batch, n, thin, burn, regression,
+ params, verbose, progress, ...)
}
#' @rdname BASiCSEstimate
diff --git a/R/BASiCS-simulate.R b/R/BASiCS-simulate.R
index 66cc4242aa349b2c58d62fe6ffd0c6b1a88f33ef..2b5ab176af7ef79a0a7cbc05b2e796c4e4396313 100644
--- a/R/BASiCS-simulate.R
+++ b/R/BASiCS-simulate.R
@@ -18,14 +18,16 @@
#'
#' @references
#' Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
-#' Single-Cell Sequencing data. PLoS Comput. Biol. (2015).
+#' Single-Cell Sequencing data. PLoS Computational Biology (2015).
#'
#' Paper: \url{10.1371/journal.pcbi.1004333}
#'
#' Code: \url{https://github.com/catavallejos/BASiCS}
#'
#' @examples
-#' sim <- BASiCSSimulate()
+#' if (requireNamespace("BASiCS", quietly = TRUE)) {
+#' sim <- BASiCSSimulate()
+#' }
#' @export
BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
@@ -46,6 +48,10 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
batch.cells <- getParam(params, "batchCells")
gene.params <- getParam(params, "gene.params")
+ if (nSpikes == 0 && nBatches == 1) {
+ stop("If there are no spikes there must be multiple batches")
+ }
+
# Sample gene.params if necessary
if (nrow(gene.params) != nGenes) {
warning("Number of gene.params not equal to nGenes, ",
@@ -57,17 +63,18 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
mu <- gene.params$Mean
delta <- gene.params$Delta
- if (nSpikes > 0) {
+ has.spikes <- nSpikes > 0
+ spike.mu <- NULL
+ if (has.spikes) {
spike.mu <- getParam(params, "spike.means")
if (length(spike.mu) != nSpikes) {
warning("Number of spike-in means not equal to nSpikes, ",
"spike.means will be sampled.")
selected <- sample(length(spike.mu), nSpikes, replace = TRUE)
spike.mu <- spike.mu[selected]
+
+ params <- setParam(params, "spike.mu", spike.mu)
}
- } else {
- # Create dummy spike-ins to get around BASiCS_Sim...
- spike.mu <- c(10, 10)
}
cell.params <- getParam(params, "cell.params")
@@ -76,6 +83,10 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
"cell.params will be sampled.")
selected <- sample(nrow(cell.params), nCells, replace = TRUE)
cell.params <- cell.params[selected, ]
+
+ cell.params$Phi <- (cell.params$Phi / sum(cell.params$Phi)) * nCells
+
+ params <- setParam(params, "cell.params", cell.params)
}
thetas <- getParam(params, "theta")
@@ -85,31 +96,32 @@ BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
batches <- unlist(batches)
if (verbose) {message("Simulating counts with BASiCS...")}
- counts.list <- list()
- for (batch in seq_len(nBatches)) {
- batch.cells <- batches == batch
- phi <- cell.params[batch.cells, "Phi"]
- phi <- (phi / sum(phi)) * sum(batch.cells)
- s <- cell.params[batch.cells, "S"]
- theta <- thetas[batch]
+ if (has.spikes) {
+ BASiCS.sim <- suppressMessages(
+ BASiCS::BASiCS_Sim(Mu = mu, Mu_spikes = spike.mu, Delta = delta,
+ Phi = cell.params$Phi, S = cell.params$S,
+ Theta = thetas, BatchInfo = batches)
+ )
+ counts <- SingleCellExperiment::counts(BASiCS.sim)
+ spike.counts <- SummarizedExperiment::assay(
+ SingleCellExperiment::altExp(BASiCS.sim)
+ )
+ counts <- rbind(counts, spike.counts)
+ } else {
+ if (verbose) {message("Simulating without spikes")}
BASiCS.sim <- suppressMessages(
- BASiCS::BASiCS_Sim(mu, spike.mu, delta, phi, s, theta)
- )
- batch.counts <- SummarizedExperiment::assay(BASiCS.sim)
- counts.list[[batch]] <- batch.counts
+ BASiCS::BASiCS_Sim(Mu = mu, Mu_spikes = NULL, Delta = delta,
+ Phi = NULL, S = cell.params$S,
+ Theta = thetas, BatchInfo = batches)
+ )
+ counts <- SingleCellExperiment::counts(BASiCS.sim)
}
- counts <- do.call(cbind, counts.list)
-
if (verbose) {message("Creating final dataset...")}
cell.names <- paste0("Cell", seq_len(nCells))
gene.names <- paste0("Gene", seq_len(nGenes))
- if (nSpikes > 0) {
+ if (has.spikes) {
gene.names <- c(gene.names, paste0("Spike", seq_len(nSpikes)))
- } else {
- # Remove dummy spikes
- counts <- counts[1:(nrow(counts) - 2), ]
- spike.mu <- numeric()
}
rownames(counts) <- gene.names
diff --git a/R/KersplatParams-methods.R b/R/KersplatParams-methods.R
new file mode 100644
index 0000000000000000000000000000000000000000..936e0661644f7a9e3a1c98455e295568a5b27e5c
--- /dev/null
+++ b/R/KersplatParams-methods.R
@@ -0,0 +1,305 @@
+#' @rdname newParams
+#' @importFrom methods new
+#' @export
+newKersplatParams <- function(...) {
+
+ if (!requireNamespace("igraph", quietly = TRUE)) {
+ stop("The Kersplat simulation requires the 'igraph' package.")
+ }
+
+ if (!requireNamespace("DropletUtils", quietly = TRUE)) {
+ stop("The Kersplat simulation requires the 'DropletUtils' package.")
+ }
+
+ msg <- paste("The Kersplat simulation is still experimental and may",
+ "produce unreliable results. Please try it and report any",
+ "issues to",
+ "https://github.com/Oshlack/splatter/issues. The development",
+ "version may have improved features.")
+ rlang:::warn_deprecated(msg, id = "warn.kersplat")
+
+ params <- new("KersplatParams")
+ params <- setParams(params, ...)
+
+ return(params)
+}
+
+setValidity("KersplatParams", function(object) {
+
+ v <- getParams(object, slotNames(object))
+
+ checks <- c(nGenes = checkmate::checkInt(v$nGenes, lower = 1),
+ nCells = checkmate::checkInt(v$nCells, lower = 1),
+ seed = checkmate::checkInt(v$seed, lower = 0),
+ mean.rate = checkmate::checkNumber(v$mean.rate, lower = 0),
+ mean.shape = checkmate::checkNumber(v$mean.shape, lower = 0),
+ mean.outProb = checkNumber(v$mean.outProb, lower = 0,
+ upper = 1),
+ mean.outLoc = checkNumber(v$mean.outLoc),
+ mean.outScale = checkNumber(v$mean.outScale, lower = 0),
+ mean.dens = checkmate::checkClass(v$mean.dens, "density"),
+ mean.method = checkmate::checkChoice(v$mean.method,
+ c("fit", "density")),
+ bcv.common = checkNumber(v$bcv.common, lower = 0),
+ bcv.df = checkNumber(v$bcv.df, lower = 0),
+ network.graph = checkmate::checkClass(v$network, "igraph",
+ null.ok = TRUE),
+ network.nRegs = checkmate::checkInt(v$network.nRegs,
+ lower = 0),
+ network.regsSet = checkmate::checkFlag(v$network.regsSet),
+ paths.nPrograms = checkmate::checkInt(v$paths.nPrograms,
+ lower = 1),
+ paths.design = checkmate::checkDataFrame(v$paths.design,
+ types = "numeric",
+ any.missing = FALSE,
+ min.rows = 1,
+ ncols = 3),
+ lib.loc = checkmate::checkNumber(v$lib.loc),
+ lib.scale = checkmate::checkNumber(v$lib.scale, lower = 0),
+ lib.dens = checkmate::checkClass(v$lib.dens, "density"),
+ lib.method = checkmate::checkChoice(v$lib.method,
+ c("fit", "density")),
+ cells.design = checkmate::checkDataFrame(v$cells.design,
+ types = "numeric",
+ any.missing = FALSE,
+ nrows = nrow(
+ v$paths.design),
+ ncols = 4),
+ doublet.prop = checkmate::check_number(v$doublet.prop,
+ lower = 0,
+ upper = 1),
+ ambient.scale = checkmate::check_number(v$ambient.scale,
+ lower = 0,
+ upper = 1),
+ ambient.nEmpty = checkmate::check_number(v$ambient.nEmpty,
+ lower = 0,
+ finite = TRUE))
+
+ if (!checkmate::testNumeric(v$mean.values, len = 0)) {
+ checks <- c(checks,
+ mean.values = checkmate::checkNumeric(v$mean.values,
+ lower = 0,
+ finite = TRUE,
+ any.missing = FALSE,
+ len = v$nGenes))
+ }
+
+ if (!all(colnames(v$paths.design) == c("Path", "From", "Steps"))) {
+ checks <- c(checks, paths.design = "Incorrect column names")
+ } else {
+ if (!(0 %in% v$paths.design$From)) {
+ checks <- c(checks, paths.design = paste("origin must be specified",
+ "in paths.design"))
+ }
+
+ paths.graph <- igraph::graph_from_data_frame(v$paths.design)
+ if (!igraph::is_simple(paths.graph)) {
+ checks <- c(checks, paths.design = "graph is not simple")
+ }
+ if (!igraph::is_connected(paths.graph)) {
+ checks <- c(checks, paths.design = "graph is not connected")
+ }
+ if (!igraph::is_dag(paths.graph)) {
+ checks <- c(checks, paths.design = "graph is not a DAG")
+ }
+ }
+
+ if (!checkmate::testList(v$paths.means, len = 0)) {
+ checks <- c(checks,
+ paths.means = checkmate::checkList(v$paths.means,
+ types = "matrix",
+ any.missing = FALSE,
+ len = nrow(v$paths.design),
+ names = "unique"))
+ }
+
+ if (!all(colnames(v$cells.design) == c("Path", "Probability", "Alpha",
+ "Beta"))) {
+ checks <- c(checks, cells.design = "Incorrect column names")
+ } else {
+ if (!all(sort(v$cells.design$Path) == sort(v$paths.design$Path))) {
+ checks <- c(checks,
+ cells.design = "Path names don't match paths.design")
+ }
+ if (sum(v$cells.design$Probability) != 1) {
+ checks <- c(checks, cells.design = "Probability must sum to 1")
+ }
+ checks <- c(checks,
+ "cells.design$Alpha" = checkmate::checkNumeric(
+ v$cells.design$Alpha,
+ lower = 0, any.missing = FALSE))
+ checks <- c(checks,
+ "cells.design$Beta" = checkmate::checkNumeric(
+ v$cells.design$Beta,
+ lower = 0, any.missing = FALSE))
+ }
+
+ if (all(checks == TRUE)) {
+ valid <- TRUE
+ } else {
+ valid <- checks[checks != TRUE]
+ valid <- paste(names(valid), valid, sep = ": ")
+ }
+
+ return(valid)
+})
+
+#' @importFrom methods show
+setMethod("show", "KersplatParams", function(object) {
+
+ pp.top <- list("Mean:" = c("(Rate)" = "mean.rate",
+ "(Shape)" = "mean.shape",
+ "(Out Prob)" = "mean.outProb",
+ "(Out Location)" = "mean.outLoc",
+ "(Out Scale)" = "mean.outScale",
+ "(Density)" = "mean.dens",
+ "[Method]" = "mean.method",
+ "[Values]*" = "mean.values"),
+ "BCV:" = c("(Common Disp)" = "bcv.common",
+ "[DoF]" = "bcv.df"))
+
+ pp.network <- list("Network:" = c("[Graph]*" = "network.graph",
+ "[nRegs]" = "network.nRegs",
+ "[regsSet]*" = "network.regsSet"))
+
+ pp.paths <- list("Paths:" = c("[nPrograms]" = "paths.nPrograms",
+ "[Design]" = "paths.design"))
+
+ pp.bot <- list("Library size:" = c("(Location)" = "lib.loc",
+ "(Scale)" = "lib.scale",
+ "(Density)" = "lib.dens",
+ "[Method]" = "lib.method"),
+ "Cells:" = c("[Design]" = "cells.design"),
+ "Doublets:" = c("[Prop]" = "doublet.prop"),
+ "Ambient:" = c("[Scale]" = "ambient.scale",
+ "[Empty]" = "ambient.nEmpty"))
+
+ paths.means <- getParam(object, "paths.means")
+ if (length(paths.means) == 0) {
+ pp.paths[[1]] <- c(pp.paths[[1]], "[Means]*" = "paths.means")
+ }
+
+ callNextMethod()
+
+ showPP(object, pp.top)
+
+ network.graph <- getParam(object, "network.graph")
+ if (is.null(network.graph)) {
+ showPP(object, pp.network)
+ } else {
+ cat(crayon::bold("Network:"), "\n")
+ cat(crayon::bold(crayon::bgYellow(crayon::blue("[GRAPH]\n"))))
+ cat(crayon::bold(crayon::green(paste(
+ "Graph with", igraph::gorder(network.graph), "nodes and",
+ igraph::gsize(network.graph), "edges\n"
+ ))))
+ show(network.graph)
+ network.values <- list("[nRegs]" = getParam(object, "network.nRegs"),
+ "[regsSet]*" = getParam(object,
+ "network.regsSet"))
+ network.default <- c(network.values$`[nRegs]` != 100,
+ network.values$`[regsSet]` != FALSE)
+ showValues(network.values, network.default)
+ }
+
+ showPP(object, pp.paths)
+
+ if (length(paths.means) != 0) {
+ cat(crayon::bgYellow(crayon::bold(crayon::blue("[MEANS]\n"))))
+ cat(crayon::bold(crayon::green(paste(
+ "List of", length(paths.means), "matrices with names:",
+ paste(names(paths.means), collapse = ", "), "\n\n"
+ ))))
+ }
+
+ showPP(object, pp.bot)
+})
+
+#' @rdname setParam
+setMethod("setParam", "KersplatParams", function(object, name, value) {
+ checkmate::assertString(name)
+
+ if (name == "nGenes") {
+ if (!is.null(getParam(object, "network.graph"))) {
+ stop("nGenes can not be changed once network.graph is set")
+ }
+ if (!length(getParam(object, "mean.values")) == 0) {
+ stop("nGenes can not be changed once mean.values is set")
+ }
+ }
+
+ if (name == "mean.values") {
+ if (!is.null(getParam(object, "network.graph"))) {
+ if (length(value) != getParam(object, "nGenes")) {
+ stop("new mean.values does not match the number of genes in ",
+ "the network")
+ }
+ } else {
+ object <- setParam(object, "nGenes", length(value))
+ }
+ }
+
+ if (name == "network.graph") {
+ checkmate::assertClass(value, "igraph")
+ if (getParam(object, "nGenes") != igraph::gorder(value)) {
+ if (!(length(getParam(object, "mean.values")) == 0)) {
+ warning("changing network.graph resets mean.values")
+ object <- setParam(object, "mean.values", numeric())
+ }
+ object <- setParamUnchecked(object, "nGenes", igraph::gorder(value))
+ }
+
+ if ("IsReg" %in% igraph::vertex_attr_names(value)) {
+ isReg <- igraph::vertex_attr(value, "IsReg")
+ checkmate::assertLogical(isReg, any.missing = FALSE)
+ object <- setParamUnchecked(object, "network.nRegs", sum(isReg))
+ object <- setParamUnchecked(object, "network.regsSet", TRUE)
+ } else {
+ object <- setParamUnchecked(object, "network.regsSet", FALSE)
+ }
+ }
+
+ if (name == "network.nRegs" && getParam(object, "network.regsSet")) {
+ stop("network.nRegs can not be changed after regulators are set")
+ }
+
+ if (name == "network.regsSet") {
+ stop("network.regsSet can not be set manually")
+ }
+
+ if (name == "paths.design" &&
+ (nrow(value) != nrow(getParam(object, "cells.design")))) {
+ warning("cells.design reset to match paths.design")
+ cells.design <- data.frame(Path = value$Path,
+ Probability = 1 / nrow(value),
+ Alpha = 1, Beta = 0)
+ object <- setParamUnchecked(object, "cells.design", cells.design)
+ }
+
+ object <- callNextMethod()
+
+ return(object)
+})
+
+#' @rdname setParams
+setMethod("setParams", "KersplatParams", function(object, update = NULL, ...) {
+
+ checkmate::assertList(update, null.ok = TRUE)
+
+ update <- c(update, list(...))
+
+ # If both cells.design and paths.design are given set cells.design first
+ # to avoid reset warning
+ if ("cells.design" %in% names(update) &&
+ "paths.design" %in% names(update)) {
+ object <- setParamUnchecked(object, "cells.design",
+ update$cells.design)
+ update$cells.design <- NULL
+ }
+
+ update <- bringItemsForward(update, c("network.graph", "paths.design"))
+
+ object <- callNextMethod(object, update)
+
+ return(object)
+})
diff --git a/R/Params-methods.R b/R/Params-methods.R
index 8725919bee7523f1c3896e900836a206a954bd0f..6bb8a0005dae65e2981a66712cdfabe90ba9e5a6 100644
--- a/R/Params-methods.R
+++ b/R/Params-methods.R
@@ -21,6 +21,24 @@ setMethod("setParamUnchecked", "Params", function(object, name, value) {
return(object)
})
+#' @rdname setParams
+setMethod("setParams", "Params", function(object, update = NULL, ...) {
+
+ checkmate::assertClass(object, classes = "Params")
+ checkmate::assertList(update, null.ok = TRUE)
+
+ update <- c(update, list(...))
+
+ if (length(update) > 0) {
+ for (name in names(update)) {
+ value <- update[[name]]
+ object <- setParam(object, name, value)
+ }
+ }
+
+ return(object)
+})
+
#' @importFrom methods slotNames
setMethod("show", "Params", function(object) {
@@ -30,8 +48,11 @@ setMethod("show", "Params", function(object) {
cat("A", crayon::bold("Params"), "object of class",
crayon::bold(class(object)), "\n")
- cat("Parameters can be (estimable) or", crayon::blue("[not estimable],"),
- "'Default' or ", crayon::bold(crayon::green("'NOT DEFAULT'")), "\n\n")
+ cat("Parameters can be (estimable) or",
+ paste0(crayon::blue("[not estimable]"), ","),
+ "'Default' or ", crayon::bold(crayon::green("'NOT DEFAULT'")), "\n")
+ cat(crayon::bgYellow(crayon::black("Secondary")), "parameters are usually",
+ "set during simulation\n\n")
showPP(object, pp)
cat(length(slotNames(object)) - 3, "additional parameters", "\n\n")
})
diff --git a/R/SCE-functions.R b/R/SCE-functions.R
index 5e4a8743c5b6d4e62e596e7b44980cbac560bbf5..609345b5f03cf2884010333b56dc728d2b4fcb09 100644
--- a/R/SCE-functions.R
+++ b/R/SCE-functions.R
@@ -142,3 +142,25 @@ addGeneLengths <- function(sce, method = c("generate", "sample"), loc = 7.9,
return(sce)
}
+
+#' Get counts
+#'
+#' Get counts matrix from a SingleCellExperiment object. If counts is missing
+#' a warning is issued and the first assay is returned.
+#'
+#' @param sce
+#'
+#' @return Counts matrix
+getCounts <- function(sce) {
+
+ checkmate::assertClass(sce, "SingleCellExperiment")
+
+ if ("counts" %in% SummarizedExperiment::assayNames(sce)) {
+ counts <- SingleCellExperiment::counts(sce)
+ } else {
+ warning("counts assay is missing, using the first assay instead")
+ counts <- SummarizedExperiment::assay(sce)
+ }
+
+ return(counts)
+}
diff --git a/R/SimpleParams-methods.R b/R/SimpleParams-methods.R
index 6ff2ded00bff46ad798ddf602856fc755083a0ef..57af469f29e2c41cc817cd47e37140627c1d9bb3 100644
--- a/R/SimpleParams-methods.R
+++ b/R/SimpleParams-methods.R
@@ -30,6 +30,7 @@ setValidity("SimpleParams", function(object) {
return(valid)
})
+#' @importFrom methods is
setMethod("show", "SimpleParams", function(object) {
pp <- list("Mean:" = c("(Rate)" = "mean.rate",
@@ -38,7 +39,7 @@ setMethod("show", "SimpleParams", function(object) {
# Mean parameters aren't estimated for the LunParams object which
# inherits from SimpleParams
- if (class(object) == "LunParams") {
+ if (is(object, "LunParams")) {
pp[["Mean:"]] <- c("[Rate]" = "mean.rate", "[Shape]" = "mean.shape")
}
diff --git a/R/SplatParams-methods.R b/R/SplatParams-methods.R
index d0db76529ac1c9b405dc3bd16473ba16f5e76057..8a82e79c88b7b991ccd2305b773143f62e4bfa21 100644
--- a/R/SplatParams-methods.R
+++ b/R/SplatParams-methods.R
@@ -54,8 +54,8 @@ setValidity("SplatParams", function(object) {
any.missing = FALSE, min.len = 1),
path.from = checkIntegerish(v$path.from, lower = 0,
upper = nGroups, len = nGroups),
- path.length = checkIntegerish(v$path.length, lower = 1,
- len = nGroups),
+ path.nSteps = checkIntegerish(v$path.nSteps, lower = 1,
+ len = nGroups),
path.skew = checkNumeric(v$path.skew, lower = 0, upper = 1,
len = nGroups),
path.nonlinearProb = checkNumber(v$path.nonlinearProb,
@@ -100,9 +100,15 @@ setValidity("SplatParams", function(object) {
})
#' @rdname setParam
-setMethod("setParam", "SplatParams",function(object, name, value) {
+setMethod("setParam", "SplatParams", function(object, name, value) {
checkmate::assertString(name)
+ if (name == "path.length") {
+ warning("path.length has been renamed path.nSteps, ",
+ "please use path.nSteps in the future.")
+ name <- "path.nSteps"
+ }
+
if (name == "nCells" || name == "nBatches") {
stop(name, " cannot be set directly, set batchCells instead")
}
@@ -169,6 +175,21 @@ setMethod("setParam", "SplatParams",function(object, name, value) {
return(object)
})
+#' @rdname setParams
+setMethod("setParams", "SplatParams", function(object, update = NULL, ...) {
+
+ checkmate::assertClass(object, classes = "SplatParams")
+ checkmate::assertList(update, null.ok = TRUE)
+
+ update <- c(update, list(...))
+
+ update <- bringItemsForward(update, c("batchCells", "group.prob"))
+
+ object <- callNextMethod(object, update)
+
+ return(object)
+})
+
#' @importFrom methods callNextMethod
setMethod("show", "SplatParams", function(object) {
@@ -196,7 +217,7 @@ setMethod("show", "SplatParams", function(object) {
"(Midpoint)" = "dropout.mid",
"(Shape)" = "dropout.shape"),
"Paths:" = c("[From]" = "path.from",
- "[Length]" = "path.length",
+ "[Steps]" = "path.nSteps",
"[Skew]" = "path.skew",
"[Non-linear]" = "path.nonlinearProb",
"[Sigma Factor]" = "path.sigmaFac"))
@@ -217,7 +238,7 @@ setMethod("expandParams", "SplatParams", function(object) {
n <- getParam(object, "nGroups")
vectors <- c("de.prob", "de.downProb", "de.facLoc", "de.facScale",
- "path.from", "path.length", "path.skew")
+ "path.from", "path.nSteps", "path.skew")
object <- callNextMethod(object, vectors, n)
diff --git a/R/ZINBParams-methods.R b/R/ZINBParams-methods.R
index 08f3f79ccdf36a1b7de28ea2cbba4c67296bdf74..e5a44c6932363d72d925cd4e823754e07496ee71 100644
--- a/R/ZINBParams-methods.R
+++ b/R/ZINBParams-methods.R
@@ -47,9 +47,9 @@ setMethod("setParam", "ZINBParams", function(object, name, value) {
if (name == "model") {
checkmate::assertClass(value, "ZinbModel")
object <- setParamUnchecked(object, "nGenes",
- zinbwave::nFeatures(value))
+ as.numeric(zinbwave::nFeatures(value)))
object <- setParamUnchecked(object, "nCells",
- zinbwave::nSamples(value))
+ as.numeric(zinbwave::nSamples(value)))
}
object <- callNextMethod()
@@ -107,7 +107,7 @@ setMethod("show", "ZINBParams", function(object) {
for (category in names(pp)) {
parameters <- pp[[category]]
values <- lapply(parameters, function(x) {slot(model, x)})
- short.values <- sapply(values, function(x) {
+ short.values <- vapply(values, function(x) {
if ("matrix" %in% class(x)) {
if (nrow(x) == 1) {
paste0(paste(head(x[1, ], n = 4), collapse = ", "), ",...")
@@ -121,10 +121,11 @@ setMethod("show", "ZINBParams", function(object) {
} else {
paste(x, collapse = ", ")
}
- })
- values <- sapply(values, paste, collapse = ", ")
+ }, c(Value = "None"))
+ values <- vapply(values, paste, c(Value = "None"), collapse = ", ")
default.values <- lapply(parameters, function(x) {slot(default, x)})
- default.values <- sapply(default.values, paste, collapse = ", ")
+ default.values <- vapply(default.values, paste, c(Value = "None"),
+ collapse = ", ")
not.default <- values != default.values
cat(crayon::bold(c("Model", category)), "\n")
showValues(short.values, not.default)
diff --git a/R/compare.R b/R/compare.R
index 3743e64e657dbdb05ce5e11c8af874655f977436..3243d8894a9063a8e89de186a4f18bafa9e03254 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -14,9 +14,9 @@
#' The returned list has three items:
#'
#' \describe{
-#' \item{\code{FeatureData}}{Combined feature data from the provided
+#' \item{\code{RowData}}{Combined row data from the provided
#' SingleCellExperiments.}
-#' \item{\code{PhenoData}}{Combined pheno data from the provided
+#' \item{\code{ColData}}{Combined column data from the provided
#' SingleCellExperiments.}
#' \item{\code{Plots}}{Comparison plots
#' \describe{
@@ -24,7 +24,7 @@
#' \item{\code{Variances}}{Boxplot of variance distribution.}
#' \item{\code{MeanVar}}{Scatter plot with fitted lines showing the
#' mean-variance relationship.}
-#' \item{\code{LibraySizes}}{Boxplot of the library size
+#' \item{\code{LibrarySizes}}{Boxplot of the library size
#' distribution.}
#' \item{\code{ZerosGene}}{Boxplot of the percentage of each gene
#' that is zero.}
@@ -32,6 +32,8 @@
#' that is zero.}
#' \item{\code{MeanZeros}}{Scatter plot with fitted lines showing
#' the mean-zeros relationship.}
+#' \item{\code{VarGeneCor}}{Heatmap of correlation of the 100 most
+#' variable genes.}
#' }
#' }
#' }
@@ -50,9 +52,12 @@
#' names(comparison)
#' names(comparison$Plots)
#' @importFrom ggplot2 ggplot aes_string geom_point geom_smooth geom_boxplot
-#' scale_y_continuous scale_y_log10 scale_x_log10 xlab ylab ggtitle
-#' theme_minimal scale_colour_manual scale_fill_manual
-#' @importFrom SingleCellExperiment cpm<-
+#' geom_violin geom_tile scale_y_continuous scale_y_log10 scale_x_log10
+#' scale_colour_manual scale_fill_manual scale_fill_distiller coord_fixed
+#' facet_wrap xlab ylab ggtitle theme_minimal
+#' @importFrom S4Vectors metadata<- metadata
+#' @importFrom SingleCellExperiment cpm<- cpm
+#' @importFrom stats cor
#' @export
compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
fits = TRUE, colours = NULL) {
@@ -74,37 +79,58 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
sce <- sces[[name]]
rowData(sce)$Dataset <- name
colData(sce)$Dataset <- name
- sce <- scater::calculateQCMetrics(sce)
- cpm(sce) <- scater::calculateCPM(sce, use_size_factors = FALSE)
+ sce <- scater::addQCPerCell(sce)
+ sce <- scater::addQCPerFeature(sce)
+ cpm(sce) <- scater::calculateCPM(sce)
sce <- addFeatureStats(sce, "counts")
sce <- addFeatureStats(sce, "cpm")
sce <- addFeatureStats(sce, "cpm", log = TRUE)
- n.features <- colData(sce)$total_features_by_counts
+ n.features <- colData(sce)$detected
colData(sce)$PctZero <- 100 * (1 - n.features / nrow(sce))
+ rowData(sce)$PctZero <- 100 - rowData(sce)$detected
+
+ var.genes <- rev(order(rowData(sce)$VarLogCPM))[seq_len(100)]
+ var.cpm <- log2(cpm(sce)[var.genes, ] + 1)
+ var.cors <- as.data.frame.table(cor(t(var.cpm), method = "spearman"))
+ colnames(var.cors) <- c("GeneA", "GeneB", "Correlation")
+ var.cors$VarGeneA <- rep(paste0("VarGene", seq_len(100)), 100)
+ var.cors$VarGeneB <- rep(paste0("VarGene", seq_len(100)), each = 100)
+ var.cors$Dataset <- name
+ var.cors <- var.cors[, c("Dataset", "GeneA", "GeneB", "VarGeneA",
+ "VarGeneB", "Correlation")]
+ metadata(sce)$VarGeneCorrelation <- var.cors
+
sces[[name]] <- sce
}
features <- rowData(sces[[1]])
cells <- colData(sces[[1]])
+ var.cors <- metadata(sces[[1]])$VarGeneCorrelation
if (length(sces) > 1) {
for (name in names(sces)[-1]) {
sce <- sces[[name]]
features <- rbindMatched(features, rowData(sce))
cells <- rbindMatched(cells, colData(sce))
+ var.cors <- rbindMatched(var.cors, metadata(sce)$VarGeneCorrelation)
}
}
features$Dataset <- factor(features$Dataset, levels = names(sces))
cells$Dataset <- factor(cells$Dataset, levels = names(sces))
+ var.cors$Dataset <- factor(var.cors$Dataset, levels = names(sces))
features <- data.frame(features)
cells <- data.frame(cells)
means <- ggplot(features,
aes_string(x = "Dataset", y = "MeanLogCPM",
colour = "Dataset")) +
- geom_boxplot() +
+ geom_violin(aes_string(fill = "Dataset"),
+ draw_quantiles = c(0.25, 0.5, 0.75),
+ colour = "white", alpha = 0.3, size = 0.8) +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
ylab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
ggtitle("Distribution of mean expression") +
theme_minimal()
@@ -112,8 +138,12 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
vars <- ggplot(features,
aes_string(x = "Dataset", y = "VarLogCPM",
colour = "Dataset")) +
- geom_boxplot() +
+ geom_violin(aes_string(fill = "Dataset"),
+ draw_quantiles = c(0.25, 0.5, 0.75),
+ colour = "white", alpha = 0.3, size = 0.8) +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
ylab(expression(paste("Variance ", log[2], "(CPM + 1)"))) +
ggtitle("Distribution of variance") +
theme_minimal()
@@ -130,21 +160,29 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
theme_minimal()
libs <- ggplot(cells,
- aes_string(x = "Dataset", y = "total_counts",
+ aes_string(x = "Dataset", y = "sum",
colour = "Dataset")) +
- geom_boxplot() +
+ geom_violin(aes_string(fill = "Dataset"),
+ draw_quantiles = c(0.25, 0.5, 0.75),
+ colour = "white", alpha = 0.3, size = 0.8) +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_y_continuous(labels = scales::comma) +
scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
ylab("Total counts per cell") +
ggtitle("Distribution of library sizes") +
theme_minimal()
z.gene <- ggplot(features,
- aes_string(x = "Dataset", y = "pct_dropout_by_counts",
+ aes_string(x = "Dataset", y = "PctZero",
colour = "Dataset")) +
- geom_boxplot() +
+ geom_violin(aes_string(fill = "Dataset"),
+ draw_quantiles = c(0.25, 0.5, 0.75),
+ colour = "white", alpha = 0.3, size = 0.8) +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_y_continuous(limits = c(0, 100)) +
scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
ylab("Percentage zeros per gene") +
ggtitle("Distribution of zeros per gene") +
theme_minimal()
@@ -152,16 +190,20 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
z.cell <- ggplot(cells,
aes_string(x = "Dataset", y = "PctZero",
colour = "Dataset")) +
- geom_boxplot() +
+ geom_violin(aes_string(fill = "Dataset"),
+ draw_quantiles = c(0.25, 0.5, 0.75),
+ colour = "white", alpha = 0.3, size = 0.8) +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_y_continuous(limits = c(0, 100)) +
scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
ylab("Percentage zeros per cell") +
ggtitle("Distribution of zeros per cell") +
theme_minimal()
mean.zeros <- ggplot(features,
- aes_string(x = "MeanCounts",
- y = "pct_dropout_by_counts",
+ aes_string(x = "mean",
+ y = "PctZero",
colour = "Dataset", fill = "Dataset")) +
geom_point(size = point.size, alpha = point.alpha) +
scale_x_log10(labels = scales::comma) +
@@ -172,20 +214,35 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
ggtitle("Mean-zeros relationship") +
theme_minimal()
+ var.correlation <- ggplot(var.cors,
+ aes_string(x = "VarGeneA", y = "VarGeneB",
+ fill = "Correlation")) +
+ geom_tile() +
+ scale_fill_distiller(palette = "RdBu", limits = c(-1, 1)) +
+ coord_fixed() +
+ facet_wrap(~ Dataset) +
+ ggtitle("Correlation - 100 variable genes") +
+ theme_minimal() +
+ theme(axis.title = element_blank(),
+ axis.text = element_blank())
+
if (fits) {
- mean.var <- mean.var + geom_smooth()
- mean.zeros <- mean.zeros + geom_smooth()
+ mean.var <- mean.var + geom_smooth(method = "gam",
+ formula = y ~ s(x, bs = "cs"))
+ mean.zeros <- mean.zeros + geom_smooth(method = "gam",
+ formula = y ~ s(x, bs = "cs"))
}
- comparison <- list(FeatureData = features,
- PhenoData = cells,
+ comparison <- list(RowData = features,
+ ColData = cells,
Plots = list(Means = means,
Variances = vars,
MeanVar = mean.var,
LibrarySizes = libs,
ZerosGene = z.gene,
ZerosCell = z.cell,
- MeanZeros = mean.zeros))
+ MeanZeros = mean.zeros,
+ VarGeneCor = var.correlation))
return(comparison)
}
@@ -217,9 +274,9 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
#'
#' \describe{
#' \item{\code{Reference}}{The SingleCellExperiment used as the reference.}
-#' \item{\code{FeatureData}}{Combined feature data from the provided
+#' \item{\code{RowData}}{Combined feature data from the provided
#' SingleCellExperiments.}
-#' \item{\code{PhenoData}}{Combined pheno data from the provided
+#' \item{\code{ColData}}{Combined column data from the provided
#' SingleCellExperiments.}
#' \item{\code{Plots}}{Difference plots
#' \describe{
@@ -227,7 +284,7 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
#' \item{\code{Variances}}{Boxplot of variance differences.}
#' \item{\code{MeanVar}}{Scatter plot showing the difference from
#' the reference variance across expression ranks.}
-#' \item{\code{LibraySizes}}{Boxplot of the library size
+#' \item{\code{LibraeySizes}}{Boxplot of the library size
#' differences.}
#' \item{\code{ZerosGene}}{Boxplot of the differences in the
#' percentage of each gene that is zero.}
@@ -301,13 +358,15 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
}
rowData(sce)$Dataset <- name
colData(sce)$Dataset <- name
- sce <- scater::calculateQCMetrics(sce)
- cpm(sce) <- scater::calculateCPM(sce, use_size_factors = FALSE)
+ sce <- scater::addQCPerCell(sce)
+ sce <- scater::addQCPerFeature(sce)
+ cpm(sce) <- scater::calculateCPM(sce)
sce <- addFeatureStats(sce, "counts")
sce <- addFeatureStats(sce, "cpm", log = TRUE)
- n.features <- colData(sce)$total_features_by_counts
+ n.features <- colData(sce)$detected
colData(sce)$PctZero <- 100 * (1 - n.features / nrow(sce))
- rowData(sce)$RankCounts <- rank(rowData(sce)$mean_counts)
+ rowData(sce)$RankCounts <- rank(rowData(sce)$mean)
+ rowData(sce)$PctZero <- 100 - rowData(sce)$detected
sces[[name]] <- sce
}
@@ -315,13 +374,13 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
ref.means <- sort(rowData(ref.sce)$MeanLogCPM)
ref.vars <- sort(rowData(ref.sce)$VarLogCPM)
- ref.libs <- sort(colData(ref.sce)$total_counts)
- ref.z.gene <- sort(rowData(ref.sce)$pct_dropout_by_counts)
+ ref.libs <- sort(colData(ref.sce)$sum)
+ ref.z.gene <- sort(rowData(ref.sce)$PctZero)
ref.z.cell <- sort(colData(ref.sce)$PctZero)
ref.rank.ord <- order(rowData(ref.sce)$RankCounts)
ref.vars.rank <- rowData(ref.sce)$VarLogCPM[ref.rank.ord]
- ref.z.gene.rank <- rowData(ref.sce)$pct_dropout_by_counts[ref.rank.ord]
+ ref.z.gene.rank <- rowData(ref.sce)$PctZero[ref.rank.ord]
for (name in names(sces)) {
sce <- sces[[name]]
@@ -332,12 +391,11 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
rowData(sce)$RefRankVarLogCPM <- ref.vars[rank(rowData(sce)$VarLogCPM)]
rowData(sce)$RankDiffVarLogCPM <- rowData(sce)$VarLogCPM -
rowData(sce)$RefRankVarLogCPM
- colData(sce)$RefRankLibSize <- ref.libs[rank(colData(sce)$total_counts)]
- colData(sce)$RankDiffLibSize <- colData(sce)$total_counts -
+ colData(sce)$RefRankLibSize <- ref.libs[rank(colData(sce)$sum)]
+ colData(sce)$RankDiffLibSize <- colData(sce)$sum -
colData(sce)$RefRankLibSize
- rowData(sce)$RefRankZeros <- ref.z.gene[rank(
- rowData(sce)$pct_dropout_by_counts)]
- rowData(sce)$RankDiffZeros <- rowData(sce)$pct_dropout_by_counts -
+ rowData(sce)$RefRankZeros <- ref.z.gene[rank(rowData(sce)$PctZero)]
+ rowData(sce)$RankDiffZeros <- rowData(sce)$PctZero -
rowData(sce)$RefRankZeros
colData(sce)$RefRankZeros <- ref.z.cell[rank(
colData(sce)$PctZero)]
@@ -346,7 +404,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
rowData(sce)$MeanRankVarDiff <- rowData(sce)$VarLogCPM -
ref.vars.rank[rowData(sce)$RankCounts]
- rowData(sce)$MeanRankZerosDiff <- rowData(sce)$pct_dropout_by_counts -
+ rowData(sce)$MeanRankZerosDiff <- rowData(sce)$PctZero -
ref.z.gene.rank[rowData(sce)$RankCounts]
sces[[name]] <- sce
@@ -375,7 +433,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "Dataset", y = "RankDiffMeanLogCPM",
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_boxplot() +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
ylab(expression(paste("Rank difference mean ", log[2], "(CPM + 1)"))) +
ggtitle("Difference in mean expression") +
@@ -385,7 +443,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "Dataset", y = "RankDiffVarLogCPM",
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_boxplot() +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
ylab(expression(paste("Rank difference variance ", log[2],
"(CPM + 1)"))) +
@@ -409,9 +467,9 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "Dataset", y = "RankDiffLibSize",
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_boxplot() +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
- ylab(paste("Rank difference libray size")) +
+ ylab(paste("Rank difference library size")) +
ggtitle("Difference in library sizes") +
theme_minimal()
@@ -419,7 +477,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "Dataset", y = "RankDiffZeros",
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_boxplot() +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
ylab(paste("Rank difference percentage zeros")) +
ggtitle("Difference in zeros per gene") +
@@ -429,7 +487,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "Dataset", y = "RankDiffZeros",
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_boxplot() +
+ geom_boxplot(notch = TRUE, width = 0.1, size = 0.8) +
scale_colour_manual(values = colours) +
ylab(paste("Rank difference percentage zeros")) +
ggtitle("Difference in zeros per cell") +
@@ -451,7 +509,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "RefRankMeanLogCPM", y = "MeanLogCPM",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point(size = point.size, alpha = point.alpha) +
+ geom_point(size = point.size) +
scale_colour_manual(values = colours) +
xlab(expression(paste("Reference mean ", log[2], "(CPM + 1)"))) +
ylab(expression(paste("Alternative mean ", log[2], "(CPM + 1)"))) +
@@ -462,7 +520,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "RefRankVarLogCPM", y = "VarLogCPM",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point(size = point.size, alpha = point.alpha) +
+ geom_point(size = point.size) +
scale_colour_manual(values = colours) +
xlab(expression(paste("Reference variance ", log[2], "(CPM + 1)"))) +
ylab(expression(paste("Alternative variance ", log[2], "(CPM + 1)"))) +
@@ -470,10 +528,10 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
theme_minimal()
libs.qq <- ggplot(cells,
- aes_string(x = "RefRankLibSize", y = "total_counts",
+ aes_string(x = "RefRankLibSize", y = "sum",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point(size = point.size, alpha = point.alpha) +
+ geom_point(size = point.size) +
scale_colour_manual(values = colours) +
xlab("Reference library size") +
ylab("Alternative library size") +
@@ -482,10 +540,10 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
z.gene.qq <- ggplot(features,
aes_string(x = "RefRankZeros",
- y = "pct_dropout_by_counts",
+ y = "PctZero",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point(size = point.size, alpha = point.alpha) +
+ geom_point(size = point.size) +
scale_colour_manual(values = colours) +
xlab("Reference percentage zeros") +
ylab("Alternative percentage zeros") +
@@ -496,7 +554,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
aes_string(x = "RefRankZeros", y = "PctZero",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point(size = point.size, alpha = point.alpha) +
+ geom_point(size = point.size) +
scale_colour_manual(values = colours) +
xlab("Reference percentage zeros") +
ylab("Alternative percentage zeros") +
@@ -504,13 +562,15 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
theme_minimal()
if (fits) {
- mean.var <- mean.var + geom_smooth()
- mean.zeros <- mean.zeros + geom_smooth()
+ mean.var <- mean.var + geom_smooth(method = "gam",
+ formula = y ~ s(x, bs = "cs"))
+ mean.zeros <- mean.zeros + geom_smooth(method = "gam",
+ formula = y ~ s(x, bs = "cs"))
}
comparison <- list(Reference = ref.sce,
- FeatureData = features,
- PhenoData = cells,
+ RowData = features,
+ ColData = cells,
Plots = list(Means = means,
Variances = vars,
MeanVar = mean.var,
@@ -717,7 +777,7 @@ makeDiffPanel <- function(diff, title = "Difference comparison",
#' \dontrun{
#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
#' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-#' comparison <- compSCEs(list(Splat = sim1, Simple = sim2))
+#' comparison <- compareSCEs(list(Splat = sim1, Simple = sim2))
#' difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
#' panel <- makeOverallPanel(comparison, difference)
#' }
@@ -806,11 +866,12 @@ makeOverallPanel <- function(comp, diff, title = "Overall comparison",
return(panel)
}
-#' Summarise diffSCESs
+#' Summarise diffSCEs
#'
#' Summarise the results of \code{\link{diffSCEs}}. Calculates the Median
-#' Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
-#' Error (RMSE) for the various properties and ranks them.
+#' Absolute Deviation (MAD), Mean Absolute Error (MAE), Root Mean Squared
+#' Error (RMSE) and Kolmogorov-Smirnov (KS) statistics for the various
+#' properties and ranks them.
#'
#' @param diff Output from \code{\link{diffSCEs}}
#'
@@ -822,146 +883,190 @@ makeOverallPanel <- function(comp, diff, title = "Overall comparison",
#' summary <- summariseDiff(difference)
#' head(summary)
#' @export
+#' @importFrom SummarizedExperiment rowData
summariseDiff <- function(diff) {
- datasets <- unique(diff$PhenoData$Dataset)
-
- fData.mads <- sapply(datasets, function(dataset) {
- df <- diff$FeatureData[diff$FeatureData$Dataset == dataset, ]
- mean <- median(abs(df$RankDiffMeanLogCPM))
- var <- median(abs(df$RankDiffVarLogCPM))
- zeros <- median(abs(df$RankDiffZeros))
- mean.var <- median(abs(df$MeanRankVarDiff))
- mean.zeros <- median(abs(df$MeanRankZerosDiff))
- return(c(Mean = mean, Variance = var, ZerosGene = zeros,
- MeanVar = mean.var, MeanZeros = mean.zeros))
- })
- fData.mads.z <- t(scale(t(fData.mads)))
+ row.stats <- c(Mean = "RankDiffMeanLogCPM",
+ Variance = "RankDiffVarLogCPM",
+ ZerosGene = "RankDiffZeros",
+ MeanVar = "MeanRankVarDiff",
+ MeanZeros = "MeanRankZerosDiff")
+
+ row.ks.stats <- c(Mean = "MeanLogCPM",
+ Variance = "VarLogCPM",
+ ZerosGene = "PctZero",
+ MeanVar = NA,
+ MeanZeros = NA)
+
+ row.mad <- summariseStats(diff$RowData, "Dataset", row.stats, "MAD")
+ row.mae <- summariseStats(diff$RowData, "Dataset", row.stats, "MAE")
+ row.rmse <- summariseStats(diff$RowData, "Dataset", row.stats, "RMSE")
+ row.ks <- summariseKS(diff$RowData,
+ SummarizedExperiment::rowData(diff$Reference),
+ "Dataset", row.ks.stats)
+
+ row.list <- list(row.mad, row.mae, row.rmse, row.ks)
+ row.list <- lapply(row.list, function(summ) {summ[, -c(1, 2)]})
+ row.summ <- data.frame(Dataset = row.mad$Dataset,
+ Statistic = row.mad$Statistic)
+ row.list <- c(row.summ, row.list)
+ row.summ <- do.call("cbind", row.list)
+
+ col.stats <- c(LibSize = "RankDiffLibSize",
+ ZerosCell = "RankDiffZeros")
+
+ col.ks.stats <- c(LibSize = "sum",
+ ZerosCell = "PctZero")
+
+ col.mad <- summariseStats(diff$ColData, "Dataset", col.stats, "MAD")
+ col.mae <- summariseStats(diff$ColData, "Dataset", col.stats, "MAE")
+ col.rmse <- summariseStats(diff$ColData, "Dataset", col.stats, "RMSE")
+ col.ks <- summariseKS(diff$ColData,
+ SummarizedExperiment::colData(diff$Reference),
+ "Dataset", col.ks.stats)
+
+ col.list <- list(col.mad, col.mae, col.rmse, col.ks)
+ col.list <- lapply(col.list, function(summ) {summ[, -c(1, 2)]})
+ col.summ <- data.frame(Dataset = col.mad$Dataset,
+ Statistic = col.mad$Statistic)
+ col.list <- c(col.summ, col.list)
+ col.summ <- do.call("cbind", col.list)
+
+ summary <- rbind(row.summ, col.summ)
- pData.mads <- sapply(datasets, function(dataset) {
- df <- diff$PhenoData[diff$PhenoData$Dataset == dataset, ]
- lib.size <- median(abs(df$RankDiffLibSize))
- zeros <- median(abs(df$RankDiffZeros))
- return(c(LibSize = lib.size, ZerosCell = zeros))
- })
- pData.mads.z <- t(scale(t(pData.mads)))
-
- mads <- data.frame(Dataset = datasets, t(fData.mads), t(pData.mads))
- mads.z <- data.frame(Dataset = datasets, t(fData.mads.z), t(pData.mads.z))
-
- fData.ranks <- matrixStats::rowRanks(fData.mads)
- pData.ranks <- matrixStats::rowRanks(pData.mads)
-
- ranks.mads <- data.frame(Dataset = datasets, t(fData.ranks), t(pData.ranks))
- colnames(ranks.mads) <- paste0(colnames(mads), "Rank")
-
- fData.maes <- sapply(datasets, function(dataset) {
- df <- diff$FeatureData[diff$FeatureData$Dataset == dataset, ]
- mean <- mean(abs(df$RankDiffMeanLogCPM))
- var <- mean(abs(df$RankDiffVarLogCPM))
- zeros <- mean(abs(df$RankDiffZeros))
- mean.var <- mean(abs(df$MeanRankVarDiff))
- mean.zeros <- mean(abs(df$MeanRankZerosDiff))
- return(c(Mean = mean, Variance = var, ZerosGene = zeros,
- MeanVar = mean.var, MeanZeros = mean.zeros))
- })
- fData.maes.z <- t(scale(t(fData.maes)))
+ return(summary)
+}
- pData.maes <- sapply(datasets, function(dataset) {
- df <- diff$PhenoData[diff$PhenoData$Dataset == dataset, ]
- lib.size <- mean(abs(df$RankDiffLibSize))
- zeros <- mean(abs(df$RankDiffZeros))
- return(c(LibSize = lib.size, ZerosCell = zeros))
- })
- pData.maes.z <- t(scale(t(pData.maes)))
-
- maes <- data.frame(Dataset = datasets, t(fData.maes), t(pData.maes))
- maes.z <- data.frame(Dataset = datasets, t(fData.maes.z), t(pData.maes.z))
-
- fData.ranks <- matrixStats::rowRanks(fData.maes)
- pData.ranks <- matrixStats::rowRanks(pData.maes)
-
- ranks.maes <- data.frame(Dataset = datasets, t(fData.ranks), t(pData.ranks))
- colnames(ranks.maes) <- paste0(colnames(mads), "Rank")
-
- fData.rmse <- sapply(datasets, function(dataset) {
- df <- diff$FeatureData[diff$FeatureData$Dataset == dataset, ]
- mean <- sqrt(mean(df$RankDiffMeanLogCPM ^ 2))
- var <- sqrt(mean(df$RankDiffVarLogCPM ^ 2))
- zeros <- sqrt(mean(df$RankDiffZeros ^ 2))
- mean.var <- sqrt(mean(df$MeanRankVarDiff ^ 2))
- mean.zeros <- sqrt(mean(df$MeanRankZerosDiff ^ 2))
- return(c(Mean = mean, Variance = var, ZerosGene = zeros,
- MeanVar = mean.var, MeanZeros = mean.zeros))
- })
- fData.rmse.z <- t(scale(t(fData.rmse)))
+#' Summarise statistics
+#'
+#' Summarise columns of a data.frame using a single measure.
+#'
+#' @param data The data.frame to summarise
+#' @param split.col Name of the column used to split the dataset
+#' @param stat.cols Names of the columns to summarise. If this vector is named
+#' those names will be used in the output.
+#' @param measure The measure to use for summarisation.
+#'
+#' @return data.frame with the summarised measure, scaled and ranked
+#'
+#' @importFrom stats aggregate
+summariseStats <- function(data, split.col, stat.cols,
+ measure = c("MAD", "MAE", "RMSE")) {
+
+ measure <- match.arg(measure)
+
+ if (is.null(names(stat.cols))) {
+ names(stat.cols) <- stat.cols
+ }
+
+ switch (measure,
+ "MAD" = {
+ measure_fun <- function(x) {median(abs(x))}
+ },
+ "MAE" = {
+ measure_fun <- function(x) {mean(abs(x))}
+ },
+ "RMSE" = {
+ measure_fun <- function(x) {sqrt(mean(abs(x ^ 2)))}
+ }
+ )
+
+ summ <- aggregate(data[, stat.cols], list(Dataset = data[[split.col]]),
+ measure_fun)
+ colnames(summ) <- c(split.col, names(stat.cols))
+
+ tidy.summ <- tidyStatSumm(summ, measure)
+
+ return(tidy.summ)
+}
- pData.rmse <- sapply(datasets, function(dataset) {
- df <- diff$PhenoData[diff$PhenoData$Dataset == dataset, ]
- lib.size <- sqrt(mean(df$RankDiffLibSize ^ 2))
- zeros <- sqrt(mean(df$RankDiffZeros ^ 2))
- return(c(LibSize = lib.size, ZerosCell = zeros))
+#' Summarise KS
+#'
+#' Summarise columns of a data.frame compared to a reference using the KS test.
+#'
+#' @param data The data.frame to summarise
+#' @param ref The reference data.frame
+#' @param split.col Name of the column used to split the dataset
+#' @param stat.cols Names of the columns to summarise. If this vector is named
+#' those names will be used in the output.
+#'
+#' @return data.frame with the summarised measure, scaled and ranked
+#' @importFrom stats ks.test
+summariseKS <- function(data, ref, split.col, stat.cols) {
+
+ if (is.null(names(stat.cols))) {
+ names(stat.cols) <- stat.cols
+ }
+
+ splits <- unique(data[[split.col]])
+
+ summ <- expand.grid(Dataset = splits, Statistic = names(stat.cols),
+ stringsAsFactors = FALSE)
+
+ ks.res <- mapply(function(split, stat.name) {
+ stat <- stat.cols[stat.name]
+ if (!is.na(stat)) {
+ data.stat <- data[data[[split.col]] == split, stat]
+ ref.stat <- ref[[stat]]
+
+ ks <- suppressWarnings(ks.test(ref.stat, data.stat))
+ ks.out <- c(KS = unname(ks$statistic), KSPVal = ks$p.value)
+ } else {
+ ks.out <- c(KS = NA, KSPVal = NA)
+ }
+
+ return(ks.out)
+ }, summ$Dataset, summ$Statistic)
+
+ summ$KS <- ks.res["KS", ]
+ summ$KSPVal <- ks.res["KSPVal", ]
+
+ ks.ranks <- lapply(split(summ, summ$Statistic), function(x) {
+ rank(x$KS)
})
- pData.rmse.z <- t(scale(t(pData.rmse)))
-
- rmse <- data.frame(Dataset = datasets, t(fData.rmse), t(pData.rmse))
- rmse.z <- data.frame(Dataset = datasets, t(fData.rmse.z), t(pData.rmse.z))
-
- fData.ranks <- matrixStats::rowRanks(fData.rmse)
- pData.ranks <- matrixStats::rowRanks(pData.rmse)
-
- ranks.rmse <- data.frame(Dataset = datasets, t(fData.ranks), t(pData.ranks))
- colnames(ranks.rmse) <- paste0(colnames(rmse), "Rank")
-
- mads <- stats::reshape(mads, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(mads)[2:8], v.names = "MAD")
-
- mads.z <- stats::reshape(mads.z, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(mads)[2:8],
- v.names = "MADScaled")
-
- ranks.mads <- stats::reshape(ranks.mads, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(ranks.mads)[2:8],
- v.names = "Rank")
-
- maes <- stats::reshape(maes, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(maes)[2:8], v.names = "MAE")
-
- maes.z <- stats::reshape(maes.z, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(mads)[2:8],
- v.names = "MAEScaled")
-
- ranks.maes <- stats::reshape(ranks.maes, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(ranks.maes)[2:8],
- v.names = "Rank")
-
- rmse <- stats::reshape(rmse, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(mads)[2:8], v.names = "RMSE")
-
- rmse.z <- stats::reshape(rmse.z, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(mads)[2:8],
- v.names = "RMSEScaled")
-
- ranks.rmse <- stats::reshape(ranks.rmse, varying = 2:8, direction = "long",
- idvar = "Dataset", timevar = "Statistic",
- times = colnames(ranks.rmse)[2:8],
- v.names = "Rank")
-
- summary <- data.frame(mads, MADScaled = mads.z$MADScaled,
- MADRank = ranks.mads$Rank,
- MAE = maes$MAE, MAEScaled = maes.z$MAEScaled,
- MAERank = ranks.maes$Rank,
- RMSE = rmse$RMSE, RMSEScaled = rmse.z$RMSEScaled,
- RMSERank = ranks.rmse$Rank)
- row.names(summary) <- NULL
+ ks.ranks <- unlist(ks.ranks)
- return(summary)
+ summ$KSRank <- ks.ranks
+ summ$KSRank[is.na(summ$KS)] <- NA
+
+ return(summ)
}
+
+#' Tidy summarised statistics
+#'
+#' Convert a statistic summary to tidy format and add ranks and scaled values
+#'
+#' @param stat.summ The summary to convert
+#' @param measure The name of the summarisation measure
+#'
+#' @return tidy data.frame with the summarised measure, scaled and ranked
+tidyStatSumm <- function(stat.summ, measure = c("MAD", "MAE", "RMSE")) {
+
+ measure <- match.arg(measure)
+
+ summ.mat <- t(stat.summ[, -1])
+ colnames(summ.mat) <- stat.summ[, 1]
+
+ scale.summ <- apply(summ.mat, 1, scale)
+ # Check if apply has returned a vector
+ if (is.vector(scale.summ)) {
+ scale.summ <- t(as.matrix(scale.summ))
+ }
+
+ rank.summ <- apply(summ.mat, 1, rank)
+ if (is.vector(rank.summ)) {
+ rank.summ <- t(as.matrix(rank.summ))
+ }
+
+ tidy.summ <- as.data.frame.table(t(summ.mat))
+ colnames(tidy.summ) <- c("Dataset", "Statistic", measure)
+
+ tidy.scale <- as.data.frame.table(scale.summ)
+ tidy.rank <- as.data.frame.table(rank.summ)
+
+ tidy.summ[[paste0(measure, "Scaled")]] <- tidy.scale[, 3]
+ tidy.summ[[paste0(measure, "Rank")]] <- tidy.rank[, 3]
+
+ return(tidy.summ)
+}
+
diff --git a/R/kersplat-estimate.R b/R/kersplat-estimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..9eaa4c08f4952ca70940970aaaa3f7909b242986
--- /dev/null
+++ b/R/kersplat-estimate.R
@@ -0,0 +1,347 @@
+#' Estimate Kersplat simulation parameters
+#'
+#' Estimate simulation parameters for the Kersplat simulation from a real
+#' dataset. See the individual estimation functions for more details on how this
+#' is done.
+#'
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#' containing count data to estimate parameters from.
+#' @param params KersplatParams object to store estimated values in.
+#' @param verbose logical. Whether to print progress messages.
+#'
+#' @seealso
+#' \code{\link{kersplatEstMean}}, \code{\link{kersplatEstBCV}},
+#' \code{\link{kersplatEstLib}}
+#'
+#' @return KersplatParams object containing the estimated parameters.
+#'
+#' @examples
+#' # Load example data
+#' library(scater)
+#' set.seed(1)
+#' sce <- mockSCE()
+#'
+#' params <- kersplatEstimate(sce)
+#' params
+#' @export
+kersplatEstimate <- function(counts, params = newKersplatParams(),
+ verbose = TRUE) {
+ UseMethod("kersplatEstimate")
+}
+
+#' @rdname kersplatEstimate
+#' @export
+kersplatEstimate.SingleCellExperiment <- function(counts,
+ params = newKersplatParams(),
+ verbose = TRUE) {
+ counts <- getCounts(counts)
+ kersplatEstimate(counts, params, verbose)
+}
+
+#' @rdname kersplatEstimate
+#' @importFrom stats median
+#' @export
+kersplatEstimate.matrix <- function(counts, params = newKersplatParams(),
+ verbose = TRUE) {
+
+ checkmate::assertClass(params, "KersplatParams")
+ checkmate::assertFlag(verbose)
+
+ # Normalise for library size and remove all zero genes
+ lib.sizes <- colSums(counts)
+ lib.med <- median(lib.sizes)
+ norm.counts <- t(t(counts) / lib.sizes * lib.med)
+ norm.counts <- norm.counts[rowSums(norm.counts > 0) > 1, ]
+
+ params <- kersplatEstMean(norm.counts, params, verbose)
+ params <- kersplatEstBCV(counts, params, verbose)
+ params <- kersplatEstLib(counts, params, verbose)
+
+ params <- setParams(params, nGenes = nrow(counts), nCells = ncol(counts))
+
+ return(params)
+}
+
+#' Estimate Kersplat means
+#'
+#' Estimate mean parameters for the Kersplat simulation
+#'
+#' @param norm.counts library size normalised counts matrix.
+#' @param params KersplatParams object to store estimated values in.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Parameters for the gamma distribution are estimated by fitting the mean
+#' normalised counts using \code{\link[fitdistrplus]{fitdist}}. All the fitting
+#' methods are tried and the fit with the best Cramer-von Mises statistic is
+#' selected. The density of the means is also estimated using
+#' \code{\link[stats]{density}}.
+#'
+#' Expression outlier genes are detected using the Median Absolute Deviation
+#' (MAD) from median method. If the log2 mean expression of a gene is greater
+#' than two MADs above the median log2 mean expression it is designated as an
+#' outlier. The proportion of outlier genes is used to estimate the outlier
+#' probability. Factors for each outlier gene are calculated by dividing mean
+#' expression by the median mean expression. A log-normal distribution is then
+#' fitted to these factors in order to estimate the outlier factor location and
+#' scale parameters using the \code{\link[fitdistrplus]{fitdist}} MLE method.
+#'
+#' @return KersplatParams object with estimated means
+#'
+#' @importFrom stats density
+kersplatEstMean <- function(norm.counts, params, verbose) {
+
+ if (verbose) {message("Estimating mean parameters...")}
+
+ means <- rowMeans(norm.counts)
+ means <- means[means != 0]
+ non.zero <- rowSums(norm.counts > 0)
+
+ fit <- selectFit(means, "gamma", non.zero, verbose)
+
+ params <- setParams(params, mean.shape = unname(fit$estimate["shape"]),
+ mean.rate = unname(fit$estimate["rate"]))
+
+ if (verbose) {message("Estimating expression outlier parameters...")}
+ lmeans <- log(means)
+ med <- median(lmeans)
+ mad <- mad(lmeans)
+
+ bound <- med + 2 * mad
+
+ outs <- which(lmeans > bound)
+
+ prob <- length(outs) / nrow(norm.counts)
+
+ params <- setParam(params, "mean.outProb", prob)
+
+ if (length(outs) > 1) {
+ facs <- means[outs] / median(means)
+ #fit <- selectFit(facs, "lnorm", verbose = verbose)
+ fit <- fitdistrplus::fitdist(facs, "lnorm")
+
+ params <- setParams(params,
+ mean.outLoc = unname(fit$estimate["meanlog"]),
+ mean.outScale = unname(fit$estimate["sdlog"]))
+ }
+
+ params <- setParams(params, mean.dens = density(lmeans))
+
+ return(params)
+}
+
+#' Estimate Kersplat BCV parameters
+#'
+#' Estimate Biological Coefficient of Variation (BCV) parameters for the
+#' Kersplat simulation
+#'
+#' @param counts counts matrix.
+#' @param params KersplatParams object to store estimated values in.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' The \code{\link[edgeR]{estimateDisp}} function is used to estimate the common
+#' dispersion across the dataset. An exponential correction is applied based on
+#' fitting an exponential relationship between simulated and estimated values.
+#' If this results in a negative dispersion a simpler linear correction is
+#' applied instead.
+#'
+#' @return KersplatParams object with estimated BCV parameters
+kersplatEstBCV <- function(counts, params, verbose) {
+
+ if (verbose) {message("Estimating BCV parameters...")}
+
+ # Add dummy design matrix to avoid print statement
+ design <- matrix(1, ncol(counts), 1)
+ disps <- edgeR::estimateDisp(counts, design = design)
+ raw <- disps$common.dispersion
+
+ mean.rate <- getParam(params, "mean.rate")
+ mean.shape <- getParam(params, "mean.shape")
+
+ # Caculate factors for correction based on mean parameters
+ # Coefficents come from fitting
+ # RawEst ~
+ # (A1 * mean.rate + A2 * mean.shape + A3 * mean.rate *
+ # E_mean.shape + A4) *
+ # ((B1 * mean.rate + B2 * mean.shape + B3 * mean.rate *
+ # mean.shape + B4) ^ SimBCVCommon) +
+ # (C1 * mean.rate + C2 * mean.shape + C3 * mean.rate *
+ # mean.shape + C4)
+ # Using minpack.lm::nlsLM
+ A <- -0.6 * mean.rate - 2.9 * mean.shape +
+ 0.4 * mean.rate * mean.shape + 9.5
+ B <- 0.15 * mean.rate + 0.25 * mean.shape -
+ 0.1 * mean.rate * mean.shape + 1.2
+ C <- 0.9 * mean.rate + 4.5 * mean.shape -
+ 0.6 * mean.rate * mean.shape - 10.6
+ Y <- (raw - C) / A
+
+ message("Raw: ", raw, " A: ", A, " B: ", B, " C: ", C, " Y: ", Y)
+
+ # Check if Y <= 0 to avoid problems when taking log
+ if (Y <= 0) {
+ Y <- 0.0001
+ }
+
+ corrected <- log(Y, base = B)
+
+ # Dispersion cannot be negative so apply a simpler correction to those.
+ # Coefficients come from fitting
+ # SimBCVCommon ~ EstRaw
+ # Using lm (negative values only)
+ if (corrected < 0) {
+ warning("Exponential corrected BCV is negative.",
+ "Using linear correction.")
+ corrected <- -0.1 + 0.1 * raw
+ }
+
+ if (corrected < 0) {
+ warning("Linear corrected BCV is negative.",
+ "Using existing bcv.common.")
+ corrected <- getParam(params, "bcv.common")
+ }
+
+ params <- setParams(params, bcv.common = corrected)
+
+ return(params)
+}
+
+#' Estimate Kersplat library size parameters
+#'
+#' Estimate the library size parameters for the Kersplat simulation
+#'
+#' @param counts counts matrix.
+#' @param params KersplatParams object to store estimated values in.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Parameters for the log-normal distribution are estimated by fitting the
+#' library sizes using \code{\link[fitdistrplus]{fitdist}}. All the fitting
+#' methods are tried and the fit with the best Cramer-von Mises statistic is
+#' selected. The density of the library sizes is also estimated using
+#' \code{\link[stats]{density}}.
+#'
+#' @return KersplatParams object with library size parameters
+#'
+#' @importFrom stats density
+kersplatEstLib <- function(counts, params, verbose) {
+
+ if (verbose) {message("Estimating library size parameters...")}
+
+ lib.sizes <- colSums(counts)
+
+ fit <- selectFit(lib.sizes, "lnorm", verbose = verbose)
+
+ lib.loc <- unname(fit$estimate["meanlog"])
+ lib.scale <- unname(fit$estimate["sdlog"])
+
+ dens <- density(lib.sizes)
+
+ params <- setParams(params, lib.loc = lib.loc, lib.scale = lib.scale,
+ lib.dens = dens)
+
+ return(params)
+}
+
+#' Select fit
+#'
+#' Try a variety of fitting methods and select the best one
+#'
+#' @param data The data to fit
+#' @param distr Name of the distribution to fit
+#' @param weights Optional vector of weights
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' The distribution is fitted to the data using each of the
+#' \code{\link[fitdistrplus]{fitdist}} fitting methods. The fit with the
+#' smallest Cramer-von Mises statistic is selected.
+#'
+#' @return The selected fit object
+selectFit <- function(data, distr, weights = NULL, verbose = TRUE) {
+
+ checkmate::assertNumeric(data, finite = TRUE, any.missing = FALSE)
+ checkmate::assertString(distr)
+ checkmate::assertNumeric(weights, finite = TRUE, any.missing = TRUE,
+ len = length(data), null.ok = TRUE)
+ checkmate::assertFlag(verbose)
+
+ # Sink output that sometimes happens when fitting
+ sink(tempfile())
+ on.exit(sink())
+
+ fits <- list()
+
+ try(
+ fits$`MLE` <- fitdistrplus::fitdist(data, distr, method = "mle"),
+ silent = TRUE
+ )
+
+ try(
+ fits$`MME` <- fitdistrplus::fitdist(data, distr, method = "mme"),
+ silent = TRUE
+ )
+
+ try(
+ fits$`QME` <- fitdistrplus::fitdist(data, distr, method = "qme",
+ probs = c(1/3, 2/3)),
+ silent = TRUE
+ )
+
+ try(
+ fits$`MGE (CvM)` <- fitdistrplus::fitdist(data, distr, method = "mge",
+ gof = "CvM"),
+ silent = TRUE
+ )
+
+ try(
+ fits$`MGE (KS)` <- fitdistrplus::fitdist(data, distr, method = "mge",
+ gof = "KS"),
+ silent = TRUE
+ )
+
+ try(
+ fits$`MGE (AD)` <- fitdistrplus::fitdist(data, distr, method = "mge",
+ gof = "AD"),
+ silent = TRUE
+ )
+
+ if (!is.null(weights)) {
+ try(suppressWarnings(
+ fits$`Weighted MLE` <- fitdistrplus::fitdist(data, distr,
+ method = "mle",
+ weights = weights)
+ ), silent = TRUE
+ )
+
+ try(suppressWarnings(
+ fits$`Weighted MME` <- fitdistrplus::fitdist(data, distr,
+ method = "mme",
+ weights = weights)
+ ), silent = TRUE
+ )
+
+ try(suppressWarnings(
+ fits$`Weighted QME` <- fitdistrplus::fitdist(data, distr,
+ method = "qme",
+ probs = c(1/3, 2/3),
+ weights = weights)
+ ), silent = TRUE
+ )
+ }
+
+ scores <- fitdistrplus::gofstat(fits)$cvm
+
+ # Flatten in case scores is a list
+ scores.flat <- unlist(scores)
+ selected <- which(scores.flat == min(scores.flat, na.rm = TRUE))
+
+ if (verbose) {
+ # Work around to get name in case scores is a list
+ name <- names(fits)[names(scores) == names(scores.flat)[selected]]
+ message("Selected ", name, " fit")
+ }
+
+ return(fits[[selected]])
+}
diff --git a/R/kersplat-simulate.R b/R/kersplat-simulate.R
new file mode 100644
index 0000000000000000000000000000000000000000..1971042405f0faf50145ef5d44abdfaca5ccee01
--- /dev/null
+++ b/R/kersplat-simulate.R
@@ -0,0 +1,936 @@
+#' Kersplat simulation
+#'
+#' Simulate scRNA-seq count data using the Kersplat model
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#' @param ... any additional parameter settings to override what is provided in
+#' \code{params}.
+#'
+#' @details
+#'
+#' This functions is for simulating data in a single step. It consists of a
+#' call to \code{\link{kersplatSetup}} followed by a call to
+#' \code{\link{kersplatSample}}. Please see the documentation for those
+#' functions for more details of the individual steps.
+#'
+#' @seealso
+#' \code{\link{kersplatSetup}}, \code{\link{kersplatSample}}
+#'
+#' @return SingleCellExperiment containing simulated counts and intermediate
+#' values
+#'
+#' @examples
+#' sim <- kersplatSimulate()
+#'
+#' @export
+kersplatSimulate <- function(params = newKersplatParams(), verbose = TRUE,
+ ...) {
+
+ params <- kersplatSetup(params, verbose, ...)
+ sim <- kersplatSample(params, verbose)
+
+ return(sim)
+}
+
+#' Kersplat setup
+#'
+#' Setup the parameters required for the Kersplat simulation
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#' @param ... any additional parameter settings to override what is provided in
+#' \code{params}.
+#'
+#' @details
+#' The first stage is a two-step Kersplat simulation is to generate some of the
+#' intermediate parameters. The resulting parameters allow multiple simulated
+#' datasets to be generated from the same biological structure (using
+#' \code{\link{kersplatSample}}). As with all the other parameters these values
+#' can be manually overwritten if desired.
+#'
+#' The setup involves the following steps:
+#' \enumerate{
+#' \item Generate a gene network (if not already present)
+#' \item Select regulator genes (if not already present)
+#' \item Simulate gene means (if not already present)
+#' \item Simulate cell paths
+#' }
+#'
+#' The resulting \code{\link{KersplatParams}} object will have the following
+#' parameters set (if they weren't already).
+#'
+#' \itemize{
+#' \item \code{mean.values}
+#' \item \code{network.graph}
+#' \item \code{network.regsSet}
+#' \item \code{paths.means}
+#' }
+#'
+#' See \code{\link{KersplatParams}} for more details about these parameters and
+#' the functions for the individual steps for more details about the process.
+#'
+#' @seealso
+#' \code{\link{kersplatGenNetwork}}, \code{\link{kersplatSelectRegs}},
+#' \code{\link{kersplatSimGeneMeans}}, \code{\link{kersplatSimPaths}},
+#' \code{\link{KersplatParams}}
+#'
+#' @return A complete KersplatParams object
+#' @export
+#'
+#' @examples
+#' params <- kersplatSetup()
+kersplatSetup <- function(params = newKersplatParams(), verbose = TRUE, ...) {
+
+ checkmate::assertClass(params, "KersplatParams")
+ params <- setParams(params, ...)
+
+ # Set random seed
+ seed <- getParam(params, "seed")
+ set.seed(seed)
+
+ if (verbose) {message("Setting up parameters...")}
+ params <- kersplatGenNetwork(params, verbose)
+ params <- kersplatSelectRegs(params, verbose)
+ params <- kersplatSimGeneMeans(params, verbose)
+ params <- kersplatSimPaths(params, verbose)
+
+ return(params)
+}
+
+#' Kersplat sample
+#'
+#' Sample cells for the Kersplat simulation
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' The second stage is a two-step Kersplat simulation is to generate cells based
+#' on a complete \code{\link{KersplatParams}} object.
+#' intermediate parameters.
+#'
+#' The sampling process involves the following steps:
+#' \enumerate{
+#' \item Simulate library sizes for each cell
+#' \item Simulate means for each cell
+#' \item Simulate endogenous counts for each cell
+#' \item Simulate ambient counts for each cell
+#' \item Simulate final counts for each cell
+#' }
+#'
+#' The final output is a
+#' \code{\link[SingleCellExperiment]{SingleCellExperiment}} object that
+#' contains the simulated counts but also the values for various intermediate
+#' steps. These are stored in the \code{\link{colData}} (for cell specific
+#' information), \code{\link{rowData}} (for gene specific information) or
+#' \code{\link{assays}} (for gene by cell matrices) slots. This additional
+#' information includes:
+#' \describe{
+#' \item{\code{colData}}{
+#' \describe{
+#' \item{Cell}{Unique cell identifier.}
+#' \item{Type}{Whether the cell is a Cell, Doublet or Empty.}
+#' \item{CellLibSize}{The expected number of endogenous counts for
+#' that cell.}
+#' \item{AmbientLibSize}{The expected number of ambient counts for
+#' that cell.}
+#' \item{Path}{The path the cell belongs to.}
+#' \item{Step}{How far along the path each cell is.}
+#' \item{Path1}{For doublets the path of the first partner in the
+#' doublet (otherwise \code{NA}).}
+#' \item{Step1}{For doublets the step of the first partner in the
+#' doublet (otherwise \code{NA}).}
+#' \item{Path2}{For doublets the path of the second partner in the
+#' doublet (otherwise \code{NA}).}
+#' \item{Step2}{For doublets the step of the second partner in the
+#' doublet (otherwise \code{NA}).}
+#' }
+#' }
+#' \item{\code{rowData}}{
+#' \describe{
+#' \item{Gene}{Unique gene identifier.}
+#' \item{BaseMean}{The base expression level for that gene.}
+#' \item{AmbientMean}{The ambient expression level for that gene.}
+#' }
+#' }
+#' \item{\code{assays}}{
+#' \describe{
+#' \item{CellMeans}{The mean expression of genes in each cell
+#' after any differential expression and adjusted for expected
+#' library size.}
+#' \item{CellCounts}{Endogenous count matrix.}
+#' \item{AmbientCounts}{Ambient count matrix.}
+#' \item{counts}{Final count matrix.}
+#' }
+#' }
+#' }
+#'
+#' Values that have been added by Splatter are named using \code{UpperCamelCase}
+#' in order to differentiate them from the values added by analysis packages
+#' which typically use \code{underscore_naming}.
+#'
+#' @seealso
+#' \code{\link{kersplatSimLibSizes}}, \code{\link{kersplatSimCellMeans}},
+#' \code{\link{kersplatSimCellCounts}}, \code{\link{kersplatSimAmbientCounts}},
+#' \code{\link{kersplatSimCounts}}
+#'
+#' @return SingleCellExperiment object containing the simulated counts and
+#' intermediate values.
+#' @export
+#'
+#' @examples
+#' params <- kersplatSetup()
+#' sim <- kersplatSample(params)
+kersplatSample <- function(params, verbose = TRUE) {
+
+ # Check that parameters are set up
+ checkmate::assertClass(params, "KersplatParams")
+ network.graph <- getParam(params, "network.graph")
+ if (is.null(network.graph)) {
+ stop("'network.graph' not set, run kersplatSetup first")
+ }
+ network.regsSet <- getParam(params, "network.regsSet")
+ if (!network.regsSet) {
+ stop("network regulators not set, run kersplatSetup first")
+ }
+ mean.values <- getParam(params, "mean.values")
+ if (length(mean.values) == 0) {
+ stop("'mean.values' not set, run kersplatSetup first")
+ }
+ paths.means <- getParam(params, "paths.means")
+ if (length(mean.values) == 0) {
+ stop("'paths.means' not set, run kersplatSetup first")
+ }
+
+ if (verbose) {message("Creating simulation object...")}
+ nGenes <- getParam(params, "nGenes")
+ gene.names <- paste0("Gene", seq_len(nGenes))
+
+ nCells <- getParam(params, "nCells")
+ doublet.prop <- getParam(params, "doublet.prop")
+ nDoublets <- floor(nCells * doublet.prop)
+ if (doublet.prop > 0) {
+ nCells <- nCells - nDoublets
+ cell.names <- c(paste0("Cell", seq_len(nCells)),
+ paste0("Doublet", seq_len(nDoublets)))
+ } else {
+ cell.names <- paste0("Cell", seq_len(nCells))
+ }
+
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ if (nEmpty > 0) {
+ empty.names <- paste0("Empty", seq_len(nEmpty))
+ cell.names <- c(cell.names, empty.names)
+ }
+
+ cells <- data.frame(Cell = cell.names,
+ Type = rep(c("Cell", "Doublet", "Empty"),
+ c(nCells, nDoublets, nEmpty)),
+ row.names = cell.names)
+ features <- data.frame(Gene = gene.names,
+ BaseMean = getParam(params, "mean.values"),
+ row.names = gene.names)
+ sim <- SingleCellExperiment(rowData = features, colData = cells,
+ metadata = list(Params = params))
+
+ sim <- kersplatSimLibSizes(sim, params, verbose)
+ sim <- kersplatSimCellMeans(sim, params, verbose)
+ sim <- kersplatSimCellCounts(sim, params, verbose)
+ sim <- kersplatSimAmbientCounts(sim, params, verbose)
+ sim <- kersplatSimCounts(sim, params, verbose)
+
+ return(sim)
+
+}
+
+#' Generate Kersplat gene network
+#'
+#' Generate a gene network for the Kersplat simulation
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Currently a very simple approach is used which needs to be improved. A
+#' network is generated using the \code{\link[igraph]{sample_forestfire}}
+#' function and edge weights are sampled from a standard normal distribution.
+#'
+#' @return KersplatParams object with gene network
+kersplatGenNetwork <- function(params, verbose) {
+
+ nGenes <- getParam(params, "nGenes")
+ network.graph <- getParam(params, "network.graph")
+
+ if (!is.null(network.graph)) {
+ if (verbose) {message("Using provided gene network...")}
+ return(params)
+ }
+
+ if (verbose) {message("Generating gene network...")}
+
+ graph.raw <- igraph::sample_forestfire(nGenes, 0.1)
+ graph.data <- igraph::get.data.frame(graph.raw)
+ graph.data <- graph.data[, c("from", "to")]
+ graph.data$weight <- rnorm(nrow(graph.data))
+ graph <- igraph::graph.data.frame(graph.data)
+
+ params <- setParam(params, "network.graph", graph)
+
+ return(params)
+}
+
+#' Select Kersplat regulators
+#'
+#' Select regulator genes in the gene network for a Kersplat simulation
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Regulators are randomly selected, weighted according to the difference
+#' between their out degree and in degree. This is an arbitrary weighting and
+#' may be improved or replace in the future.
+#'
+#' @return KersplatParams object with gene regulators
+kersplatSelectRegs <- function(params, verbose) {
+
+ network.regsSet <- getParam(params, "network.regsSet")
+
+ if (network.regsSet) {
+ if (verbose) {message("Using selected regulators...")}
+ return(params)
+ }
+
+ if (verbose) {message("Selecting regulators...")}
+ network.nRegs <- getParam(params, "network.nRegs")
+ network.graph <- getParam(params, "network.graph")
+
+ out.degree <- igraph::degree(network.graph, mode = "out")
+ in.degree <- igraph::degree(network.graph, mode = "in")
+ reg.prob <- out.degree - in.degree
+ reg.prob <- reg.prob + rnorm(length(reg.prob))
+ reg.prob[reg.prob <= 0] <- 1e-10
+ reg.prob <- reg.prob / sum(reg.prob)
+ reg.nodes <- names(rev(sort(reg.prob))[seq_len(network.nRegs)])
+ is.reg <- igraph::V(network.graph)$name %in% reg.nodes
+ network.graph <- igraph::set_vertex_attr(network.graph, "IsReg",
+ value = is.reg)
+
+ params <- setParam(params, "network.graph", network.graph)
+
+ return(params)
+}
+
+#' Simulate Kersplat gene means
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Gene means are simulated in one of two ways depending on the value of the
+#' \code{mean.method} parameter.
+#'
+#' If \code{mean.method} is "fit" (default) then means are sampled from a Gamma
+#' distribution with shape equals \code{mean.shape} and rate equals
+#' \code{mean.rate}. Expression outliers are then added by replacing some
+#' values with the median multiplied by a factor from a log-normal distribution.
+#' This is the same process used for the Splat simulation.
+#'
+#' If \code{mean.method} is "density" then means are sampled from the
+#' density object in the \code{mean.density} parameter using a rejection
+#' sampling method. This approach is more flexible but may violate some
+#' statistical assumptions.
+#'
+#' @return KersplatParams object with gene means
+kersplatSimGeneMeans <- function(params, verbose) {
+
+ mean.values <- getParam(params, "mean.values")
+
+ # Generate means
+ if (length(mean.values) != 0) {
+ if (verbose) {message("Using defined means...")}
+ return(params)
+ }
+
+ if (verbose) {message("Simulating means...")}
+ nGenes <- getParam(params, "nGenes")
+ mean.method <- getParam(params, "mean.method")
+
+ if (mean.method == "fit") {
+ if (verbose) {message("Sampling from gamma distribution...")}
+ mean.shape <- getParam(params, "mean.shape")
+ mean.rate <- getParam(params, "mean.rate")
+ mean.outProb <- getParam(params, "mean.outProb")
+ mean.outLoc <- getParam(params, "mean.outLoc")
+ mean.outScale <- getParam(params, "mean.outScale")
+
+ mean.values <- rgamma(nGenes, shape = mean.shape, rate = mean.rate)
+
+ outlier.facs <- getLNormFactors(nGenes, mean.outProb, 0, mean.outLoc,
+ mean.outScale)
+ median.means.gene <- median(mean.values)
+ outlier.means <- median.means.gene * outlier.facs
+ is.outlier <- outlier.facs != 1
+ mean.values[is.outlier] <- outlier.means[is.outlier]
+ } else if (mean.method == "density") {
+ if (verbose) {message("Sampling from density object...")}
+ mean.dens <- getParam(params, "mean.dens")
+
+ mean.values <- exp(sampleDensity(nGenes, mean.dens, lower = -Inf))
+ }
+
+ params <- setParam(params, "mean.values", mean.values)
+
+ return(params)
+}
+
+#' Simulate Kersplat paths
+#'
+#' Simulate gene means for each step along each path of a Kersplat simulation
+#'
+#' @param params KersplatParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' The method of simulating paths is inspired by the method used in the PROSSTT
+#' simulation. Changes in expression are controlled by \code{paths.nPrograms}
+#' regulatory programs. Each of the regulatory genes in the gene network has
+#' some association with each program. This is analogous to there being changes
+#' in the environment (the programs) which are sensed by receptors (regulatory
+#' genes) and cause changes in expression downstream. For each path a random
+#' walk is generated for each program and the changes passed on to the
+#' regulatory genes. At each step the changes propagate through the network
+#' according to the weights on edges between genes. This algorithm is fairly
+#' simple but should result in correlation relationships between genes. However
+#' it is likely to be improved and adjusted in the future.
+#'
+#' The path structure itself is specified by the \code{paths.design} parameter.
+#' This is a \code{data.frame} with three columns: "Path", "From", and "Steps".
+#' The Path field is an ID for each path while the Steps field controls the
+#' length of each path. Increasing the number of steps will increase the
+#' difference in expression between the ends of the paths. The From field sets
+#' the originating point of each path. For example a From of \code{0, 0, 0}
+#' would indicate three paths from the origin while a From of \code{0, 1, 1}
+#' would give a branching structure with Path 1 beginning at the origin and
+#' Path 2 and Path 3 beginning at the end of Path 1.
+#'
+#' @references
+#'
+#' Papadopoulos N, Parra RG, Söding J. PROSSTT: probabilistic simulation of
+#' single-cell RNA-seq data for complex differentiation processes.
+#' Bioinformatics (2019). \url{https://doi.org/10.1093/bioinformatics/btz078}.
+#'
+#' @return KersplatParams object with path means
+kersplatSimPaths <- function(params, verbose) {
+
+ paths.means <- getParam(params, "paths.means")
+
+ if (length(paths.means) != 0) {
+ if (verbose) {message("Using defined path means...")}
+ return(params)
+ }
+
+ if (verbose) {message("Simulating paths...")}
+ nGenes <- getParam(params, "nGenes")
+ paths.design <- getParam(params, "paths.design")
+ network.graph <- getParam(params, "network.graph")
+ network.weights <- igraph::as_adjacency_matrix(network.graph,
+ attr = "weight")
+ network.nRegs <- getParam(params, "network.nRegs")
+ network.isReg <- igraph::vertex_attr(network.graph, "IsReg")
+ paths.nPrograms <- getParam(params, "paths.nPrograms")
+
+ programs.weights <- matrix(rnorm(network.nRegs * paths.nPrograms),
+ nrow = network.nRegs, ncol = paths.nPrograms)
+ paths.changes <- vector("list", nrow(paths.design))
+ paths.factors <- vector("list", nrow(paths.design))
+
+ paths.graph <- igraph::graph_from_data_frame(paths.design)
+ paths.order <- names(igraph::topo_sort(paths.graph, mode = "in"))
+ paths.order <- as.numeric(paths.order)
+ # Remove the origin because it is not a path
+ paths.order <- paths.order[paths.order != 0]
+
+ for (path in paths.order) {
+ if (verbose) {message("Simulating path ", path, "...")}
+ nSteps <- paths.design$Steps[path]
+ from <- paths.design$From[path]
+ changes <- matrix(0, nrow = nGenes, ncol = nSteps + 1)
+
+ if (from != 0) {
+ from.changes <- paths.changes[[from]]
+ changes[, 1] <- from.changes[, ncol(from.changes)]
+ }
+
+ for (step in seq_len(nSteps) + 1) {
+ programs.changes <- rnorm(paths.nPrograms, sd = 0.01)
+ reg.changes <- as.vector(programs.weights %*% programs.changes)
+ changes[network.isReg, step] <- reg.changes
+ change <- as.vector(changes[, step - 1] %*% network.weights)
+ changes[, step] <- changes[, step] + change
+ }
+
+ if (from == 0) {
+ changes <- changes[, seq_len(nSteps)]
+ factors <- matrixStats::rowCumsums(changes)
+ } else {
+ changes <- changes[, seq_len(nSteps) + 1]
+ from.factors <- paths.factors[[from]][, ncol(paths.factors[[from]])]
+ factors <- matrixStats::rowCumsums(changes) + from.factors
+ }
+ paths.changes[[path]] <- changes
+ paths.factors[[path]] <- factors
+ }
+
+ mean.values <- getParam(params, "mean.values")
+ paths.means <- lapply(paths.factors, function(x) {
+ (2 ^ x) * mean.values
+ })
+
+ names(paths.means) <- paste0("Path", paths.design$Path)
+ params <- setParam(params, "paths.means", paths.means)
+
+ return(params)
+}
+
+#' Simulate Kersplat library sizes
+#'
+#' Generate library sizes for cells in the Kersplat simulation
+#'
+#' @param sim SingleCellExperiment containing simulation.
+#' @param params KersplatParams object with simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Library sizes are simulated in one of two ways depending on the value of the
+#' \code{lib.method} parameter.
+#'
+#' If \code{lib.method} is "fit" (default) then means are sampled from a
+#' log-normal distribution with meanlog equals \code{lib.loc} and sdlog equals
+#' \code{lib.scale}.
+#'
+#' If \code{mean.method} is "density" then library sizes are sampled from the
+#' density object in the \code{lib.density} parameter using a rejection
+#' sampling method. This approach is more flexible but may violate some
+#' statistical assumptions.
+#'
+#' Ambient library sizes are also generated from a log-normal distribution based
+#' on the parameters for the cell library size and adjusted using the
+#' \code{ambient.scale} parameter.
+#'
+#' @return SingleCellExperiment with library sizes
+kersplatSimLibSizes <- function(sim, params, verbose) {
+
+ if (verbose) {message("Simulating library sizes...")}
+ nCells <- getParam(params, "nCells")
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ is.doublet <- colData(sim)$Type == "Doublet"
+ lib.method <- getParam(params, "lib.method")
+
+ if (lib.method == "fit") {
+ if (verbose) {message("Sampling from log-normal distribution...")}
+ lib.loc <- getParam(params, "lib.loc")
+ lib.scale <- getParam(params, "lib.scale")
+
+ cell.lib.sizes <- rlnorm(nCells, lib.loc, lib.scale)
+ } else if (lib.method == "density") {
+ if (verbose) {message("Sampling from density object...")}
+ lib.dens <- getParam(params, "lib.dens")
+
+ cell.lib.sizes <- sampleDensity(nCells, lib.dens)
+ }
+
+ cell.lib.sizes <- c(cell.lib.sizes, rep(0, nEmpty))
+ cell.lib.sizes[is.doublet] <- 1.5 * cell.lib.sizes[is.doublet]
+ colData(sim)$CellLibSize <- cell.lib.sizes
+
+ ambient.scale <- getParam(params, "ambient.scale")
+ if (ambient.scale > 0) {
+ ambient.loc <- log(exp(lib.loc) * ambient.scale)
+
+ ambient.lib.sizes <- rlnorm(nCells + nEmpty, ambient.loc, 0.3)
+ colData(sim)$AmbientLibSize <- ambient.lib.sizes
+ }
+
+ return(sim)
+}
+
+#' Simulate Kersplat cell means
+#'
+#' Simulate endogenous counts for each cell in a Kersplat simulation
+#'
+#' @param sim SingleCellExperiment containing simulation.
+#' @param params KersplatParams object with simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Cells are first assigned to a path and a step along that path. This is
+#' controlled by the \code{cells.design} parameter which is a \code{data.frame}
+#' with the columns "Path", "Probability", "Alpha" and "Beta". The Path field
+#' is an ID for each path and the Probability field is the probability that a
+#' cell will come from that path (must sum to 1). The Alpha and Beta parameters
+#' control the density of cells along the path. After they are assigned to paths
+#' the step for each cell is sampled from a Beta distribution with parameters
+#' shape1 equals Alpha and shape2 equals beta. This approach is very flexible
+#' and allows almost any distribution of cells along a path. The distribution
+#' can be viewed using \code{hist(rbeta(10000, Alpha, Beta), breaks = 100)}.
+#' Some useful combinations of parameters are:
+#'
+#' \describe{
+#' \item{\code{Alpha = 1}, \code{Beta = 1}}{Uniform distribution along the
+#' path}
+#' \item{\code{Alpha = 0}, \code{Beta = 1}}{All cells at the start of the
+#' path.}
+#' \item{\code{Alpha = 1}, \code{Beta = 0}}{All cells at the end of the
+#' path.}
+#' \item{\code{Alpha = 0}, \code{Beta = 0}}{Cells only at each end of the
+#' path.}
+#' \item{\code{Alpha = 1}, \code{Beta = 2}}{Linear skew towards the start
+#' of the path}
+#' \item{\code{Alpha = 0.5}, \code{Beta = 1}}{Curved skew towards the start
+#' of the path}
+#' \item{\code{Alpha = 2}, \code{Beta = 1}}{Linear skew towards the end
+#' of the path}
+#' \item{\code{Alpha = 1}, \code{Beta = 0.5}}{Curved skew towards the end
+#' of the path}
+#' \item{\code{Alpha = 0.5}, \code{Beta = 0.5}}{Curved skew towards both
+#' ends of the path}
+#' \item{\code{Alpha = 0.5}, \code{Beta = 0.5}}{Curved skew away from both
+#' ends of the path}
+#' }
+#'
+#' Once cells are assigned to paths and steps the correct means are extracted
+#' from the \code{paths.means} parameter and adjusted based on each cell's
+#' library size. An adjustment for BCV is then applied. Doublets are also
+#' simulated at this stage by selecting two path/step combinations and averaging
+#' the means.
+#'
+#' @return SingleCellExperiment with cell means
+kersplatSimCellMeans <- function(sim, params, verbose) {
+
+ cell.names <- colData(sim)$Cell
+ gene.names <- rowData(sim)$Gene
+ nGenes <- getParam(params, "nGenes")
+ nDoublets <- sum(colData(sim)$Type == "Doublet")
+ nCells <- getParam(params, "nCells") - nDoublets
+ cells.design <- getParam(params, "cells.design")
+ paths.design <- getParam(params, "paths.design")
+ paths.means <- getParam(params, "paths.means")
+ cell.lib.sizes <- colData(sim)$CellLibSize
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ not.empty <- colData(sim)$Type != "Empty"
+
+ if (verbose) {message("Assigning cells to paths...")}
+ cells.paths <- sample(cells.design$Path, nCells, replace = TRUE,
+ prob = cells.design$Probability)
+
+ if (verbose) {message("Assigning cells to steps...")}
+ paths.cells.design <- merge(paths.design, cells.design)
+ steps.probs <- apply(paths.cells.design, 1, function(path) {
+ steps <- path["Steps"]
+ probs <- getBetaStepProbs(path["Steps"], path["Alpha"], path["Beta"])
+
+ # Return a list to avoid getting a matrix if all path lengths are equal
+ return(list(probs))
+ })
+ # Remove unnecessary list level
+ steps.probs <- lapply(steps.probs, "[[", 1)
+ names(steps.probs) <- paths.cells.design$Path
+
+ cells.steps <- vapply(cells.paths, function(path) {
+ probs <- steps.probs[[path]]
+ step <- sample(seq_len(length(probs)), 1, prob = probs)
+ return(step)
+ }, c(Step = 0))
+
+ if (verbose) {message("Simulating cell means...")}
+ cells.means <- vapply(seq_len(nCells), function(cell) {
+ path <- cells.paths[cell]
+ step <- cells.steps[cell]
+ means <- paths.means[[path]][, step]
+ return(means)
+ }, as.numeric(seq_len(nGenes)))
+
+ if (nDoublets > 0) {
+ if (verbose) {message("Assigning doublets...")}
+ doublet.paths1 <- sample(cells.design$Path, nDoublets, replace = TRUE,
+ prob = cells.design$Probability)
+ doublet.paths2 <- sample(cells.design$Path, nDoublets, replace = TRUE,
+ prob = cells.design$Probability)
+
+ doublet.steps1 <- vapply(doublet.paths1, function(path) {
+ probs <- steps.probs[[path]]
+ step <- sample(seq_len(length(probs)), 1, prob = probs)
+ return(step)
+ }, c(Step1 = 0))
+ doublet.steps2 <- vapply(doublet.paths2, function(path) {
+ probs <- steps.probs[[path]]
+ step <- sample(seq_len(length(probs)), 1, prob = probs)
+ return(step)
+ }, c(Step2 = 0))
+
+ if (verbose) {message("Simulating doublet means...")}
+ doublet.means1 <- vapply(seq_len(nDoublets), function(doublet) {
+ path <- doublet.paths1[doublet]
+ step <- doublet.steps1[doublet]
+ means <- paths.means[[path]][, step]
+ return(means)
+ }, as.numeric(seq_len(nGenes)))
+ doublet.means2 <- vapply(seq_len(nDoublets), function(doublet) {
+ path <- doublet.paths2[doublet]
+ step <- doublet.steps2[doublet]
+ means <- paths.means[[path]][, step]
+ return(means)
+ }, as.numeric(seq_len(nGenes)))
+ doublet.means <- (doublet.means1 + doublet.means2) * 0.5
+
+ cells.means <- cbind(cells.means, doublet.means)
+ }
+
+ # Adjust mean based on library size
+ cells.props <- t(t(cells.means) / colSums(cells.means))
+ cells.means <- t(t(cells.props) * cell.lib.sizes[not.empty])
+
+ if (verbose) {message("Applying BCV adjustment...")}
+ nGenes <- getParam(params, "nGenes")
+ bcv.common <- getParam(params, "bcv.common")
+ bcv.df <- getParam(params, "bcv.df")
+
+ if (is.finite(bcv.df)) {
+ bcv <- (bcv.common + (1 / sqrt(cells.means))) *
+ sqrt(bcv.df / rchisq(nGenes, df = bcv.df))
+ } else {
+ warning("'bcv.df' is infinite. This parameter will be ignored.")
+ bcv <- (bcv.common + (1 / sqrt(cells.means)))
+ }
+
+ cells.means <- matrix(rgamma(
+ as.numeric(nGenes) * as.numeric(nCells + nDoublets),
+ shape = 1 / (bcv ^ 2), scale = cells.means * (bcv ^ 2)),
+ nrow = nGenes, ncol = nCells + nDoublets)
+
+ empty.means <- matrix(0, nrow = nGenes, ncol = nEmpty)
+ cells.means <- cbind(cells.means, empty.means)
+
+ colnames(cells.means) <- cell.names
+ rownames(cells.means) <- gene.names
+
+ colData(sim)$Path <- factor(c(cells.paths, rep(NA, nDoublets),
+ rep(NA, nEmpty)))
+ colData(sim)$Step <- c(cells.steps, rep(NA, nDoublets), rep(NA, nEmpty))
+
+ if (nDoublets > 0) {
+ colData(sim)$Path1 <- factor(c(rep(NA, nCells), doublet.paths1,
+ rep(NA, nEmpty)))
+ colData(sim)$Step1 <- c(rep(NA, nCells), doublet.steps1,
+ rep(NA, nEmpty))
+ colData(sim)$Path2 <- factor(c(rep(NA, nCells), doublet.paths2,
+ rep(NA, nEmpty)))
+ colData(sim)$Step2 <- c(rep(NA, nCells), doublet.steps2,
+ rep(NA, nEmpty))
+ }
+
+ assays(sim)$CellMeans <- cells.means
+
+ return(sim)
+}
+
+#' Simulate Kersplat cell counts
+#'
+#' Simulate cell counts for the Kersplat simulation
+#'
+#' @param sim SingleCellExperiment containing simulation.
+#' @param params KersplatParams object with simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' Counts are sampled from a Poisson distribution with lambda equal to the
+#' cell means matrix.
+#'
+#' @return SingleCellExperiment with cell counts
+kersplatSimCellCounts <- function(sim, params, verbose) {
+
+ if (verbose) {message("Simulating cell counts...")}
+ cell.names <- colData(sim)$Cell
+ gene.names <- rowData(sim)$Gene
+ nGenes <- getParam(params, "nGenes")
+ nCells <- getParam(params, "nCells")
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ cells.means <- assays(sim)$CellMeans
+
+ cell.counts <- matrix(rpois(
+ as.numeric(nGenes) * as.numeric(nCells + nEmpty),
+ lambda = cells.means),
+ nrow = nGenes, ncol = nCells + nEmpty)
+
+ colnames(cell.counts) <- cell.names
+ rownames(cell.counts) <- gene.names
+ assays(sim)$CellCounts <- cell.counts
+
+ return(sim)
+}
+
+#' Simulate Kersplat ambient counts
+#'
+#' @param sim SingleCellExperiment containing simulation.
+#' @param params KersplatParams object with simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' The overall expression profile to calculated by averaging the cell counts
+#' of the (non-empty) cells. This is then multiplied by the ambient library
+#' sizes to get a mean for each cell. Counts are then sampled from a Poisson
+#' distribution using these means.
+#'
+#' @return SingleCellExperiment with ambient counts
+kersplatSimAmbientCounts <- function(sim, params, verbose) {
+
+ if (verbose) {message("Simulating ambient counts...")}
+ cell.names <- colData(sim)$Cell
+ gene.names <- rowData(sim)$Gene
+ nGenes <- getParam(params, "nGenes")
+ nCells <- getParam(params, "nCells")
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ cell.counts <- assays(sim)$CellCounts
+ not.empty <- colData(sim)$Type != "Empty"
+ ambient.lib.sizes <- colData(sim)$AmbientLibSize
+
+ not.empty.means <- rowMeans(cell.counts[, not.empty])
+ ambient.props <- not.empty.means / sum(not.empty.means)
+
+ ambient.means <- ambient.props %*% t(ambient.lib.sizes)
+
+ ambient.counts <- matrix(rpois(
+ as.numeric(nGenes) * as.numeric(nCells + nEmpty),
+ lambda = ambient.means),
+ nrow = nGenes, ncol = nCells + nEmpty)
+
+ colnames(ambient.counts) <- cell.names
+ rownames(ambient.counts) <- gene.names
+ assays(sim)$AmbientCounts <- ambient.counts
+ rowData(sim)$AmbientMean <- not.empty.means
+
+ return(sim)
+}
+
+#' Simulate Kersplat final counts
+#'
+#' Simulate the final counts matrix for a Kersplat simulation
+#'
+#' @param sim SingleCellExperiment containing simulation.
+#' @param params KersplatParams object with simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#'
+#' @details
+#' The cell counts matrix and ambient counts matrix are added together. The
+#' result is then downsampled to the cell library size (for cells and doublets)
+#' or the ambient library size (for empty cells) using the
+#' \code{\link[DropletUtils]{downsampleMatrix}} function.
+#'
+#' @seealso \code{\link[DropletUtils]{downsampleMatrix}}
+#'
+#' @return SingleCellExperiment with counts matrix
+kersplatSimCounts <- function(sim, params, verbose) {
+
+ if (verbose) {message("Simulating final counts...")}
+ cell.lib.sizes <- colData(sim)$CellLibSize
+ ambient.lib.sizes <- colData(sim)$AmbientLibSize
+ empty <- colData(sim)$Type == "Empty"
+ cell.counts <- assays(sim)$CellCounts
+ ambient.counts <- assays(sim)$AmbientCounts
+
+ lib.sizes <- cell.lib.sizes
+ lib.sizes[empty] <- ambient.lib.sizes[empty]
+
+ counts <- cell.counts + ambient.counts
+
+ down.prop <- lib.sizes / colSums(counts)
+ # Avoid proportion creeping over 1 for empty cells
+ down.prop <- min(down.prop, 1)
+
+ counts <- DropletUtils::downsampleMatrix(counts, down.prop)
+
+ assays(sim)$counts <- counts
+
+ return(sim)
+}
+
+#' Get Beta step probabilities
+#'
+#' Use a Beta distribution for set probabilities along a path
+#'
+#' @param steps Number of steps
+#' @param alpha Alpha parameter
+#' @param beta Beta parameter
+#'
+#' @details
+#' The density is sampled from a Beta distribution between 0 and 1. Infinite
+#' densities at edges are adjusted and then the values are scaled to give
+#' probabilities.
+#'
+#' @return Vector of probabilities
+#'
+#' @importFrom stats dbeta
+getBetaStepProbs <- function(steps, alpha, beta) {
+ dens <- dbeta(seq(0, 1, length.out = steps), alpha, beta)
+
+ # Adjust for infinite values at edge of distribution
+ dens.inf <- !is.finite(dens)
+ if (any(dens.inf) && all(dens[!dens.inf] == 0)) {
+ dens[dens.inf] <- 1
+ }
+ if (!is.finite(dens[1])) {
+ dens[1] <- 1.1 * dens[2]
+ }
+ if (!is.finite(dens[steps])) {
+ dens[steps] <- 1.1 * dens[steps - 1]
+ }
+
+ probs <- dens / sum(dens)
+
+ return(probs)
+}
+
+#' Sample density
+#'
+#' Sample from a density object using rejection sampling
+#'
+#' @param n Number of values to sample
+#' @param dens Density object to sample from
+#' @param lower Lower x-axis bound on sampled values
+#'
+#' @details
+#' Random points (x and y) are generated inside the range of the density object.
+#' If they value is less than the density for that x value (and x is greater
+#' than \code{lower}) then that x value is retained. Ten thousand points are
+#' generated at a time until enough valid values have been sampled.
+#'
+#' @return Vector of sampled values
+#'
+#' @importFrom stats approxfun
+sampleDensity <- function(n, dens, lower = 0) {
+
+ xmin <- min(dens$x)
+ xmax <- max(dens$x)
+ ymin <- min(dens$y)
+ ymax <- max(dens$y)
+
+ boundary <- approxfun(dens$x, dens$y)
+
+ values <- c()
+ nsel <- 0
+
+ while(nsel < n) {
+ x <- runif(1e4, xmin, xmax)
+ y <- runif(1e4, ymin, ymax)
+ sel <- y < boundary(x) & x > lower
+
+ nsel <- nsel + sum(sel)
+ values <- c(values, x[sel])
+ }
+
+ values <- values[seq_len(n)]
+
+ return(values)
+}
diff --git a/R/listSims.R b/R/listSims.R
index f30b1188d42fe861308be77573bc0d04dfff1d66..891bb4087e08db729c27f812ba8071e7d17adb8f 100644
--- a/R/listSims.R
+++ b/R/listSims.R
@@ -31,6 +31,11 @@ listSims <- function(print = TRUE) {
"The Splat simulation with differentiation paths. Each
path can have it's own length, skew and probability. Genes
can change in non-linear ways."),
+ c("Kersplat", "kersplat", "",
+ "Oshlack/splatter",
+ "The Kersplat simulation extends the Splat model by adding a
+ gene network, more complex cell structure, doublets and
+ empty cells (Experimental)."),
c("Simple", "simple", "10.1186/s13059-017-1305-0",
"Oshlack/splatter",
"A simple simulation with gamma means and negative binomial
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index 298c84ba27f35cfb6b09c83c7191ec2434a09735..140019bb1520da99981c8c98ff7943bfb7fed61a 100644
--- a/R/lun-estimate.R
+++ b/R/lun-estimate.R
@@ -16,9 +16,10 @@
#' @examples
#' # Load example data
#' library(scater)
-#' data("sc_example_counts")
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' params <- lunEstimate(sc_example_counts)
+#' params <- lunEstimate(sce)
#' params
#' @export
lunEstimate <- function(counts, params = newLunParams()) {
@@ -28,7 +29,7 @@ lunEstimate <- function(counts, params = newLunParams()) {
#' @rdname lunEstimate
#' @export
lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
- counts <- BiocGenerics::counts(counts)
+ counts <- getCounts(counts)
lunEstimate(counts, params)
}
diff --git a/R/lun-simulate.R b/R/lun-simulate.R
index b94c6567a32fba326b779c1ef1a4ec011eb793e1..526733e179c2a213a4fe2b827f1969e9882ee826 100644
--- a/R/lun-simulate.R
+++ b/R/lun-simulate.R
@@ -105,9 +105,11 @@ lunSimulate <- function(params = newLunParams(), verbose = TRUE, ...) {
rownames(cell.means) <- gene.names
if (verbose) {message("Simulating counts...")}
- counts <- matrix(rnbinom(nGenes * nCells, mu = cell.means,
- size = 1 / count.disp),
- nrow = nGenes, ncol = nCells)
+ counts <- matrix(rnbinom(
+ as.numeric(nGenes) * as.numeric(nCells),
+ mu = cell.means, size = 1 / count.disp
+ ),
+ nrow = nGenes, ncol = nCells)
if (verbose) {message("Creating final dataset...")}
rownames(counts) <- gene.names
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index aaedad7852ef48ac0d8f66e1fc21c2957d263b70..f9332d9a39324e3da3a5157fe91a20e36d75eb14 100644
--- a/R/lun2-estimate.R
+++ b/R/lun2-estimate.R
@@ -22,11 +22,11 @@
#' \dontrun{
#' # Load example data
#' library(scater)
-#' data("sc_example_counts")
-#' data("sc_example_cell_info")
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' plates <- factor(sc_example_cell_info$Mutation_Status)
-#' params <- lun2Estimate(sc_example_counts, plates, min.size = 20)
+#' plates <- as.numeric(factor(colData(sce)$Mutation_Status))
+#' params <- lun2Estimate(sce, plates, min.size = 20)
#' params
#' }
#' @importFrom BiocParallel bplapply SerialParam
@@ -43,8 +43,9 @@ lun2Estimate.SingleCellExperiment <- function(counts, plates,
params = newLun2Params(),
min.size = 200, verbose = TRUE,
BPPARAM = SerialParam()) {
- counts <- BiocGenerics::counts(counts)
- lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose)
+ counts <- getCounts(counts)
+ lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose,
+ BPPARAM = BPPARAM)
}
#' @rdname lun2Estimate
diff --git a/R/lun2-simulate.R b/R/lun2-simulate.R
index ec5ff3b11545cb519bda2c2f64405cbfcc3eb13c..68cc68471f5f06d92ac3fa3e23e302077f3ca731 100644
--- a/R/lun2-simulate.R
+++ b/R/lun2-simulate.R
@@ -19,9 +19,9 @@
#' Library size factors are also applied and optionally a zero-inflated
#' negative-binomial can be used.
#'
-#' If the number of genes to simulate differs from the number of provied gene
+#' If the number of genes to simulate differs from the number of provided gene
#' parameters or the number of cells to simulate differs from the number of
-#' library sizes the relevant paramters will be sampled with a warning. This
+#' library sizes the relevant parameters will be sampled with a warning. This
#' allows any number of genes or cells to be simulated regardless of the
#' number in the dataset used in the estimation step but has the downside that
#' some genes or cells may be simulated multiple times.
@@ -145,7 +145,7 @@ lun2Simulate <- function(params = newLun2Params(), zinb = FALSE,
}
}
- if (verbose) {message("Simulating libray size factors...")}
+ if (verbose) {message("Simulating library size factors...")}
lib.facs <- lib.sizes / mean(lib.sizes)
lib.facs <- sample(lib.facs, nCells, replace = TRUE) * lib.mod
cells$LibSizeFac <- lib.facs
diff --git a/R/mfa-estimate.R b/R/mfa-estimate.R
index 62aa212951ec26e51ad7f7aaea05c27ee585e1d2..dcff5ae6f42ad2ec954fae2dcc53b67eeb402d95 100644
--- a/R/mfa-estimate.R
+++ b/R/mfa-estimate.R
@@ -16,11 +16,14 @@
#'
#' @examples
#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("mfa", quietly = TRUE)) {
+#' library(mfa)
+#' synth <- create_synthetic(C = 20, G = 5, zero_negative = TRUE,
+#' model_dropout = TRUE)
#'
-#' params <- mfaEstimate(sc_example_counts)
-#' params
+#' params <- mfaEstimate(synth$X)
+#' params
+#' }
#' @export
mfaEstimate <- function(counts, params = newMFAParams()) {
UseMethod("mfaEstimate")
@@ -30,7 +33,7 @@ mfaEstimate <- function(counts, params = newMFAParams()) {
#' @export
mfaEstimate.SingleCellExperiment <- function(counts,
params = newMFAParams()) {
- counts <- BiocGenerics::counts(counts)
+ counts <- getCounts(counts)
mfaEstimate(counts, params)
}
diff --git a/R/mfa-simulate.R b/R/mfa-simulate.R
index 8f6a7a29312d30dd87f942fd66aead64a81db5b1..eb7e1d1867e076eee377d2bfa88b6f7a407a7a8d 100644
--- a/R/mfa-simulate.R
+++ b/R/mfa-simulate.R
@@ -27,7 +27,9 @@
#' Code: \url{https://github.com/kieranrcampbell/mfa}
#'
#' @examples
-#' sim <- mfaSimulate()
+#' if (requireNamespace("mfa", quietly = TRUE)) {
+#' sim <- mfaSimulate()
+#' }
#' @export
mfaSimulate <- function(params = newMFAParams(), verbose = TRUE, ...) {
diff --git a/R/params-functions.R b/R/params-functions.R
index c17fa35a8cd4ac3eb91e3a8d0b382c94f126d835..eed27d1e542fd901a2a80f0b06bd81049fc4c418 100644
--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -15,52 +15,10 @@ getParams <- function(params, names) {
checkmate::assertClass(params, classes = "Params")
checkmate::assertCharacter(names, min.len = 1, any.missing = FALSE)
- sapply(names, getParam, object = params, simplify = FALSE)
-}
-
-#' Set parameters
-#'
-#' Set multiple parameters in a Params object.
-#'
-#' @param params Params object to set parameters in.
-#' @param update list of parameters to set where \code{names(update)} are the
-#' names of the parameters to set and the items in the list are values.
-#' @param ... additional parameters to set. These are combined with any
-#' parameters specified in \code{update}.
-#'
-#' @details
-#' Each parameter is set by a call to \code{\link{setParam}}. If the same
-#' parameter is specified multiple times it will be set multiple times.
-#' Parameters can be specified using a list via \code{update} (useful when
-#' collecting parameter values in some way) or individually (useful when setting
-#' them manually), see examples.
-#'
-#' @return Params object with updated values.
-#' @examples
-#' params <- newSimpleParams()
-#' params
-#' # Set individually
-#' params <- setParams(params, nGenes = 1000, nCells = 50)
-#' params
-#' # Set via update list
-#' params <- setParams(params, list(mean.rate = 0.2, mean.shape = 0.8))
-#' params
-#' @export
-setParams <- function(params, update = NULL, ...) {
+ params.list <- lapply(names, getParam, object = params)
+ names(params.list) <- names
- checkmate::assertClass(params, classes = "Params")
- checkmate::assertList(update, null.ok = TRUE)
-
- update <- c(update, list(...))
-
- if (length(update) > 0) {
- for (name in names(update)) {
- value <- update[[name]]
- params <- setParam(params, name, value)
- }
- }
-
- return(params)
+ return(params.list)
}
#' Set parameters UNCHECKED
@@ -115,13 +73,18 @@ showPP <- function(params, pp) {
for (category in names(pp)) {
parameters <- pp[[category]]
values <- getParams(params, parameters)
- is.df <- sapply(values, is.data.frame)
+ is.df <- vapply(values, is.data.frame, FALSE)
default.values <- getParams(default, parameters)
- not.default <- sapply(seq_along(values), function(i) {
+ not.default <- vapply(seq_along(values), function(i) {
!identical(values[i], default.values[i])
- })
+ }, FALSE)
+ empty.values <- vapply(values, function(x) {
+ is.null(x) || length(x) == 0
+ }, FALSE)
+ values[empty.values] <- "Not set"
+ names(values) <- names(parameters)
cat(crayon::bold(category), "\n")
if (sum(!is.df) > 0) {
showValues(values[!is.df], not.default[!is.df])
@@ -133,13 +96,15 @@ showPP <- function(params, pp) {
}
}
-#' Show vales
+#' Show values
#'
-#' Function used for pretty printing scale or vector parameters.
+#' Function used for pretty printing scalar or vector parameters.
#'
#' @param values list of values to show.
#' @param not.default logical vector giving which have changed from the default.
#'
+#' @return Print values
+#'
#' @importFrom utils head
showValues <- function(values, not.default) {
@@ -147,13 +112,22 @@ showValues <- function(values, not.default) {
checkmate::check_logical(not.default, any.missing = FALSE,
len = length(values))
- short.values <- sapply(values, function(x) {
- if (length(x) > 4) {
- paste0(paste(head(x, n = 4), collapse = ", "), ",...")
+ short.values <- vapply(values, function(x) {
+ if (is.list(x)) {
+ classes <- class(x)
+ if (length(classes) == 1 && classes == "list") {
+ paste("List with", length(x), "items")
+ } else {
+ paste("Object of class", paste(classes, collapse = ", "))
+ }
} else {
- paste(x, collapse = ", ")
+ if (length(x) > 4) {
+ paste0(paste(head(x, n = 4), collapse = ", "), ",...")
+ } else {
+ paste(x, collapse = ", ")
+ }
}
- })
+ }, c(Value = "None"))
names(short.values)[not.default] <- toupper(names(values[not.default]))
@@ -163,15 +137,19 @@ showValues <- function(values, not.default) {
items.per.line <- floor(screen.width / (max.len + 2))
short.names <- names(short.values)
- short.values <- crayon::col_align(short.values, max.len, "right")
- short.names <- crayon::col_align(short.names, max.len, "right")
-
not.est <- !grepl("\\(", short.names)
+ secondary <- grepl("\\*", short.names)
+ short.names <- gsub("\\*", "", short.names)
+
short.names[not.est] <- crayon::blue(short.names[not.est])
+ short.names[secondary] <- crayon::bgYellow(short.names[secondary])
short.names[not.default] <- crayon::bold(short.names[not.default])
short.values[not.default] <- crayon::green(short.values[not.default])
short.values[not.default] <- crayon::bold(short.values[not.default])
+ short.values <- crayon::col_align(short.values, max.len, "right")
+ short.names <- crayon::col_align(short.names, max.len, "right")
+
names(short.values) <- short.names
values.list <- split(short.values,
@@ -190,6 +168,8 @@ showValues <- function(values, not.default) {
#' @param dfs list of data.frames to show.
#' @param not.default logical vector giving which have changed from the default.
#'
+#' @return Print data.frame parameters
+#'
#' @importFrom utils head
showDFs <- function(dfs, not.default) {
@@ -218,6 +198,8 @@ showDFs <- function(dfs, not.default) {
cat(paste0("\n", name, "\n"))
cat(msg, "\n")
print(head(df, n = 4))
- cat("# ... with", nrow(df) - 4, "more rows\n")
+ if (nrow(df) > 4) {
+ cat("# ... with", nrow(df) - 4, "more rows\n")
+ }
}
}
diff --git a/R/pheno-estimate.R b/R/pheno-estimate.R
index cccf02fd575db38a2a210602b7f2501a480aee72..47c92d75a9089370bd9da372a80087e5579e6c9e 100644
--- a/R/pheno-estimate.R
+++ b/R/pheno-estimate.R
@@ -15,12 +15,15 @@
#' @return PhenoParams object containing the estimated parameters.
#'
#' @examples
-#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("phenopath", quietly = TRUE)) {
+#' # Load example data
+#' library(scater)
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' params <- phenoEstimate(sc_example_counts)
-#' params
+#' params <- phenoEstimate(sce)
+#' params
+#' }
#' @export
phenoEstimate <- function(counts, params = newPhenoParams()) {
UseMethod("phenoEstimate")
@@ -30,7 +33,7 @@ phenoEstimate <- function(counts, params = newPhenoParams()) {
#' @export
phenoEstimate.SingleCellExperiment <- function(counts,
params = newPhenoParams()) {
- counts <- BiocGenerics::counts(counts)
+ counts <- getCounts(counts)
phenoEstimate(counts, params)
}
diff --git a/R/pheno-simulate.R b/R/pheno-simulate.R
index 56c2e99ddb5d45834214c941892dfc40a68221a1..8e068a3fc110a523509165d95ef6021010541ebd 100644
--- a/R/pheno-simulate.R
+++ b/R/pheno-simulate.R
@@ -29,8 +29,9 @@
#' Code: \url{https://github.com/kieranrcampbell/phenopath}
#'
#' @examples
-#' sim <- phenoSimulate()
-#'
+#' if (requireNamespace("phenopath", quietly = TRUE)) {
+#' sim <- phenoSimulate()
+#' }
#' @export
#' @importFrom SingleCellExperiment SingleCellExperiment
phenoSimulate <- function(params = newPhenoParams(), verbose = TRUE, ...) {
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index e8e1ccc8b4020eca5d7bb186e750a92ec8eed8a2..87ecaa0ebdfaf44fba2d6b3b1d269b3bde31b261 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -24,15 +24,16 @@
#' @return SCDDParams object containing the estimated parameters.
#'
#' @examples
-#' \dontrun{
-#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("scDD", quietly = TRUE)) {
+#' library(scater)
+#' set.seed(1)
+#' sce <- mockSCE(ncells = 20, ngenes = 100)
#'
-#' conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
-#' params <- scDDEstimate(sc_example_counts, conditions = conditions)
-#' params
+#' colData(sce)$condition <- sample(1:2, ncol(sce), replace = TRUE)
+#' params <- scDDEstimate(sce, condition = "condition")
+#' params
#' }
+#'
#' @importFrom BiocParallel SerialParam
#' @export
scDDEstimate <- function(counts, #conditions, condition,
@@ -72,6 +73,7 @@ scDDEstimate.SingleCellExperiment <- function(counts,
verbose = TRUE,
BPPARAM = SerialParam(),
condition = "condition", ...) {
+
scDDEstimate.default(counts, params, verbose, BPPARAM,
condition = condition)
}
diff --git a/R/scDD-simulate.R b/R/scDD-simulate.R
index abcb8ffcb805014c56a841d279142ce3cbf1fa1b..4c3be4aaf46fa3f1f9b95f96da56addfd2e2f91b 100644
--- a/R/scDD-simulate.R
+++ b/R/scDD-simulate.R
@@ -103,7 +103,7 @@ scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
colnames(counts) <- cell.names
cells <- data.frame(Cell = cell.names,
- Condition = rep(1:2, each = nCells))
+ Condition = rep(seq_len(2), each = nCells))
rownames(cells) <- cell.names
features <- data.frame(Gene = gene.names, DEStatus = de.status,
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 1f9e6cc653bbfa215e695d09a2d3268eb7372152..c5e208fd12c2de272ad377bc61cfaddc957772e6 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -18,9 +18,10 @@
#' @examples
#' # Load example data
#' library(scater)
-#' data("sc_example_counts")
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' params <- simpleEstimate(sc_example_counts)
+#' params <- simpleEstimate(sce)
#' params
#' @export
simpleEstimate <- function(counts, params = newSimpleParams()) {
@@ -31,7 +32,7 @@ simpleEstimate <- function(counts, params = newSimpleParams()) {
#' @export
simpleEstimate.SingleCellExperiment <- function(counts,
params = newSimpleParams()) {
- counts <- BiocGenerics::counts(counts)
+ counts <- getCounts(counts)
simpleEstimate(counts, params)
}
diff --git a/R/simple-simulate.R b/R/simple-simulate.R
index 3c074cee3ab9c42de8a42376d500121e6555b879..13391c808de637dd4616132d15f860cb0d68b202 100644
--- a/R/simple-simulate.R
+++ b/R/simple-simulate.R
@@ -43,9 +43,10 @@ simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
means <- rgamma(nGenes, shape = mean.shape, rate = mean.rate)
if (verbose) {message("Simulating counts...")}
- counts <- matrix(rnbinom(nGenes * nCells, mu = means,
- size = 1 / count.disp),
- nrow = nGenes, ncol = nCells)
+ counts <- matrix(rnbinom(
+ as.numeric(nGenes) * as.numeric(nCells),
+ mu = means, size = 1 / count.disp),
+ nrow = nGenes, ncol = nCells)
if (verbose) {message("Creating final dataset...")}
cell.names <- paste0("Cell", seq_len(nCells))
@@ -61,7 +62,7 @@ simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
sim <- SingleCellExperiment(assays = list(counts = counts),
rowData = features,
colData = cells,
- metadata = list(params = params))
+ metadata = list(Params = params))
return(sim)
}
diff --git a/R/sparseDC-estimate.R b/R/sparseDC-estimate.R
index 0c0f793f38b6c71d0e8ec68ae034063e36c78eca..f2847995f84f4064c86a959223c3984a435d1f1d 100644
--- a/R/sparseDC-estimate.R
+++ b/R/sparseDC-estimate.R
@@ -7,7 +7,7 @@
#' containing count data to estimate parameters from.
#' @param conditions numeric vector giving the condition each cell belongs to.
#' @param nclusters number of cluster present in the dataset.
-#' @param norm logical, whether to libray size normalise counts before
+#' @param norm logical, whether to library size normalise counts before
#' estimation. Set this to FALSE if counts is already normalised.
#' @param params PhenoParams object to store estimated values in.
#'
@@ -24,16 +24,17 @@
#' @return SparseParams object containing the estimated parameters.
#'
#' @examples
-#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("SparseDC", quietly = TRUE)) {
+#' # Load example data
+#' library(scater)
+#' set.seed(1)
+#' sce <- mockSCE(ncells = 20, ngenes = 100)
#'
-#' set.seed(1)
-#' conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
+#' conditions <- sample(1:2, ncol(sce), replace = TRUE)
#'
-#' params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
-#' nclusters = 3)
-#' params
+#' params <- sparseDCEstimate(sce, conditions, nclusters = 3)
+#' params
+#' }
#' @export
sparseDCEstimate <- function(counts, conditions, nclusters, norm = TRUE,
params = newSparseDCParams()) {
@@ -45,8 +46,8 @@ sparseDCEstimate <- function(counts, conditions, nclusters, norm = TRUE,
sparseDCEstimate.SingleCellExperiment <- function(counts, conditions, nclusters,
norm = TRUE,
params = newSparseDCParams()) {
- counts <- BiocGenerics::counts(counts)
- sparseDCEstimate(counts, params)
+ counts <- getCounts(counts)
+ sparseDCEstimate(counts, conditions, nclusters, norm, params)
}
#' @rdname sparseDCEstimate
diff --git a/R/sparseDC-simulate.R b/R/sparseDC-simulate.R
index 6b410ed1215e8f01a1282900408717c9530ccb77..abd69b3e389450a911d00272dbc88fe63724591b 100644
--- a/R/sparseDC-simulate.R
+++ b/R/sparseDC-simulate.R
@@ -31,8 +31,9 @@
#' Paper: \url{10.1093/nar/gkx1113}
#'
#' @examples
-#' sim <- sparseDCSimulate()
-#'
+#' if (requireNamespace("SparseDC", quietly = TRUE)) {
+#' sim <- sparseDCSimulate()
+#' }
#' @export
#' @importFrom SingleCellExperiment SingleCellExperiment
sparseDCSimulate <- function(params = newSparseDCParams(),
@@ -80,7 +81,8 @@ sparseDCSimulate <- function(params = newSparseDCParams(),
cells <- data.frame(Cell = cell.names,
Condition = factor(paste0("Condition",
- rep(1:2, each = nCells))),
+ rep(seq_len(2),
+ each = nCells))),
Cluster = factor(paste0("Cluster",
c(sparsedc.sim$clusters1,
sparsedc.sim$clusters2))),
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index 0af1ceda491b3fecd84b28a77dbc5fe15a539eed..179f7dca8de6f68d85268bb3ff28f7907d1f8a34 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -18,9 +18,10 @@
#' @examples
#' # Load example data
#' library(scater)
-#' data("sc_example_counts")
+#' set.seed(1)
+#' sce <- mockSCE()
#'
-#' params <- splatEstimate(sc_example_counts)
+#' params <- splatEstimate(sce)
#' params
#' @export
splatEstimate <- function(counts, params = newSplatParams()) {
@@ -31,7 +32,7 @@ splatEstimate <- function(counts, params = newSplatParams()) {
#' @export
splatEstimate.SingleCellExperiment <- function(counts,
params = newSplatParams()) {
- counts <- BiocGenerics::counts(counts)
+ counts <- getCounts(counts)
splatEstimate(counts, params)
}
@@ -69,7 +70,7 @@ splatEstimate.matrix <- function(counts, params = newSplatParams()) {
#' @param params SplatParams object to store estimated values in.
#'
#' @details
-#' Parameter for the gamma distribution are estimated by fitting the mean
+#' Parameters for the gamma distribution are estimated by fitting the mean
#' normalised counts using \code{\link[fitdistrplus]{fitdist}}. The 'maximum
#' goodness-of-fit estimation' method is used to minimise the Cramer-von Mises
#' distance. This can fail in some situations, in which case the 'method of
@@ -110,7 +111,7 @@ splatEstMean <- function(norm.counts, params) {
#' @param counts counts matrix to estimate parameters from.
#' @param params splatParams object to store estimated values in.
#'
-#' @return splatParams object with estimated values.
+#' @return SplatParams object with estimated values.
#'
#' @importFrom stats shapiro.test
splatEstLib <- function(counts, params) {
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index fbf9ff108ee00818bad3dd531425f9c704bb8568..927e0c69896e71f2fa8729bf814cfac360a60b19 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -42,7 +42,7 @@
#' \code{\link{assays}} (for gene by cell matrices) slots. This additional
#' information includes:
#' \describe{
-#' \item{\code{phenoData}}{
+#' \item{\code{colData}}{
#' \describe{
#' \item{Cell}{Unique cell identifier.}
#' \item{Group}{The group or path the cell belongs to.}
@@ -50,7 +50,7 @@
#' \item{Step (paths only)}{how far along the path each cell is.}
#' }
#' }
-#' \item{\code{featureData}}{
+#' \item{\code{rowData}}{
#' \describe{
#' \item{Gene}{Unique gene identifier.}
#' \item{BaseGeneMean}{The base expression level for that gene.}
@@ -66,7 +66,7 @@
#' non-linear changes in expression along a path.}
#' }
#' }
-#' \item{\code{assayData}}{
+#' \item{\code{assays}}{
#' \describe{
#' \item{BatchCellMeans}{The mean expression of genes in each cell
#' after adding batch effects.}
@@ -185,7 +185,7 @@ splatSimulate <- function(params = newSplatParams(),
if (method != "single") {
groups <- sample(seq_len(nGroups), nCells, prob = group.prob,
replace = TRUE)
- colData(sim)$Group <- group.names[groups]
+ colData(sim)$Group <- factor(group.names[groups], levels = group.names)
}
if (verbose) {message("Simulating library sizes...")}
@@ -396,7 +396,7 @@ splatSimBatchCellMeans <- function(sim, params) {
#'
#' Simulate differential expression. Differential expression factors for each
#' group are produced using \code{\link{getLNormFactors}} and these are added
-#' along with updated means for each group. For paths care is taked to make sure
+#' along with updated means for each group. For paths care is taken to make sure
#' they are simulated in the correct order.
#'
#' @param sim SingleCellExperiment to add differential expression to.
@@ -502,7 +502,7 @@ splatSimGroupCellMeans <- function(sim, params) {
cell.names <- colData(sim)$Cell
gene.names <- rowData(sim)$Gene
groups <- colData(sim)$Group
- group.names <- sort(unique(groups))
+ group.names <- levels(groups)
exp.lib.sizes <- colData(sim)$ExpLibSize
batch.means.cell <- assays(sim)$BatchCellMeans
@@ -530,7 +530,7 @@ splatSimPathCellMeans <- function(sim, params) {
cell.names <- colData(sim)$Cell
gene.names <- rowData(sim)$Gene
path.from <- getParam(params, "path.from")
- path.length <- getParam(params, "path.length")
+ path.nSteps <- getParam(params, "path.nSteps")
path.skew <- getParam(params, "path.skew")
path.nonlinearProb <- getParam(params, "path.nonlinearProb")
path.sigmaFac <- getParam(params, "path.sigmaFac")
@@ -558,7 +558,7 @@ splatSimPathCellMeans <- function(sim, params) {
rowData(sim)[[paste0("SigmaFacPath", idx)]] <- sigma.facs
}
- # Generate paths. Each path is a matrix with path.length columns and
+ # Generate paths. Each path is a matrix with path.nSteps columns and
# nGenes rows where the expression from each genes changes along the path.
path.steps <- lapply(seq_along(path.from), function(idx) {
from <- path.from[idx]
@@ -575,7 +575,7 @@ splatSimPathCellMeans <- function(sim, params) {
sigma.facs <- rowData(sim)[[paste0("SigmaFacPath", idx)]]
# Build Brownian bridges from start to end
- steps <- buildBridges(facs.start, facs.end, n = path.length[idx],
+ steps <- buildBridges(facs.start, facs.end, n = path.nSteps[idx],
sigma.fac = sigma.facs)
return(t(steps))
@@ -584,14 +584,14 @@ splatSimPathCellMeans <- function(sim, params) {
# Randomly assign a position in the appropriate path to each cell
path.probs <- lapply(seq_len(nGroups), function(idx) {
probs <- seq(path.skew[idx], 1 - path.skew[idx],
- length = path.length[idx])
+ length = path.nSteps[idx])
probs <- probs / sum(probs)
return(probs)
})
- steps <- sapply(factor(groups), function(path) {
- step <- sample(seq_len(path.length[path]), 1, prob = path.probs[[path]])
- })
+ steps <- vapply(factor(groups), function(path) {
+ step <- sample(seq_len(path.nSteps[path]), 1, prob = path.probs[[path]])
+ }, c(Step = 0))
# Collect the underlying expression levels for each cell
cell.facs.gene <- lapply(seq_len(nCells), function(idx) {
@@ -646,9 +646,10 @@ splatSimBCVMeans <- function(sim, params) {
bcv <- (bcv.common + (1 / sqrt(base.means.cell)))
}
- means.cell <- matrix(rgamma(nGenes * nCells, shape = 1 / (bcv ^ 2),
- scale = base.means.cell * (bcv ^ 2)),
- nrow = nGenes, ncol = nCells)
+ means.cell <- matrix(rgamma(
+ as.numeric(nGenes) * as.numeric(nCells),
+ shape = 1 / (bcv ^ 2), scale = base.means.cell * (bcv ^ 2)),
+ nrow = nGenes, ncol = nCells)
colnames(means.cell) <- cell.names
rownames(means.cell) <- gene.names
@@ -680,8 +681,10 @@ splatSimTrueCounts <- function(sim, params) {
nCells <- getParam(params, "nCells")
cell.means <- assays(sim)$CellMeans
- true.counts <- matrix(rpois(nGenes * nCells, lambda = cell.means),
- nrow = nGenes, ncol = nCells)
+ true.counts <- matrix(rpois(
+ as.numeric(nGenes) * as.numeric(nCells),
+ lambda = cell.means),
+ nrow = nGenes, ncol = nCells)
colnames(true.counts) <- cell.names
rownames(true.counts) <- gene.names
@@ -693,7 +696,7 @@ splatSimTrueCounts <- function(sim, params) {
#' Simulate dropout
#'
-#' A logistic function is used to form a relationshop between the expression
+#' A logistic function is used to form a relationship between the expression
#' level of a gene and the probability of dropout, giving a probability for each
#' gene in each cell. These probabilities are used in a Bernoulli distribution
#' to decide which counts should be dropped.
@@ -750,7 +753,7 @@ splatSimDropout <- function(sim, params) {
}
if ("Group" %in% colnames(colData(sim))) {
- groups <- as.numeric(factor(colData(sim)$Group))
+ groups <- as.numeric(colData(sim)$Group)
} else {
stop("dropout.type is set to 'group' but groups have not ",
"been simulated")
@@ -770,11 +773,11 @@ splatSimDropout <- function(sim, params) {
if (dropout.type != "none") {
- # Generate probabilites based on expression
- drop.prob <- sapply(seq_len(nCells), function(idx) {
+ # Generate probabilities based on expression
+ drop.prob <- vapply(seq_len(nCells), function(idx) {
eta <- log(cell.means[, idx])
return(logistic(eta, x0 = dropout.mid[idx], k = dropout.shape[idx]))
- })
+ }, as.numeric(seq_len(nGenes)))
# Decide which counts to keep
keep <- matrix(rbinom(nCells * nGenes, 1, 1 - drop.prob),
@@ -831,7 +834,7 @@ getLNormFactors <- function(n.facs, sel.prob, neg.prob, fac.loc, fac.scale) {
#' Identify the correct order to process paths so that preceding paths have
#' already been simulated.
#'
-#' @param path.from vector giving the path endpoints that each path orginates
+#' @param path.from vector giving the path endpoints that each path originates
#' from.
#'
#' @return Vector giving the order to process paths in.
diff --git a/R/utils.R b/R/utils.R
index 0a9098758d0d6490b3749452eb1189717b071104..96fec570540fa8669b4b7436820720aecbf32441 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -6,7 +6,7 @@
#' @param x0 midpoint parameter. Gives the centre of the function.
#' @param k shape parameter. Gives the slope of the function.
#'
-#' @return Value of logistic funciton with given parameters
+#' @return Value of logistic function with given parameters
logistic <- function(x, x0, k) {
1 / (1 + exp(-k * (x - x0)))
}
@@ -31,6 +31,33 @@ rbindMatched <- function(df1, df2) {
return(combined)
}
+#' Bring items forward
+#'
+#' Move selected items to the start of a list.
+#'
+#' @param ll list to adjust item order.
+#' @param items vector of items to bring to the front. Any not in the list will
+#' be ignored.
+#'
+#' @return list with selected items first
+bringItemsForward <- function(ll, items) {
+
+ checkmate::check_list(ll, min.len = 1, names = "unique")
+ checkmate::check_character(items, any.missing = FALSE, min.len = 1,
+ unique = TRUE)
+
+ items <- items[items %in% names(ll)]
+
+ if (length(items) > 0) {
+ ll.front <- ll[items]
+ ll.back <- ll[!(names(ll) %in% items)]
+
+ ll <- c(ll.front, ll.back)
+ }
+
+ return(ll)
+}
+
#' Winsorize vector
#'
#' Set outliers in a numeric vector to a specified percentile.
diff --git a/R/zinb-estimate.R b/R/zinb-estimate.R
index 866c3505762cfca877f2e08cddf8efb0ed515ba9..b978fbdbdcb149e52f032317d7d85ad295e4b45e 100644
--- a/R/zinb-estimate.R
+++ b/R/zinb-estimate.R
@@ -9,7 +9,7 @@
#' @param design.genes design matrix of gene-level covariates.
#' @param common.disp logical. Whether or not a single dispersion for all
#' features is estimated.
-#' @param iter.init number of iterations to use for initalization.
+#' @param iter.init number of iterations to use for initialization.
#' @param iter.opt number of iterations to use for optimization.
#' @param stop.opt stopping criterion for optimization.
#' @param params ZINBParams object to store estimated values in.
@@ -28,14 +28,15 @@
#' @return ZINBParams object containing the estimated parameters.
#'
#' @examples
-#' \dontrun{
-#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("zinbwave", quietly = TRUE)) {
+#' library(scater)
+#' set.seed(1)
+#' sce <- mockSCE(ncells = 20, ngenes = 100)
#'
-#' params <- zinbEstimate(sc_example_counts)
-#' params
+#' params <- zinbEstimate(sce)
+#' params
#' }
+#'
#' @importFrom BiocParallel SerialParam
#' @export
zinbEstimate <- function(counts, design.samples = NULL, design.genes = NULL,
@@ -55,7 +56,7 @@ zinbEstimate.SingleCellExperiment <- function(counts, design.samples = NULL,
params = newZINBParams(),
verbose = TRUE,
BPPARAM = SerialParam(), ...) {
- counts <- BiocGenerics::counts(counts)
+ counts <- getCounts(counts)
zinbEstimate(counts, design.samples, design.genes, common.disp,
iter.init, iter.opt, stop.opt, params, verbose, BPPARAM, ...)
}
diff --git a/R/zinb-simulate.R b/R/zinb-simulate.R
index 7ebefa296772125bc7d35423b2d2cf831071109c..83da9739bbc9530c141b090c81a055c073458a35 100644
--- a/R/zinb-simulate.R
+++ b/R/zinb-simulate.R
@@ -30,7 +30,9 @@
#' Code: \url{https://github.com/drisso/zinbwave}
#'
#' @examples
-#' sim <- zinbSimulate()
+#' if (requireNamespace("zinbwave", quietly = TRUE)) {
+#' sim <- zinbSimulate()
+#' }
#'
#' @export
#' @importFrom SingleCellExperiment SingleCellExperiment
diff --git a/README.md b/README.md
index 7b85bef86d225e7da1c40529f05fc5cbb8334bbc..33b0ac2075b504d11ab290a9fcbbc7044bde6edd 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@ aren't required for core functionality).
## Getting started
Once installed the best place to get started is the vignette. For most users
-the most convient way to access this is online [here][vignette].
+the most convenient way to access this is online [here][vignette].
Alternatively, if you chose to build the vignette, you can load Splatter, then
browse the vignettes:
diff --git a/_pkgdown.yml b/_pkgdown.yml
index a51d299468259182c553cc4f304d493705ee00b0..9ec49c82aff1afc44c53a813b9291fe224a5c30f 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -14,6 +14,7 @@ reference:
- '`setParam`'
- '`setParams`'
- '`BASiCSParams`'
+ - '`KersplatParams`'
- '`Lun2Params`'
- '`LunParams`'
- '`MFAParams`'
@@ -28,6 +29,7 @@ reference:
desc: Functions for estimating parameters
contents:
- '`BASiCSEstimate`'
+ - '`kersplatEstimate`'
- '`lun2Estimate`'
- '`lunEstimate`'
- '`mfaEstimate`'
@@ -46,6 +48,7 @@ reference:
desc: Functions for simulating datasets
contents:
- '`BASiCSSimulate`'
+ - '`kersplatSimulate`'
- '`lun2Simulate`'
- '`lunSimulate`'
- '`mfaSimulate`'
diff --git a/docs/404.html b/docs/404.html
new file mode 100644
index 0000000000000000000000000000000000000000..9f26cd2903c331feaec5e1bc26f7e0e946c49bd4
--- /dev/null
+++ b/docs/404.html
@@ -0,0 +1,165 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Page not found (404) • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="http://oshlack.github.io/splatter/pkgdown.css" rel="stylesheet">
+<script src="http://oshlack.github.io/splatter/pkgdown.js"></script>
+
+
+
+ <link href="http://oshlack.github.io/splatter/extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Page not found (404)" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-title-body">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="http://oshlack.github.io/splatter/index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="contents col-md-9">
+ <div class="page-header">
+ <h1>Page not found (404)</h1>
+ </div>
+
+Content not found. Please use links in the navbar.
+
+ </div>
+
+</div>
+
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 8bd38ffb016a9718c3ca5ce21ad107b9fa9d4717..679977e4aa4f5543fb4de74a90981ed5647fd697 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>License • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
@@ -32,12 +36,15 @@
<link href="extra.css" rel="stylesheet">
+
<meta property="og:title" content="License" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -55,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -63,14 +71,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -78,7 +87,7 @@
<ul class="nav navbar-nav">
<li>
<a href="index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -88,15 +97,26 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -107,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -796,13 +817,14 @@ Public License instead of this License. But first, please read
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -810,6 +832,8 @@ Public License instead of this License. But first, please read
+
</body>
</html>
+
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 043ae7079c1c83274d04e2359a79afb0cb37e0cc..5b054c57bf648ed2e43fb68c70d2bbe13d2ec6f4 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Articles • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,12 +36,15 @@
<link href="../extra.css" rel="stylesheet">
+
<meta property="og:title" content="Articles" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -55,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -63,14 +71,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -78,7 +87,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -88,15 +97,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -107,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -120,19 +141,21 @@
<p class="section-desc"></p>
<ul>
+ <li><a href="splat_params.html">Splat simulation parameters</a></li>
<li><a href="splatter.html">Introduction to Splatter</a></li>
</ul>
</div>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -140,6 +163,8 @@
+
</body>
</html>
+
diff --git a/docs/articles/splat-model.png b/docs/articles/splat-model.png
new file mode 100644
index 0000000000000000000000000000000000000000..1e5ca99ce1ce487c534d6e849c6643ee73b94a05
Binary files /dev/null and b/docs/articles/splat-model.png differ
diff --git a/docs/articles/splat_params.html b/docs/articles/splat_params.html
new file mode 100644
index 0000000000000000000000000000000000000000..de92495615ef07727693823dd6a7dcae375d422a
--- /dev/null
+++ b/docs/articles/splat_params.html
@@ -0,0 +1,721 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Splat simulation parameters • Splatter</title>
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<meta property="og:title" content="Splat simulation parameters">
+<meta property="og:description" content="">
+<meta name="twitter:card" content="summary">
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script><script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+</head>
+<body>
+ <div class="container template-article">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+<li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+<li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+<ul class="nav navbar-nav navbar-right">
+<li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+</div>
+<!--/.nav-collapse -->
+ </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header toc-ignore">
+ <h1>Splat simulation parameters</h1>
+
+ <h4 class="date">Last updated: 18 April 2019</h4>
+
+ <small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splat_params.Rmd"><code>vignettes/splat_params.Rmd</code></a></small>
+ <div class="hidden name"><code>splat_params.Rmd</code></div>
+
+ </div>
+
+
+
+<p>This vignette describes the Splat simulation model and the parameters it uses in more detail.</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"splatter"</span>)</a>
+<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">#> Loading required package: SingleCellExperiment</span></a>
+<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co">#> Warning: package 'SingleCellExperiment' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">#> Loading required package: SummarizedExperiment</span></a>
+<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">#> Warning: package 'SummarizedExperiment' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">#> Loading required package: GenomicRanges</span></a>
+<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co">#> Warning: package 'GenomicRanges' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="co">#> Loading required package: stats4</span></a>
+<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co">#> Loading required package: BiocGenerics</span></a>
+<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co">#> Warning: package 'BiocGenerics' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co">#> Loading required package: parallel</span></a>
+<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co">#> Attaching package: 'BiocGenerics'</span></a>
+<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="co">#> The following objects are masked from 'package:parallel':</span></a>
+<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-16" data-line-number="16"><span class="co">#> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,</span></a>
+<a class="sourceLine" id="cb1-17" data-line-number="17"><span class="co">#> clusterExport, clusterMap, parApply, parCapply, parLapply,</span></a>
+<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co">#> parLapplyLB, parRapply, parSapply, parSapplyLB</span></a>
+<a class="sourceLine" id="cb1-19" data-line-number="19"><span class="co">#> The following objects are masked from 'package:stats':</span></a>
+<a class="sourceLine" id="cb1-20" data-line-number="20"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-21" data-line-number="21"><span class="co">#> IQR, mad, sd, var, xtabs</span></a>
+<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co">#> The following objects are masked from 'package:base':</span></a>
+<a class="sourceLine" id="cb1-23" data-line-number="23"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-24" data-line-number="24"><span class="co">#> anyDuplicated, append, as.data.frame, basename, cbind,</span></a>
+<a class="sourceLine" id="cb1-25" data-line-number="25"><span class="co">#> colnames, dirname, do.call, duplicated, eval, evalq, Filter,</span></a>
+<a class="sourceLine" id="cb1-26" data-line-number="26"><span class="co">#> Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,</span></a>
+<a class="sourceLine" id="cb1-27" data-line-number="27"><span class="co">#> mapply, match, mget, order, paste, pmax, pmax.int, pmin,</span></a>
+<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="co">#> pmin.int, Position, rank, rbind, Reduce, rownames, sapply,</span></a>
+<a class="sourceLine" id="cb1-29" data-line-number="29"><span class="co">#> setdiff, sort, table, tapply, union, unique, unsplit, which,</span></a>
+<a class="sourceLine" id="cb1-30" data-line-number="30"><span class="co">#> which.max, which.min</span></a>
+<a class="sourceLine" id="cb1-31" data-line-number="31"><span class="co">#> Loading required package: S4Vectors</span></a>
+<a class="sourceLine" id="cb1-32" data-line-number="32"><span class="co">#> Warning: package 'S4Vectors' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-33" data-line-number="33"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-34" data-line-number="34"><span class="co">#> Attaching package: 'S4Vectors'</span></a>
+<a class="sourceLine" id="cb1-35" data-line-number="35"><span class="co">#> The following object is masked from 'package:base':</span></a>
+<a class="sourceLine" id="cb1-36" data-line-number="36"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-37" data-line-number="37"><span class="co">#> expand.grid</span></a>
+<a class="sourceLine" id="cb1-38" data-line-number="38"><span class="co">#> Loading required package: IRanges</span></a>
+<a class="sourceLine" id="cb1-39" data-line-number="39"><span class="co">#> Warning: package 'IRanges' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-40" data-line-number="40"><span class="co">#> Loading required package: GenomeInfoDb</span></a>
+<a class="sourceLine" id="cb1-41" data-line-number="41"><span class="co">#> Warning: package 'GenomeInfoDb' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-42" data-line-number="42"><span class="co">#> Loading required package: Biobase</span></a>
+<a class="sourceLine" id="cb1-43" data-line-number="43"><span class="co">#> Warning: package 'Biobase' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-44" data-line-number="44"><span class="co">#> Welcome to Bioconductor</span></a>
+<a class="sourceLine" id="cb1-45" data-line-number="45"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-46" data-line-number="46"><span class="co">#> Vignettes contain introductory material; view with</span></a>
+<a class="sourceLine" id="cb1-47" data-line-number="47"><span class="co">#> 'browseVignettes()'. To cite Bioconductor, see</span></a>
+<a class="sourceLine" id="cb1-48" data-line-number="48"><span class="co">#> 'citation("Biobase")', and for packages 'citation("pkgname")'.</span></a>
+<a class="sourceLine" id="cb1-49" data-line-number="49"><span class="co">#> Loading required package: DelayedArray</span></a>
+<a class="sourceLine" id="cb1-50" data-line-number="50"><span class="co">#> Warning: package 'DelayedArray' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-51" data-line-number="51"><span class="co">#> Loading required package: matrixStats</span></a>
+<a class="sourceLine" id="cb1-52" data-line-number="52"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-53" data-line-number="53"><span class="co">#> Attaching package: 'matrixStats'</span></a>
+<a class="sourceLine" id="cb1-54" data-line-number="54"><span class="co">#> The following objects are masked from 'package:Biobase':</span></a>
+<a class="sourceLine" id="cb1-55" data-line-number="55"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-56" data-line-number="56"><span class="co">#> anyMissing, rowMedians</span></a>
+<a class="sourceLine" id="cb1-57" data-line-number="57"><span class="co">#> Loading required package: BiocParallel</span></a>
+<a class="sourceLine" id="cb1-58" data-line-number="58"><span class="co">#> Warning: package 'BiocParallel' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-59" data-line-number="59"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-60" data-line-number="60"><span class="co">#> Attaching package: 'DelayedArray'</span></a>
+<a class="sourceLine" id="cb1-61" data-line-number="61"><span class="co">#> The following objects are masked from 'package:matrixStats':</span></a>
+<a class="sourceLine" id="cb1-62" data-line-number="62"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-63" data-line-number="63"><span class="co">#> colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</span></a>
+<a class="sourceLine" id="cb1-64" data-line-number="64"><span class="co">#> The following objects are masked from 'package:base':</span></a>
+<a class="sourceLine" id="cb1-65" data-line-number="65"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-66" data-line-number="66"><span class="co">#> aperm, apply, rowsum</span></a>
+<a class="sourceLine" id="cb1-67" data-line-number="67"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"scater"</span>)</a>
+<a class="sourceLine" id="cb1-68" data-line-number="68"><span class="co">#> Warning: package 'scater' was built under R version 3.6.1</span></a>
+<a class="sourceLine" id="cb1-69" data-line-number="69"><span class="co">#> Loading required package: ggplot2</span></a>
+<a class="sourceLine" id="cb1-70" data-line-number="70"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"ggplot2"</span>)</a></code></pre></div>
+<div id="the-base-splat-model" class="section level1">
+<h1 class="hasAnchor">
+<a href="#the-base-splat-model" class="anchor"></a>The base Splat model</h1>
+<p>This figure, taken from the Splatter publication, describes the core of the Splat simulation model.</p>
+<div class="figure">
+<img src="splat-model.png" alt="Splat simulation model"><p class="caption">Splat simulation model</p>
+</div>
+<p>The Splat simulation uses a hierarchical probabilistic where different aspects of a dataset are generated from appropriate statistical distributions. The first stage generates a mean expression level for each gene. These are originally chosen from a Gamma distribution. For some genes that are selected to be outliers with high expression a factor is generated from a log-normal distribution. These factors are then multiplied by the median gene mean to create new means for those genes.</p>
+<p>The next stage incorporates variation in the counts per cell. An expected library size (total counts) is chosen for each cell from a log-normal distribution. The library sizes are then used to scale the gene means for each cell, resulting in a range a counts per cell in the simulated dataset. The gene means are then further adjusted to enforce a relationship between the mean expression level and the variability.</p>
+<p>The final cell by gene matrix of gene means is then used to generate a count matrix using a Poisson distribution. The result is a synthetic dataset consisting of counts from a Gamma-Poisson (or negative-binomial) distribution. An additional optional step can be used to replicate a “dropout†effect. A probability of dropout is generated using a logistic function based on the underlying mean expression level. A Bernoulli distribution is then used to create a dropout matrix which sets some of the generated counts to zero.</p>
+<p>The model described here will generate a single population of cells but the Splat simulation has been designed to be as flexible as possible and can create scenarios including multiple groups of cells (cell types), continuous paths between cell types and multiple experimental batches. The parameters used to create these types of simulations and how they interact with the model are described below.</p>
+</div>
+<div id="splat-simulation-parameters" class="section level1">
+<h1 class="hasAnchor">
+<a href="#splat-simulation-parameters" class="anchor"></a>Splat simulation parameters</h1>
+<p>Within Splatter the parameters for the Splat simulation model are held in the <code>SplatParams</code> object. Let’s create one of these objects and see what it looks like.</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
+<a class="sourceLine" id="cb2-2" data-line-number="2">params</a>
+<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co">#> A Params object of class SplatParams </span></a>
+<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT' </span></a>
+<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#> Secondary parameters are usually set during simulation</span></a>
+<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co">#> Global: </span></a>
+<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co">#> (Genes) (Cells) [Seed] </span></a>
+<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co">#> 10000 100 955861 </span></a>
+<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#> 28 additional parameters </span></a>
+<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co">#> Batches: </span></a>
+<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co">#> [Batches] [Batch Cells] [Location] [Scale] </span></a>
+<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co">#> 1 100 0.1 0.1 </span></a>
+<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co">#> Mean: </span></a>
+<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co">#> (Rate) (Shape) </span></a>
+<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co">#> 0.3 0.6 </span></a>
+<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co">#> Library size: </span></a>
+<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co">#> (Location) (Scale) (Norm) </span></a>
+<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co">#> 11 0.2 FALSE </span></a>
+<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co">#> Exprs outliers: </span></a>
+<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co">#> (Probability) (Location) (Scale) </span></a>
+<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co">#> 0.05 4 0.5 </span></a>
+<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co">#> Groups: </span></a>
+<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co">#> [Groups] [Group Probs] </span></a>
+<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co">#> 1 1 </span></a>
+<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co">#> Diff expr: </span></a>
+<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co">#> [Probability] [Down Prob] [Location] [Scale] </span></a>
+<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co">#> 0.1 0.5 0.1 0.4 </span></a>
+<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-37" data-line-number="37"><span class="co">#> BCV: </span></a>
+<a class="sourceLine" id="cb2-38" data-line-number="38"><span class="co">#> (Common Disp) (DoF) </span></a>
+<a class="sourceLine" id="cb2-39" data-line-number="39"><span class="co">#> 0.1 60 </span></a>
+<a class="sourceLine" id="cb2-40" data-line-number="40"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-41" data-line-number="41"><span class="co">#> Dropout: </span></a>
+<a class="sourceLine" id="cb2-42" data-line-number="42"><span class="co">#> [Type] (Midpoint) (Shape) </span></a>
+<a class="sourceLine" id="cb2-43" data-line-number="43"><span class="co">#> none 0 -1 </span></a>
+<a class="sourceLine" id="cb2-44" data-line-number="44"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb2-45" data-line-number="45"><span class="co">#> Paths: </span></a>
+<a class="sourceLine" id="cb2-46" data-line-number="46"><span class="co">#> [From] [Steps] [Skew] [Non-linear] </span></a>
+<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="co">#> 0 100 0.5 0.1 </span></a>
+<a class="sourceLine" id="cb2-48" data-line-number="48"><span class="co">#> [Sigma Factor] </span></a>
+<a class="sourceLine" id="cb2-49" data-line-number="49"><span class="co">#> 0.8</span></a></code></pre></div>
+<p>Like all the parameter objects in Splatter printing this object displays all the parameters required for this simulation. As we haven’t set any of the parameters the default values are shown but if we were to change any of them they would be highlighted. We can also see which parameters can be estimated by the Splat estimation procedure and which can’t. The default values have been chosen to be fairly realistic but it is recommended that estimation is used to get a simulation that is more like the data you are interested in. Parameters can be modified by setting them in the <code>SplatParams</code> object or by providing them directly to the simulation function.</p>
+<p>The rest of this section provides details of all this parameters and explains how they can be used with examples.</p>
+<div id="global-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#global-parameters" class="anchor"></a>Global parameters</h2>
+<p>These parameters are used in every simulation model and control global features of the dataset produced.</p>
+<div id="ngenes---number-of-genes" class="section level3">
+<h3 class="hasAnchor">
+<a href="#ngenes---number-of-genes" class="anchor"></a><code>nGenes</code> - Number of genes</h3>
+<p>The number of genes to simulate.</p>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># Set the number of genes to 1000</span></a>
+<a class="sourceLine" id="cb3-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">1000</span>)</a>
+<a class="sourceLine" id="cb3-3" data-line-number="3"></a>
+<a class="sourceLine" id="cb3-4" data-line-number="4">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/dim.html">dim</a></span>(sim)</a>
+<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#> [1] 1000 100</span></a></code></pre></div>
+</div>
+<div id="ncells---number-of-cells" class="section level3">
+<h3 class="hasAnchor">
+<a href="#ncells---number-of-cells" class="anchor"></a><code>nCells</code> - Number of cells</h3>
+<p>The number of genes to simulate. In the Splat simulation this cannot be set directly but must be controlled using the <code>batchCells</code> parameter.</p>
+</div>
+<div id="seed---random-seed" class="section level3">
+<h3 class="hasAnchor">
+<a href="#seed---random-seed" class="anchor"></a><code>seed</code> - Random seed</h3>
+<p>Seed to use for generating random numbers including selecting values from distributions. By changing this value multiple simulated datasets with the same parameters can be produced. Simulations produced using the same set of parameters and random seed should be identical but there may be differences between operating systems, software versions etc.</p>
+</div>
+</div>
+<div id="batch-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#batch-parameters" class="anchor"></a>Batch parameters</h2>
+<p>These parameters control experimental batches in the simulated dataset. The overall effect of how batch effects are included in the model is similar to technical replicates (i.e. the same biological sample sequenced multiple times). This means that the underlying structure is consistent between batches but a global technical signature is added may separate them.</p>
+<div id="nbatches---number-of-batches" class="section level3">
+<h3 class="hasAnchor">
+<a href="#nbatches---number-of-batches" class="anchor"></a><code>nBatches</code> - Number of batches</h3>
+<p>The number of batches in the simulation. This cannot be set directly but is controlled by setting <code>batchCells</code>.</p>
+</div>
+<div id="batchcells---cells-per-batch" class="section level3">
+<h3 class="hasAnchor">
+<a href="#batchcells---cells-per-batch" class="anchor"></a><code>batchCells</code> - Cells per batch</h3>
+<p>A vector specifying the number of cells in each batch. The number of batches (<code>nBatches</code>) is equal to the length of the vector and the number of cells (<code>nCells</code>) is equal to the sum.</p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># Simulation with two batches of 100 cells</span></a>
+<a class="sourceLine" id="cb4-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">batchCells =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">100</span>, <span class="dv">100</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb4-3" data-line-number="3"></a>
+<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co"># PCA plot using scater</span></a>
+<a class="sourceLine" id="cb4-5" data-line-number="5">sim <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim)</a>
+<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb4-9" data-line-number="9"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a>
+<a class="sourceLine" id="cb4-10" data-line-number="10"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/batches-1.png" width="700"></p>
+</div>
+<div id="batch-facloc---batch-factor-location-and-batch-facscale---batch-factor-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#batch-facloc---batch-factor-location-and-batch-facscale---batch-factor-scale" class="anchor"></a><code>batch.facLoc</code> - Batch factor location and <code>batch.facScale</code> - Batch factor scale</h3>
+<p>Batches are specified by generating a small scaling factor for each gene in each batch from a log-normal distribution. These factors are then applied to the underlying gene means in each batch. Modifying these parameters affects how different the batches are from each other by generating bigger or smaller factors.</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># Simulation with small batch effects</span></a>
+<a class="sourceLine" id="cb5-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">batchCells =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">100</span>, <span class="dv">100</span>),</a>
+<a class="sourceLine" id="cb5-3" data-line-number="3"> <span class="dt">batch.facLoc =</span> <span class="fl">0.001</span>, <span class="dt">batch.facScale =</span> <span class="fl">0.001</span>,</a>
+<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb5-5" data-line-number="5">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Small batch effects"</span>)</a>
+<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/batch-factors-1.png" width="700"></p>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co"># Simulation with big batch effects</span></a>
+<a class="sourceLine" id="cb6-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">batchCells =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">100</span>, <span class="dv">100</span>),</a>
+<a class="sourceLine" id="cb6-4" data-line-number="4"> <span class="dt">batch.facLoc =</span> <span class="fl">0.5</span>, <span class="dt">batch.facScale =</span> <span class="fl">0.5</span>,</a>
+<a class="sourceLine" id="cb6-5" data-line-number="5"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb6-6" data-line-number="6">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb6-8" data-line-number="8"></a>
+<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Big batch effects"</span>)</a>
+<a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/batch-factors-2.png" width="700"></p>
+</div>
+</div>
+<div id="mean-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#mean-parameters" class="anchor"></a>Mean parameters</h2>
+<p>These parameters control the distribution that is used to generate the underlying original gene means.</p>
+<div id="mean-shape---mean-shape-and-mean-rate---mean-rate" class="section level3">
+<h3 class="hasAnchor">
+<a href="#mean-shape---mean-shape-and-mean-rate---mean-rate" class="anchor"></a><code>mean.shape</code> - Mean shape and <code>mean.rate</code> - Mean rate</h3>
+<p>These parameters control the Gamma distribution that gene means are drawn from. The relationship between shape and rate can be complex and it is often better to use values estimated from a real dataset than to try and manually set them. Although these parameters control the base gene means the means in the final simulation will depend upon other parts of the model, particularly the simulated total counts per cell (library sizes).</p>
+</div>
+</div>
+<div id="library-size-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#library-size-parameters" class="anchor"></a>Library size parameters</h2>
+<p>These parameters control the expected number of counts for each cell. Note that because of sampling the actual counts per cell in the final simulation may be different. Turning on the dropout effect will also effect this. We use the term “library size†here for consistency but expected total counts would be more appropriate.</p>
+<div id="lib-loc---library-size-location-and-lib-scale---library-size-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#lib-loc---library-size-location-and-lib-scale---library-size-scale" class="anchor"></a><code>lib.loc</code> - Library size location and <code>lib.scale</code> - Library size scale</h3>
+<p>These parameters control the shape of the distribution that is used to generate library sizes for each cell. Increasing <code>lib.loc</code> will lead to more counts per cell and increasing <code>lib.scale</code> will result in more variability in the counts per cell.</p>
+</div>
+<div id="lib-norm---library-size-distribution" class="section level3">
+<h3 class="hasAnchor">
+<a href="#lib-norm---library-size-distribution" class="anchor"></a><code>lib.norm</code> - Library size distribution</h3>
+<p>The default (and recommended) distribution used for library sizes in the Splat simulation is a log-normal. However, in rare cases a normal distribution might be more appropriate. Setting <code>lib.norm</code> to <code>TRUE</code> will use a normal distribution instead of a log-normal.</p>
+</div>
+</div>
+<div id="expression-outlier-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#expression-outlier-parameters" class="anchor"></a>Expression outlier parameters</h2>
+<p>When developing the Splat simulation we found that while the Gamma distribution was generally a good match for gene means for some datasets it did not properly capture highly expressed genes. For this reason we added expression outliers to the Splat model.</p>
+<div id="out-prob---expression-outlier-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#out-prob---expression-outlier-probability" class="anchor"></a><code>out.prob</code> - Expression outlier probability</h3>
+<p>This parameter controls the probability that genes will be selected to be expression outliers. Higher values will results in more outlier genes.</p>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="co"># Few outliers</span></a>
+<a class="sourceLine" id="cb7-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">out.prob =</span> <span class="fl">0.001</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/as.data.frame.html">as.data.frame</a></span>(<span class="kw">rowData</span>(sim1)),</a>
+<a class="sourceLine" id="cb7-4" data-line-number="4"> <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> <span class="kw"><a href="https://rdrr.io/r/base/Log.html">log10</a></span>(GeneMean), <span class="dt">fill =</span> OutlierFactor <span class="op">!=</span><span class="st"> </span><span class="dv">1</span>)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html">geom_histogram</a></span>(<span class="dt">bins =</span> <span class="dv">100</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Few outliers"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/outlier-prob-1.png" width="700"></p>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co"># Lots of outliers</span></a>
+<a class="sourceLine" id="cb8-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">out.prob =</span> <span class="fl">0.2</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/as.data.frame.html">as.data.frame</a></span>(<span class="kw">rowData</span>(sim2)),</a>
+<a class="sourceLine" id="cb8-5" data-line-number="5"> <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> <span class="kw"><a href="https://rdrr.io/r/base/Log.html">log10</a></span>(GeneMean), <span class="dt">fill =</span> OutlierFactor <span class="op">!=</span><span class="st"> </span><span class="dv">1</span>)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb8-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_histogram.html">geom_histogram</a></span>(<span class="dt">bins =</span> <span class="dv">100</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb8-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Lots of outliers"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/outlier-prob-2.png" width="700"></p>
+</div>
+<div id="out-facloc---expression-outlier-factor-location-and-out-facscale---expression-outlier-factor-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#out-facloc---expression-outlier-factor-location-and-out-facscale---expression-outlier-factor-scale" class="anchor"></a><code>out.facLoc</code> - Expression outlier factor location and <code>out.facScale</code> - Expression outlier factor scale</h3>
+<p>The expression outlier factors are drawn from a log-normal distribution controlled by these parameters. The generated factors are applied to the median mean expression rather than the existing mean for the selected genes. This is to be consistent with the estimation procedure for these factors and to make sure that the final means are outliers. For example to avoid the situation where a factor is applied to a lowly expressed gene, making it just moderately expressed rather than an expression outlier.</p>
+</div>
+<div id="group-parameters" class="section level3">
+<h3 class="hasAnchor">
+<a href="#group-parameters" class="anchor"></a>Group parameters</h3>
+<p>Up until this stage of the simulation only a single population of cells is considered but we often want to simulate datasets with multiple kinds of cells. We do this by assigning cells to groups.</p>
+</div>
+<div id="ngroups---number-of-groups" class="section level3">
+<h3 class="hasAnchor">
+<a href="#ngroups---number-of-groups" class="anchor"></a><code>nGroups</code> - Number of groups</h3>
+<p>The number of groups to simulate. This parameter cannot be set directly and is controlled using <code>group.prob</code>.</p>
+</div>
+<div id="group-prob---group-probabilities" class="section level3">
+<h3 class="hasAnchor">
+<a href="#group-prob---group-probabilities" class="anchor"></a><code>group.prob</code> - Group probabilities</h3>
+<p>A vector giving the probability that cells will be assigned to groups. The length of the vector gives the number of groups (<code>nGroups</code>) and the probabilities must sum to 1. Adjusting the number and relative values of the probabilities changes the number and relative sizes of the groups. To simulate groups we also need to use the <code>splatSimulateGroups</code> function or set <code>method = "groups"</code>.</p>
+<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">params.groups <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">batchCells =</span> <span class="dv">500</span>, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a>
+<a class="sourceLine" id="cb9-2" data-line-number="2"></a>
+<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="co"># One small group, one big group</span></a>
+<a class="sourceLine" id="cb9-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.9</span>, <span class="fl">0.1</span>),</a>
+<a class="sourceLine" id="cb9-5" data-line-number="5"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb9-6" data-line-number="6">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb9-9" data-line-number="9"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb9-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"One small group, one big group"</span>)</a>
+<a class="sourceLine" id="cb9-11" data-line-number="11"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/groups-1.png" width="700"></p>
+<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># Five groups</span></a>
+<a class="sourceLine" id="cb10-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb10-4" data-line-number="4"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>),</a>
+<a class="sourceLine" id="cb10-5" data-line-number="5"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb10-6" data-line-number="6">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb10-7" data-line-number="7"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb10-8" data-line-number="8"></a>
+<a class="sourceLine" id="cb10-9" data-line-number="9"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb10-10" data-line-number="10"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb10-11" data-line-number="11"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Five groups"</span>)</a>
+<a class="sourceLine" id="cb10-12" data-line-number="12"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/groups-2.png" width="700"></p>
+<p><strong>Note:</strong> Once there are more than three or four groups it becomes difficult to properly view them in PCA space. We use PCA here for simplicity but generally a non-linear dimensionality reduction such as t-SNE or UMAP is a more useful way to visualise the groups.</p>
+</div>
+<div id="differential-expression-parameters" class="section level3">
+<h3 class="hasAnchor">
+<a href="#differential-expression-parameters" class="anchor"></a>Differential expression parameters</h3>
+<p>Different groups are created by modifying the base expression levels of selected genes. The process for doing this is to simulate differential expression (DE) between each group and a fictional base cell. Altering the differential expression parameters controls how similar groups are to each other.</p>
+</div>
+<div id="de-prob---de-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#de-prob---de-probability" class="anchor"></a><code>de.prob</code> - DE probability</h3>
+<p>This parameter controls the probability that a gene will be selected to be differentially expressed.</p>
+<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="co"># Few DE genes</span></a>
+<a class="sourceLine" id="cb11-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb11-3" data-line-number="3"> <span class="dt">de.prob =</span> <span class="fl">0.01</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb11-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb11-5" data-line-number="5"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb11-6" data-line-number="6"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb11-7" data-line-number="7"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb11-8" data-line-number="8"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Few DE genes"</span>)</a>
+<a class="sourceLine" id="cb11-9" data-line-number="9"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/de-prob-1.png" width="700"></p>
+<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="co"># Lots of DE genes</span></a>
+<a class="sourceLine" id="cb12-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb12-4" data-line-number="4"> <span class="dt">de.prob =</span> <span class="fl">0.3</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb12-5" data-line-number="5">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb12-6" data-line-number="6"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb12-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb12-8" data-line-number="8"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb12-9" data-line-number="9"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb12-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Lots of DE genes"</span>)</a>
+<a class="sourceLine" id="cb12-11" data-line-number="11"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/de-prob-2.png" width="700"></p>
+</div>
+<div id="de-downprob---down-regulation-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#de-downprob---down-regulation-probability" class="anchor"></a><code>de.downProb</code> - Down-regulation probability</h3>
+<p>A selected DE gene can be either down-regulated (has a factor less than one) or up-regulated (has a factor greater than one). This parameter controls the probability that a selected gene will be down-regulated.</p>
+</div>
+<div id="de-facloc---de-factor-location-and-de-facscale---de-factor-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#de-facloc---de-factor-location-and-de-facscale---de-factor-scale" class="anchor"></a><code>de.facLoc</code> - DE factor location and <code>de.facScale</code> - DE factor scale</h3>
+<p>Differential expression factors are produced from a log-normal distribution in a similar way to batch effect factors and expression outlier factors. Changing these parameters can result in more or less extreme differences between groups.</p>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="co"># Small DE factors</span></a>
+<a class="sourceLine" id="cb13-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb13-3" data-line-number="3"> <span class="dt">de.facLoc =</span> <span class="fl">0.01</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb13-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb13-5" data-line-number="5"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb13-6" data-line-number="6"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb13-7" data-line-number="7"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb13-8" data-line-number="8"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Small DE factors"</span>)</a>
+<a class="sourceLine" id="cb13-9" data-line-number="9"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/de-factors-1.png" width="700"></p>
+<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="co"># Big DE factors</span></a>
+<a class="sourceLine" id="cb14-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb14-4" data-line-number="4"> <span class="dt">de.facLoc =</span> <span class="fl">0.3</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb14-5" data-line-number="5">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb14-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb14-9" data-line-number="9"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb14-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Big DE factors"</span>)</a>
+<a class="sourceLine" id="cb14-11" data-line-number="11"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/de-factors-2.png" width="700"></p>
+<p>Just looking at the PCA plots this effect seems similar to adjusting <code>de.prob</code> but the effect is achieved in a different way. A higher <code>de.prob</code> means that more genes are differentially expressed but changing the DE factors changes the level of DE for the same number of genes.</p>
+</div>
+<div id="complex-differential-expression" class="section level3">
+<h3 class="hasAnchor">
+<a href="#complex-differential-expression" class="anchor"></a>Complex differential expression</h3>
+<p>Each of the differential expression parameters can be specified for each group by providing a vector of values. These vectors must be the same length as <code>group.prob</code>. Specifying parameters as vectors allows more complex simulations where groups are more or less different to each other rather than being equally distinct. Here are some examples of different DE scenarios.</p>
+<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="co"># Different DE probs</span></a>
+<a class="sourceLine" id="cb15-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb15-3" data-line-number="3"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>),</a>
+<a class="sourceLine" id="cb15-4" data-line-number="4"> <span class="dt">de.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.01</span>, <span class="fl">0.01</span>, <span class="fl">0.1</span>, <span class="fl">0.1</span>, <span class="fl">0.3</span>),</a>
+<a class="sourceLine" id="cb15-5" data-line-number="5"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb15-6" data-line-number="6">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"Different DE probabilities"</span>,</a>
+<a class="sourceLine" id="cb15-12" data-line-number="12"> <span class="dt">caption =</span> <span class="kw"><a href="https://rdrr.io/r/base/paste.html">paste</a></span>(<span class="st">"Groups 1 and 2 have very few DE genes,"</span>,</a>
+<a class="sourceLine" id="cb15-13" data-line-number="13"> <span class="st">"Groups 3 and 4 have the default number,"</span>,</a>
+<a class="sourceLine" id="cb15-14" data-line-number="14"> <span class="st">"Group 5 has many DE genes"</span>))</a>
+<a class="sourceLine" id="cb15-15" data-line-number="15"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/complex-de-1.png" width="700"></p>
+<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"> </a>
+<a class="sourceLine" id="cb16-2" data-line-number="2"></a>
+<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="co"># Different DE factors</span></a>
+<a class="sourceLine" id="cb16-4" data-line-number="4">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb16-5" data-line-number="5"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>),</a>
+<a class="sourceLine" id="cb16-6" data-line-number="6"> <span class="dt">de.facLoc =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.01</span>, <span class="fl">0.01</span>, <span class="fl">0.1</span>, <span class="fl">0.1</span>, <span class="fl">0.2</span>),</a>
+<a class="sourceLine" id="cb16-7" data-line-number="7"> <span class="dt">de.facScale =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.2</span>, <span class="fl">0.5</span>, <span class="fl">0.2</span>, <span class="fl">0.5</span>, <span class="fl">0.4</span>),</a>
+<a class="sourceLine" id="cb16-8" data-line-number="8"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb16-9" data-line-number="9">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb16-10" data-line-number="10"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb16-11" data-line-number="11"></a>
+<a class="sourceLine" id="cb16-12" data-line-number="12"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb16-13" data-line-number="13"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb16-14" data-line-number="14"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb16-15" data-line-number="15"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"Different DE factors"</span>,</a>
+<a class="sourceLine" id="cb16-16" data-line-number="16"> <span class="dt">caption =</span> <span class="kw"><a href="https://rdrr.io/r/base/paste.html">paste</a></span>(<span class="st">"Group 1 has factors with small location (value),"</span>,</a>
+<a class="sourceLine" id="cb16-17" data-line-number="17"> <span class="st">"and scale (variability),"</span>,</a>
+<a class="sourceLine" id="cb16-18" data-line-number="18"> <span class="st">"Group 2 has small location and greater scale.</span><span class="ch">\n</span><span class="st">"</span>,</a>
+<a class="sourceLine" id="cb16-19" data-line-number="19"> <span class="st">"Groups 3 and 4 have greater location with small,"</span>,</a>
+<a class="sourceLine" id="cb16-20" data-line-number="20"> <span class="st">"and large scales"</span>,</a>
+<a class="sourceLine" id="cb16-21" data-line-number="21"> <span class="st">"Group 5 has bigger factors with moderate"</span>,</a>
+<a class="sourceLine" id="cb16-22" data-line-number="22"> <span class="st">"variability"</span>))</a>
+<a class="sourceLine" id="cb16-23" data-line-number="23"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/complex-de-2.png" width="700"></p>
+<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="co"># Combination of everything</span></a>
+<a class="sourceLine" id="cb17-3" data-line-number="3">sim3 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb17-4" data-line-number="4"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.05</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.2</span>, <span class="fl">0.35</span>),</a>
+<a class="sourceLine" id="cb17-5" data-line-number="5"> <span class="dt">de.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.3</span>, <span class="fl">0.1</span>, <span class="fl">0.2</span>, <span class="fl">0.01</span>, <span class="fl">0.1</span>),</a>
+<a class="sourceLine" id="cb17-6" data-line-number="6"> <span class="dt">de.downProb =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.1</span>, <span class="fl">0.4</span>, <span class="fl">0.9</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb17-7" data-line-number="7"> <span class="dt">de.facLoc =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.6</span>, <span class="fl">0.1</span>, <span class="fl">0.1</span>, <span class="fl">0.01</span>, <span class="fl">0.2</span>),</a>
+<a class="sourceLine" id="cb17-8" data-line-number="8"> <span class="dt">de.facScale =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.1</span>, <span class="fl">0.4</span>, <span class="fl">0.2</span>, <span class="fl">0.5</span>, <span class="fl">0.4</span>),</a>
+<a class="sourceLine" id="cb17-9" data-line-number="9"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb17-10" data-line-number="10">sim3 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim3)</a>
+<a class="sourceLine" id="cb17-11" data-line-number="11"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb17-12" data-line-number="12"></a>
+<a class="sourceLine" id="cb17-13" data-line-number="13"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb17-14" data-line-number="14"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb17-15" data-line-number="15"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim3, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb17-16" data-line-number="16"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"Different DE factors"</span>,</a>
+<a class="sourceLine" id="cb17-17" data-line-number="17"> <span class="dt">caption =</span> <span class="kw"><a href="https://rdrr.io/r/base/paste.html">paste</a></span>(</a>
+<a class="sourceLine" id="cb17-18" data-line-number="18"> <span class="st">"Group 1 is small with many very up-regulated DE genes,"</span>,</a>
+<a class="sourceLine" id="cb17-19" data-line-number="19"> <span class="st">"Group 2 has the default DE parameters,</span><span class="ch">\n</span><span class="st">"</span>,</a>
+<a class="sourceLine" id="cb17-20" data-line-number="20"> <span class="st">"Group 3 has many down-regulated DE genes,"</span>,</a>
+<a class="sourceLine" id="cb17-21" data-line-number="21"> <span class="st">"Group 4 has very few DE genes,"</span>,</a>
+<a class="sourceLine" id="cb17-22" data-line-number="22"> <span class="st">"Group 5 is large with moderate DE factors"</span>)</a>
+<a class="sourceLine" id="cb17-23" data-line-number="23"> )</a>
+<a class="sourceLine" id="cb17-24" data-line-number="24"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/complex-de-3.png" width="700"></p>
+</div>
+</div>
+<div id="biological-coefficient-of-variation-bcv-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#biological-coefficient-of-variation-bcv-parameters" class="anchor"></a>Biological Coefficient of Variation (BCV) parameters</h2>
+<p>The BCV parameters control the variability of the genes in the simulated dataset.</p>
+<div id="bcv-common---common-bcv" class="section level3">
+<h3 class="hasAnchor">
+<a href="#bcv-common---common-bcv" class="anchor"></a><code>bcv.common</code> - Common BCV</h3>
+<p>The <code>bcv.common</code> parameter controls the underlying common variability across all genes in the dataset.</p>
+</div>
+<div id="bcv-df---bcv-degrees-of-freedom" class="section level3">
+<h3 class="hasAnchor">
+<a href="#bcv-df---bcv-degrees-of-freedom" class="anchor"></a><code>bcv.df</code> - BCV Degrees of Freedom</h3>
+<p>This parameter sets the degrees of freedom used in the BCV inverse chi-squared distribution. Changing this changes the effect of mean expression on the variability of a gene.</p>
+</div>
+</div>
+<div id="dropout-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#dropout-parameters" class="anchor"></a>Dropout parameters</h2>
+<p>These parameters control whether additional dropout is added to increase the number of zeros in the simulated dataset and if it is how that is applied.</p>
+<div id="dropout-type---dropout-type" class="section level3">
+<h3 class="hasAnchor">
+<a href="#dropout-type---dropout-type" class="anchor"></a><code>dropout.type</code> - Dropout type</h3>
+<p>This parameter determines the kind of dropout effect to simulate. Setting it to <code>"none"</code> means no dropout, “<code>experiment</code>†is global dropout using the same set of parameters for every cell, <code>"batch"</code> uses the same parameters for every cell in the same batch, <code>"group"</code> uses the same parameters for every cell in the same group and <code>"cell"</code> uses a different set of parameters for every cell.</p>
+</div>
+<div id="dropout-mid---dropout-mid-point-and-dropout-shape---dropout-shape" class="section level3">
+<h3 class="hasAnchor">
+<a href="#dropout-mid---dropout-mid-point-and-dropout-shape---dropout-shape" class="anchor"></a><code>dropout.mid</code> - Dropout mid point and <code>dropout.shape</code> - Dropout shape</h3>
+<p>The probability that a particular count in a particular cell is set to zero is related to the mean expression of that gene in that cell. This relationship is represented using a logistic function with these parameters. The <code>dropout.mid</code> parameter control the point at which the probability is equal to 0.5 and the <code>dropout.shape</code> controls how it changes with increasing expression. These parameters must be vectors of the appropriate length depending on the selected dropout type.</p>
+</div>
+</div>
+<div id="path-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#path-parameters" class="anchor"></a>Path parameters</h2>
+<p>For many uses simulating groups is sufficient but in some cases it is more appropriate to simulate continuous changes between cell types. The number of paths and the probability of assigning cells to them is still controlled by the <code>group.prob</code> parameter and the amount of change along a path is controlled by the DE parameters but other aspects of the <code>splatSimulatePaths</code> model are controlled by these parameters.</p>
+<div id="path-from---path-origin" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-from---path-origin" class="anchor"></a><code>path.from</code> - Path origin</h3>
+<p>This parameter controls the order of differentiation paths. It is a vector the same length as <code>group.prob</code> giving the starting position of each path. For example a <code>path.from</code> of <code><a href="https://rdrr.io/r/base/c.html">c(0, 1, 1, 3)</a></code> would indicate the Path 1 starts at the origin (0), Path 2 starts at the end of Path 1, Path 3 also starts at the end of Path 1 (a branch point) and Path 4 starts at the end of Path 3.</p>
+<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="co"># Linear paths</span></a>
+<a class="sourceLine" id="cb18-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb18-3" data-line-number="3"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.25</span>, <span class="fl">0.25</span>, <span class="fl">0.25</span>, <span class="fl">0.25</span>),</a>
+<a class="sourceLine" id="cb18-4" data-line-number="4"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>,</a>
+<a class="sourceLine" id="cb18-5" data-line-number="5"> <span class="dt">path.from =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>),</a>
+<a class="sourceLine" id="cb18-6" data-line-number="6"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb18-7" data-line-number="7">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb18-8" data-line-number="8"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb18-9" data-line-number="9"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb18-10" data-line-number="10"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb18-11" data-line-number="11"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Linear paths"</span>)</a>
+<a class="sourceLine" id="cb18-12" data-line-number="12"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-1.png" width="700"></p>
+<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># Branching path</span></a>
+<a class="sourceLine" id="cb19-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb19-4" data-line-number="4"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.25</span>, <span class="fl">0.25</span>, <span class="fl">0.25</span>, <span class="fl">0.25</span>),</a>
+<a class="sourceLine" id="cb19-5" data-line-number="5"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>,</a>
+<a class="sourceLine" id="cb19-6" data-line-number="6"> <span class="dt">path.from =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">3</span>),</a>
+<a class="sourceLine" id="cb19-7" data-line-number="7"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb19-8" data-line-number="8">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb19-9" data-line-number="9"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb19-10" data-line-number="10"></a>
+<a class="sourceLine" id="cb19-11" data-line-number="11"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb19-12" data-line-number="12"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Branching path"</span>)</a>
+<a class="sourceLine" id="cb19-14" data-line-number="14"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-2.png" width="700"></p>
+</div>
+<div id="path-nsteps---number-of-steps" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-nsteps---number-of-steps" class="anchor"></a><code>path.nSteps</code> - Number of steps</h3>
+<p>A path is created by using the same differential expression procedure as used for groups to generate an end point. Interpolation is then used to create a series of steps between the start and end points. This parameter controls the number of steps along a path and therefore how discrete or smooth it is.</p>
+<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="co"># Few steps</span></a>
+<a class="sourceLine" id="cb20-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups, <span class="dt">path.nSteps =</span> <span class="dv">3</span>,</a>
+<a class="sourceLine" id="cb20-3" data-line-number="3"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb20-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb20-5" data-line-number="5"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb20-6" data-line-number="6"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Step"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Few steps"</span>)</a>
+<a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-steps-1.png" width="700"></p>
+<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"></a>
+<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="co"># Lots of steps</span></a>
+<a class="sourceLine" id="cb21-3" data-line-number="3">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups, <span class="dt">path.nSteps =</span> <span class="dv">1000</span>,</a>
+<a class="sourceLine" id="cb21-4" data-line-number="4"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb21-5" data-line-number="5">sim2 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim2)</a>
+<a class="sourceLine" id="cb21-6" data-line-number="6"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb21-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb21-8" data-line-number="8"><span class="co">#> Warning in .local(object, ...): 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb21-9" data-line-number="9"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb21-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Step"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Lots of steps"</span>)</a>
+<a class="sourceLine" id="cb21-11" data-line-number="11"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-steps-2.png" width="700"></p>
+</div>
+<div id="path-skew---path-skew" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-skew---path-skew" class="anchor"></a><code>path.skew</code> - Path skew</h3>
+<p>By default cells are evenly distributed along a path but it sometimes be useful to introduce a skew in the distribution, For example you may want to simulate a scenario with few stem-like cells and many differentiated cells. Setting <code>path.skew</code> to 0 will mean that all cells come from the end point while higher values up to 1 will skew them towards the start point.</p>
+<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="co"># Skew towards the end</span></a>
+<a class="sourceLine" id="cb22-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups, <span class="dt">path.skew =</span> <span class="fl">0.1</span>,</a>
+<a class="sourceLine" id="cb22-3" data-line-number="3"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb22-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim1)</a>
+<a class="sourceLine" id="cb22-5" data-line-number="5"><span class="co">#> Warning in .local(object, ...): using library sizes as size factors</span></a>
+<a class="sourceLine" id="cb22-6" data-line-number="6"><span class="co">#> Warning: 'centreSizeFactors' is deprecated.</span></a>
+<a class="sourceLine" id="cb22-7" data-line-number="7"><span class="co">#> See help("Deprecated")</span></a>
+<a class="sourceLine" id="cb22-8" data-line-number="8"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Step"</span>) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">ggtitle</a></span>(<span class="st">"Skewed towards the end"</span>)</a>
+<a class="sourceLine" id="cb22-9" data-line-number="9"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-skew-1.png" width="700"></p>
+</div>
+<div id="path-nonlinearprob---non-linear-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-nonlinearprob---non-linear-probability" class="anchor"></a><code>path.nonlinearProb</code> - Non-linear probability</h3>
+<p>Most genes are interpolated in a linear way along a path but in reality this may not always be the case. For example it is easy to imagine a gene that is lowly-expressed at the start of a process, highly-expressed in the middle and lowly-expressed again at the end. The <code>path.nonlinearProb</code> parameter controls the probability that a gene will change in a non-linear way along a path.</p>
+</div>
+<div id="path-sigmafac---path-skew" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-sigmafac---path-skew" class="anchor"></a><code>path.sigmaFac</code> - Path skew</h3>
+<p>Non-linear changes along a path are achieved by building a Brownian bridge between the two end points. A Brownian bridge is Brownian motion controlled in such a way that the end points are fixed. The <code>path.sigmaFac</code> parameter controls how extreme each step in the Brownian motion is and therefore how much the interpolation differs from a linear path.</p>
+</div>
+</div>
+</div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+
+ <div id="tocnav">
+ <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+<li><a href="#the-base-splat-model">The base Splat model</a></li>
+ <li>
+<a href="#splat-simulation-parameters">Splat simulation parameters</a><ul class="nav nav-pills nav-stacked">
+<li><a href="#global-parameters">Global parameters</a></li>
+ <li><a href="#batch-parameters">Batch parameters</a></li>
+ <li><a href="#mean-parameters">Mean parameters</a></li>
+ <li><a href="#library-size-parameters">Library size parameters</a></li>
+ <li><a href="#expression-outlier-parameters">Expression outlier parameters</a></li>
+ <li><a href="#biological-coefficient-of-variation-bcv-parameters">Biological Coefficient of Variation (BCV) parameters</a></li>
+ <li><a href="#dropout-parameters">Dropout parameters</a></li>
+ <li><a href="#path-parameters">Path parameters</a></li>
+ </ul>
+</li>
+ </ul>
+</div>
+ </div>
+
+</div>
+
+
+
+ <footer><div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+</div>
+
+
+
+
+ </body>
+</html>
diff --git a/docs/articles/splat_params_files/figure-html/batch-factors-1.png b/docs/articles/splat_params_files/figure-html/batch-factors-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..2b68de288c52a725de60a1e7e5ce2e814a928a4e
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/batch-factors-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/batch-factors-2.png b/docs/articles/splat_params_files/figure-html/batch-factors-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..ef687bbe1dde681f4e683cb7d3d0c54cb896b9a1
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/batch-factors-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/batches-1.png b/docs/articles/splat_params_files/figure-html/batches-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..1fd467285baf657faa79657a5fba210601a4190a
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/batches-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/complex-de-1.png b/docs/articles/splat_params_files/figure-html/complex-de-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..2a4fe3ef2537a84b531994e90a4825e5e8360dfe
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/complex-de-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/complex-de-2.png b/docs/articles/splat_params_files/figure-html/complex-de-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..950f97174e6087ba3b68ee3453de0dcf362c7f47
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/complex-de-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/complex-de-3.png b/docs/articles/splat_params_files/figure-html/complex-de-3.png
new file mode 100644
index 0000000000000000000000000000000000000000..7829df335afab905c2e4f094e461cc5c3c10480f
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/complex-de-3.png differ
diff --git a/docs/articles/splat_params_files/figure-html/de-factors-1.png b/docs/articles/splat_params_files/figure-html/de-factors-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..7d095a738e94ec635c1f0145cc7b11ac33052dda
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/de-factors-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/de-factors-2.png b/docs/articles/splat_params_files/figure-html/de-factors-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..17c9095d3e7b11618a906ef234218e4a1a79c15a
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/de-factors-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/de-prob-1.png b/docs/articles/splat_params_files/figure-html/de-prob-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..cad320d0e16d95f3d7f8bedafd6a477eeafdadb9
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/de-prob-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/de-prob-2.png b/docs/articles/splat_params_files/figure-html/de-prob-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..695b9255602c544d71ca05da75bfce69c96d1d64
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/de-prob-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/groups-1.png b/docs/articles/splat_params_files/figure-html/groups-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..a9a1d42543b67f46d73381d8d81bb9ec7a620f2a
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/groups-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/groups-2.png b/docs/articles/splat_params_files/figure-html/groups-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..34fdb069c796adcf2241ca1842e5323a8b6066d5
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/groups-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/outlier-prob-1.png b/docs/articles/splat_params_files/figure-html/outlier-prob-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..69b0defb163c0a0fb16861be87b9d6268122fc19
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/outlier-prob-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/outlier-prob-2.png b/docs/articles/splat_params_files/figure-html/outlier-prob-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..4928eea2e2fcac690fbab4b36748b5634a6792e3
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/outlier-prob-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/paths-1.png b/docs/articles/splat_params_files/figure-html/paths-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..7c73dc68e32e1f4cee8487522b67a7373797a223
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/paths-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/paths-2.png b/docs/articles/splat_params_files/figure-html/paths-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..ca6e4616a0304e2037246dd97a97036e529950f6
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/paths-2.png differ
diff --git a/docs/articles/splat_params_files/figure-html/paths-skew-1.png b/docs/articles/splat_params_files/figure-html/paths-skew-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..fafb6dbdbcbd8b8a2a27e7361f1529f72f41e773
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/paths-skew-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/paths-steps-1.png b/docs/articles/splat_params_files/figure-html/paths-steps-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..fe555ac7d30fa917dc52c0de453b40a0b4761553
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/paths-steps-1.png differ
diff --git a/docs/articles/splat_params_files/figure-html/paths-steps-2.png b/docs/articles/splat_params_files/figure-html/paths-steps-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..aba4ab9b21ea639a88da5f54f172df7857b9173b
Binary files /dev/null and b/docs/articles/splat_params_files/figure-html/paths-steps-2.png differ
diff --git a/docs/articles/splatter-logo-small.png b/docs/articles/splatter-logo-small.png
index cd78c46e70f630623a5916269309b09f5f438e0b..0c606de481f139402d10d5b10dbb07394aa51260 100644
Binary files a/docs/articles/splatter-logo-small.png and b/docs/articles/splatter-logo-small.png differ
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index a4b3f324eac313f90a96afff2f366e377afd4b9b..85228f2dc3f4b610ad3d269cd7a95940161eaec2 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -1,19 +1,20 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Introduction to Splatter • Splatter</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<meta property="og:title" content="Introduction to Splatter">
<meta property="og:description" content="">
<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script><script>
@@ -29,14 +30,15 @@
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -44,7 +46,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -54,6 +56,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+<li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -61,7 +75,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -74,13 +88,14 @@
<!--/.navbar -->
+
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2018-11-02</h4>
+ <h4 class="date">2019-10-11</h4>
<small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splatter.Rmd"><code>vignettes/splatter.Rmd</code></a></small>
<div class="hidden name"><code>splatter.Rmd</code></div>
@@ -97,24 +112,28 @@
<h1 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h1>
<p>Splatter can be installed from Bioconductor:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="op">!</span><span class="kw">requireNamespace</span>(<span class="st">"BiocManager"</span>, <span class="dt">quietly=</span><span class="ot">TRUE</span>))</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2"> <span class="kw">install.packages</span>(<span class="st">"BiocManager"</span>)</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3">BiocManager<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/ns-load.html">requireNamespace</a></span>(<span class="st">"BiocManager"</span>, <span class="dt">quietly=</span><span class="ot">TRUE</span>))</a>
+<a class="sourceLine" id="cb1-2" data-line-number="2"> <span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"BiocManager"</span>)</a>
+<a class="sourceLine" id="cb1-3" data-line-number="3">BiocManager<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/BiocManager/man/install.html">install</a></span>(<span class="st">"splatter"</span>)</a></code></pre></div>
<p>To install the most recent development version from Github use:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">BiocManager<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,</a>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">BiocManager<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/BiocManager/man/install.html">install</a></span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">build_vignettes =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
</div>
<div id="quickstart" class="section level1">
<h1 class="hasAnchor">
<a href="#quickstart" class="anchor"></a>Quickstart</h1>
-<p>Assuming you already have a matrix of count data similar to that you wish to simulate there are two simple steps to creating a simulated data set with Splatter. Here is an example using the example dataset in the <code>scater</code> package:</p>
+<p>Assuming you already have a matrix of count data similar to that you wish to simulate there are two simple steps to creating a simulated data set with Splatter. Here is an example a mock dataset generated with the <code>scater</code> package:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># Load package</span></a>
-<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw">library</span>(splatter)</a></code></pre></div>
+<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(splatter)</a></code></pre></div>
<pre><code>## Loading required package: SingleCellExperiment</code></pre>
+<pre><code>## Warning: package 'SingleCellExperiment' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: SummarizedExperiment</code></pre>
+<pre><code>## Warning: package 'SummarizedExperiment' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: GenomicRanges</code></pre>
+<pre><code>## Warning: package 'GenomicRanges' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: stats4</code></pre>
<pre><code>## Loading required package: BiocGenerics</code></pre>
+<pre><code>## Warning: package 'BiocGenerics' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: parallel</code></pre>
<pre><code>##
## Attaching package: 'BiocGenerics'</code></pre>
@@ -129,28 +148,32 @@
<pre><code>## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind,
-## colMeans, colnames, colSums, dirname, do.call, duplicated,
-## eval, evalq, Filter, Find, get, grep, grepl, intersect,
-## is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
-## paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
-## Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
-## table, tapply, union, unique, unsplit, which, which.max,
-## which.min</code></pre>
+## colnames, dirname, do.call, duplicated, eval, evalq, Filter,
+## Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
+## mapply, match, mget, order, paste, pmax, pmax.int, pmin,
+## pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
+## setdiff, sort, table, tapply, union, unique, unsplit, which,
+## which.max, which.min</code></pre>
<pre><code>## Loading required package: S4Vectors</code></pre>
+<pre><code>## Warning: package 'S4Vectors' was built under R version 3.6.1</code></pre>
<pre><code>##
## Attaching package: 'S4Vectors'</code></pre>
<pre><code>## The following object is masked from 'package:base':
##
## expand.grid</code></pre>
<pre><code>## Loading required package: IRanges</code></pre>
+<pre><code>## Warning: package 'IRanges' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: GenomeInfoDb</code></pre>
+<pre><code>## Warning: package 'GenomeInfoDb' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: Biobase</code></pre>
+<pre><code>## Warning: package 'Biobase' was built under R version 3.6.1</code></pre>
<pre><code>## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.</code></pre>
<pre><code>## Loading required package: DelayedArray</code></pre>
+<pre><code>## Warning: package 'DelayedArray' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: matrixStats</code></pre>
<pre><code>##
## Attaching package: 'matrixStats'</code></pre>
@@ -158,6 +181,7 @@
##
## anyMissing, rowMedians</code></pre>
<pre><code>## Loading required package: BiocParallel</code></pre>
+<pre><code>## Warning: package 'BiocParallel' was built under R version 3.6.1</code></pre>
<pre><code>##
## Attaching package: 'DelayedArray'</code></pre>
<pre><code>## The following objects are masked from 'package:matrixStats':
@@ -165,29 +189,25 @@
## colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</code></pre>
<pre><code>## The following objects are masked from 'package:base':
##
-## aperm, apply</code></pre>
-<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1"><span class="co"># Load example data</span></a>
-<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw">library</span>(scater)</a></code></pre></div>
+## aperm, apply, rowsum</code></pre>
+<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1"><span class="co"># Create mock data</span></a>
+<a class="sourceLine" id="cb39-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(scater)</a></code></pre></div>
+<pre><code>## Warning: package 'scater' was built under R version 3.6.1</code></pre>
<pre><code>## Loading required package: ggplot2</code></pre>
-<pre><code>##
-## Attaching package: 'scater'</code></pre>
-<pre><code>## The following object is masked from 'package:S4Vectors':
-##
-## rename</code></pre>
-<pre><code>## The following object is masked from 'package:stats':
-##
-## filter</code></pre>
-<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)</a>
-<a class="sourceLine" id="cb34-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
-<a class="sourceLine" id="cb34-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a>
-<a class="sourceLine" id="cb34-4" data-line-number="4"><span class="co"># Simulate data using estimated parameters</span></a>
-<a class="sourceLine" id="cb34-5" data-line-number="5">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
+<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/Random.html">set.seed</a></span>(<span class="dv">1</span>)</a>
+<a class="sourceLine" id="cb42-2" data-line-number="2">sce <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/mockSCE.html">mockSCE</a></span>()</a>
+<a class="sourceLine" id="cb42-3" data-line-number="3"></a>
+<a class="sourceLine" id="cb42-4" data-line-number="4"><span class="co"># Estimate parameters from mock data</span></a>
+<a class="sourceLine" id="cb42-5" data-line-number="5">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sce)</a></code></pre></div>
+<pre><code>## NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</code></pre>
+<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" data-line-number="1"><span class="co"># Simulate data using estimated parameters</span></a>
+<a class="sourceLine" id="cb44-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
<pre><code>## Getting parameters...</code></pre>
<pre><code>## Creating simulation object...</code></pre>
<pre><code>## Simulating library sizes...</code></pre>
<pre><code>## Simulating gene means...</code></pre>
<pre><code>## Simulating BCV...</code></pre>
-<pre><code>## Simulating counts..</code></pre>
+<pre><code>## Simulating counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
<p>These steps will be explained in detail in the following sections but briefly the first step takes a dataset and estimates simulation parameters from it and the second step takes those parameters and simulates a new dataset.</p>
@@ -197,139 +217,20 @@
<a href="#the-splat-simulation" class="anchor"></a>The Splat simulation</h1>
<p>Before we look at how we estimate parameters let’s first look at how Splatter simulates data and what those parameters are. We use the term ‘Splat’ to refer to the Splatter’s own simulation and differentiate it from the package itself. The core of the Splat model is a gamma-Poisson distribution used to generate a gene by cell matrix of counts. Mean expression levels for each gene are simulated from a <a href="https://en.wikipedia.org/wiki/Gamma_distribution">gamma distribution</a> and the Biological Coefficient of Variation is used to enforce a mean-variance trend before counts are simulated from a <a href="https://en.wikipedia.org/wiki/Poisson_distribution">Poisson distribution</a>. Splat also allows you to simulate expression outlier genes (genes with mean expression outside the gamma distribution) and dropout (random knock out of counts based on mean expression). Each cell is given an expected library size (simulated from a log-normal distribution) that makes it easier to match to a given dataset.</p>
<p>Splat can also simulate differential expression between groups of different types of cells or differentiation paths between different cells types where expression changes in a continuous way. These are described further in the <a href="#simulating-counts">simulating counts</a> section.</p>
-<div id="parameters" class="section level2">
-<h2 class="hasAnchor">
-<a href="#parameters" class="anchor"></a>Parameters</h2>
-<p>The parameters required for the Splat simulation are briefly described here:</p>
-<ul>
-<li>
-<strong>Global parameters</strong>
-<ul>
-<li>
-<code>nGenes</code> - The number of genes to simulate.</li>
-<li>
-<code>nCells</code> - The number of cells to simulate.</li>
-<li>
-<code>seed</code> - Seed to use for generating random numbers.</li>
-</ul>
-</li>
-<li>
-<strong>Batch parameters</strong>
-<ul>
-<li>
-<code>nBatches</code> - The number of batches to simulate.</li>
-<li>
-<code>batchCells</code> - The number of cells in each batch.</li>
-<li>
-<code>batch.facLoc</code> - Location (meanlog) parameter for the batch effects factor log-normal distribution.</li>
-<li>
-<code>batch.facScale</code> - Scale (sdlog) parameter for the batch effects factor log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Mean parameters</strong>
-<ul>
-<li>
-<code>mean.shape</code> - Shape parameter for the mean gamma distribution.</li>
-<li>
-<code>mean.rate</code> - Rate parameter for the mean gamma distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Library size parameters</strong>
-<ul>
-<li>
-<code>lib.loc</code> - Location (meanlog) parameter for the library size log-normal distribution, or mean for the normal distribution.</li>
-<li>
-<code>lib.scale</code> - Scale (sdlog) parameter for the library size log-normal distribution, or sd for the normal distribution.</li>
-<li>
-<code>lib.norm</code> - Whether to use a normal distribution instead of the usual log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Expression outlier parameters</strong>
-<ul>
-<li>
-<code>out.prob</code> - Probability that a gene is an expression outlier.</li>
-<li>
-<code>out.facLoc</code> - Location (meanlog) parameter for the expression outlier factor log-normal distribution.</li>
-<li>
-<code>out.facScale</code> - Scale (sdlog) parameter for the expression outlier factor log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Group parameters</strong>
-<ul>
-<li>
-<code>nGroups</code> - The number of groups or paths to simulate.</li>
-<li>
-<code>group.prob</code> - The probabilities that cells come from particular groups.</li>
-</ul>
-</li>
-<li>
-<strong>Differential expression parameters</strong>
-<ul>
-<li>
-<code>de.prob</code> - Probability that a gene is differentially expressed in each group or path.</li>
-<li>
-<code>de.loProb</code> - Probability that a differentially expressed gene is down-regulated.</li>
-<li>
-<code>de.facLoc</code> - Location (meanlog) parameter for the differential expression factor log-normal distribution.</li>
-<li>
-<code>de.facScale</code> - Scale (sdlog) parameter for the differential expression factor log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Biological Coefficient of Variation parameters</strong>
-<ul>
-<li>
-<code>bcv.common</code> - Underlying common dispersion across all genes.</li>
-<li>
-<code>bcv.df</code> - Degrees of Freedom for the BCV inverse chi-squared distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Dropout parameters</strong>
-<ul>
-<li>
-<code>dropout.type</code> - Type of dropout to simulate.</li>
-<li>
-<code>dropout.mid</code> - Midpoint parameter for the dropout logistic function.</li>
-<li>
-<code>dropout.shape</code> - Shape parameter for the dropout logistic function.</li>
-</ul>
-</li>
-<li>
-<strong>Differentiation path parameters</strong>
-<ul>
-<li>
-<code>path.from</code> - Vector giving the originating point of each path.</li>
-<li>
-<code>path.length</code> - Vector giving the number of steps to simulate along each path.</li>
-<li>
-<code>path.skew</code> - Vector giving the skew of each path.</li>
-<li>
-<code>path.nonlinearProb</code> - Probability that a gene changes expression in a non-linear way along the differentiation path.</li>
-<li>
-<code>path.sigmaFac</code> - Sigma factor for non-linear gene paths.</li>
-</ul>
-</li>
-</ul>
-<p>While this may look like a lot of parameters Splatter attempts to make it easy for the user, both by providing sensible defaults and making it easy to estimate many of the parameters from real data. For more details on the parameters see <code><a href="../reference/SplatParams.html">?SplatParams</a></code>.</p>
-</div>
</div>
<div id="the-splatparams-object" class="section level1">
<h1 class="hasAnchor">
<a href="#the-splatparams-object" class="anchor"></a>The <code>SplatParams</code> object</h1>
<p>All the parameters for the Splat simulation are stored in a <code>SplatParams</code> object. Let’s create a new one and see what it looks like.</p>
-<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
-<a class="sourceLine" id="cb43-2" data-line-number="2">params</a></code></pre></div>
+<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
+<a class="sourceLine" id="cb53-2" data-line-number="2">params</a></code></pre></div>
<pre><code>## A Params object of class SplatParams
## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+## Secondary parameters are usually set during simulation
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 477689
+## 10000 100 955861
##
## 28 additional parameters
##
@@ -366,26 +267,26 @@
## none 0 -1
##
## Paths:
-## [From] [Length] [Skew] [Non-linear]
+## [From] [Steps] [Skew] [Non-linear]
## 0 100 0.5 0.1
## [Sigma Factor]
## 0.8</code></pre>
-<p>As well as telling us what type of object we have (“A <code>Params</code> object of class <code>SplatParams</code>â€) and showing us the values of the parameter this output gives us some extra information. We can see which parameters can be estimated by the <code>splatEstimate</code> function (those in parentheses), which can’t be estimated (those in brackets) and which have been changed from their default values (those in ALL CAPS).</p>
+<p>As well as telling us what type of object we have (“A <code>Params</code> object of class <code>SplatParams</code>â€) and showing us the values of the parameter this output gives us some extra information. We can see which parameters can be estimated by the <code>splatEstimate</code> function (those in parentheses), which can’t be estimated (those in brackets) and which have been changed from their default values (those in ALL CAPS). For more details about the parameters of the Splat simulation refer to the <a href="splat_params.html">Splat parameters vignette</a>.</p>
<div id="getting-and-setting" class="section level2">
<h2 class="hasAnchor">
<a href="#getting-and-setting" class="anchor"></a>Getting and setting</h2>
<p>If we want to look at a particular parameter, for example the number of genes to simulate, we can extract it using the <code>getParam</code> function:</p>
-<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
<pre><code>## [1] 10000</code></pre>
<p>Alternatively, to give a parameter a new value we can use the <code>setParam</code> function:</p>
-<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
-<a class="sourceLine" id="cb47-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
+<a class="sourceLine" id="cb57-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
<pre><code>## [1] 5000</code></pre>
<p>If we want to extract multiple parameters (as a list) or set multiple parameters we can use the <code>getParams</code> or <code>setParams</code> functions:</p>
-<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
-<a class="sourceLine" id="cb49-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))</a>
-<a class="sourceLine" id="cb49-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
-<a class="sourceLine" id="cb49-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
+<a class="sourceLine" id="cb59-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))</a>
+<a class="sourceLine" id="cb59-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
+<a class="sourceLine" id="cb59-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</a></code></pre></div>
<pre><code>## $nGenes
## [1] 8000
##
@@ -394,15 +295,16 @@
##
## $mean.shape
## [1] 0.6</code></pre>
-<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
-<a class="sourceLine" id="cb51-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)</a>
-<a class="sourceLine" id="cb51-3" data-line-number="3">params</a></code></pre></div>
+<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
+<a class="sourceLine" id="cb61-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)</a>
+<a class="sourceLine" id="cb61-3" data-line-number="3">params</a></code></pre></div>
<pre><code>## A Params object of class SplatParams
## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+## Secondary parameters are usually set during simulation
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 477689
+## 8000 100 955861
##
## 28 additional parameters
##
@@ -439,14 +341,14 @@
## none 0 -1
##
## Paths:
-## [From] [Length] [Skew] [Non-linear]
+## [From] [Steps] [Skew] [Non-linear]
## 0 100 0.5 0.1
## [Sigma Factor]
## 0.8</code></pre>
<p>The parameters with have changed are now shown in ALL CAPS to indicate that they been changed form the default.</p>
<p>We can also set parameters directly when we call <code>newSplatParams</code>:</p>
-<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)</a>
-<a class="sourceLine" id="cb53-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)</a>
+<a class="sourceLine" id="cb63-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</a></code></pre></div>
<pre><code>## $lib.loc
## [1] 12
##
@@ -458,23 +360,27 @@
<h1 class="hasAnchor">
<a href="#estimating-parameters" class="anchor"></a>Estimating parameters</h1>
<p>Splat allows you to estimate many of it’s parameters from a data set containing counts using the <code>splatEstimate</code> function.</p>
-<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
-<a class="sourceLine" id="cb55-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" data-line-number="1"><span class="co"># Get the mock counts matrix</span></a>
+<a class="sourceLine" id="cb65-2" data-line-number="2">counts <-<span class="st"> </span><span class="kw">counts</span>(sce)</a>
+<a class="sourceLine" id="cb65-3" data-line-number="3"></a>
+<a class="sourceLine" id="cb65-4" data-line-number="4"><span class="co"># Check that counts is an integer matrix</span></a>
+<a class="sourceLine" id="cb65-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/class.html">class</a></span>(counts)</a></code></pre></div>
<pre><code>## [1] "matrix"</code></pre>
-<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
-<pre><code>## [1] "integer"</code></pre>
-<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
-<a class="sourceLine" id="cb59-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
-<pre><code>## [1] 2000 40</code></pre>
-<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
-<a class="sourceLine" id="cb61-2" data-line-number="2">sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/typeof.html">typeof</a></span>(counts)</a></code></pre></div>
+<pre><code>## [1] "double"</code></pre>
+<div class="sourceCode" id="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
+<a class="sourceLine" id="cb69-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/dim.html">dim</a></span>(counts)</a></code></pre></div>
+<pre><code>## [1] 2000 200</code></pre>
+<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
+<a class="sourceLine" id="cb71-2" data-line-number="2">counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell_001 Cell_002 Cell_003 Cell_004 Cell_005
-## Gene_0001 0 123 2 0 0
-## Gene_0002 575 65 3 1561 2311
-## Gene_0003 0 0 0 0 1213
-## Gene_0004 0 1 0 0 0
-## Gene_0005 0 0 11 0 0</code></pre>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
+## Gene_0001 0 5 7 276 50
+## Gene_0002 12 0 0 0 0
+## Gene_0003 97 292 58 64 541
+## Gene_0004 0 0 0 170 19
+## Gene_0005 105 123 174 565 1061</code></pre>
+<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(counts)</a></code></pre></div>
+<pre><code>## NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</code></pre>
<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take a <code>SingleCellExperiment</code> object. The estimation process has the following steps:</p>
<ol style="list-style-type: decimal">
<li>Mean parameters are estimated by fitting a gamma distribution to the mean expression levels.</li>
@@ -489,82 +395,86 @@
<h1 class="hasAnchor">
<a href="#simulating-counts" class="anchor"></a>Simulating counts</h1>
<p>Once we have a set of parameters we are happy with we can use <code>splatSimulate</code> to simulate counts. If we want to make small adjustments to the parameters we can provide them as additional arguments, alternatively if we don’t supply any parameters the defaults will be used:</p>
-<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a></code></pre></div>
<pre><code>## Getting parameters...</code></pre>
<pre><code>## Creating simulation object...</code></pre>
<pre><code>## Simulating library sizes...</code></pre>
<pre><code>## Simulating gene means...</code></pre>
<pre><code>## Simulating BCV...</code></pre>
-<pre><code>## Simulating counts..</code></pre>
+<pre><code>## Simulating counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
-<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">sim</a></code></pre></div>
+<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" data-line-number="1">sim</a></code></pre></div>
<pre><code>## class: SingleCellExperiment
-## dim: 1000 40
+## dim: 1000 200
## metadata(1): Params
## assays(6): BatchCellMeans BaseCellMeans ... TrueCounts counts
## rownames(1000): Gene1 Gene2 ... Gene999 Gene1000
## rowData names(4): Gene BaseGeneMean OutlierFactor GeneMean
-## colnames(40): Cell1 Cell2 ... Cell39 Cell40
+## colnames(200): Cell1 Cell2 ... Cell199 Cell200
## colData names(3): Cell Batch ExpLibSize
## reducedDimNames(0):
-## spikeNames(0):</code></pre>
-<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
-<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" data-line-number="1"><span class="co"># Access the counts</span></a>
-<a class="sourceLine" id="cb75-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+## spikeNames(0):
+## altExpNames(0):</code></pre>
+<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 200 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionally a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
+<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" data-line-number="1"><span class="co"># Access the counts</span></a>
+<a class="sourceLine" id="cb86-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 55 2 0 11 0
-## Gene2 1 2 0 0 0
-## Gene3 7 2 2 74 8
-## Gene4 0 69 6 0 114
-## Gene5 1 70 40 0 0</code></pre>
-<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="co"># Information about genes</span></a>
-<a class="sourceLine" id="cb77-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+## Gene1 388 184 496 70 977
+## Gene2 115 24 30 62 30
+## Gene3 353 311 356 172 265
+## Gene4 0 0 0 0 0
+## Gene5 66 88 687 488 91</code></pre>
+<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="co"># Information about genes</span></a>
+<a class="sourceLine" id="cb88-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## 1 Gene1 76.9025430673341 1 76.9025430673341
-## 2 Gene2 11.5038956210654 1 11.5038956210654
-## 3 Gene3 9.5216589952532 1 9.5216589952532
-## 4 Gene4 740.124978536434 1 740.124978536434
-## 5 Gene5 71.5386607136642 1 71.5386607136642
-## 6 Gene6 1.06151313409539 1 1.06151313409539</code></pre>
-<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1"><span class="co"># Information about cells</span></a>
-<a class="sourceLine" id="cb79-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## Gene1 Gene1 182.541749248015 1 182.541749248015
+## Gene2 Gene2 45.4848226172007 1 45.4848226172007
+## Gene3 Gene3 247.661694059157 1 247.661694059157
+## Gene4 Gene4 0.133237587005808 1 0.133237587005808
+## Gene5 Gene5 170.361660833028 1 170.361660833028
+## Gene6 Gene6 281.100703006627 1 281.100703006627</code></pre>
+<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="co"># Information about cells</span></a>
+<a class="sourceLine" id="cb90-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 510286.263476612
-## Cell2 Cell2 Batch1 1202024.11389745
-## Cell3 Cell3 Batch1 183908.161529651
-## Cell4 Cell4 Batch1 154585.938029774
-## Cell5 Cell5 Batch1 619536.71187027
-## Cell6 Cell6 Batch1 266676.834832325</code></pre>
-<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
-<a class="sourceLine" id="cb81-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
+## Cell1 Cell1 Batch1 347367.472875596
+## Cell2 Cell2 Batch1 357315.685032967
+## Cell3 Cell3 Batch1 344451.277578974
+## Cell4 Cell4 Batch1 348810.103710477
+## Cell5 Cell5 Batch1 356933.764212043
+## Cell6 Cell6 Batch1 343192.242624294</code></pre>
+<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
+<a class="sourceLine" id="cb92-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/names.html">names</a></span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
-<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
-<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 5.333124e+01 2.598563 1.529988e-01 11.676286605 3.982157e-03
-## Gene2 7.665400e-01 7.586450 1.614969e-25 0.372529598 6.068763e-03
-## Gene3 6.121509e+00 1.784225 6.033250e+00 74.377980371 6.435478e+00
-## Gene4 8.789318e-06 69.991629 7.918106e+00 0.026909108 1.193434e+02
-## Gene5 8.940025e-02 94.814168 3.921096e+01 0.008752188 1.123261e-01</code></pre>
+<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
+<a class="sourceLine" id="cb94-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 390.52352662 198.5368335 530.58433564 8.478547e+01 1006.4132206
+## Gene2 123.88369156 18.7047056 33.40839148 5.484398e+01 28.5096579
+## Gene3 347.21277069 341.6968857 364.20100579 1.501884e+02 254.1098498
+## Gene4 0.02443122 0.0208686 0.01504628 7.542940e-04 0.5873028
+## Gene5 69.56325232 85.8830537 670.02282798 5.116404e+02 89.9774291</code></pre>
<p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
-<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
-<a class="sourceLine" id="cb85-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
+<a class="sourceLine" id="cb96-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
-<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
+<pre><code>## Warning: 'centreSizeFactors' is deprecated.
+## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
+<a class="sourceLine" id="cb99-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim)</a></code></pre></div>
+<pre><code>## Warning: call 'runPCA' explicitly to compute results</code></pre>
<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
<p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
<p>For more details about the <code>SingleCellExperiment</code> object refer to the [vignette] <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SCE-vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
<p>The <code>splatSimulate</code> function outputs the following additional information about the simulation:</p>
<ul>
<li>
-<strong>Cell information (<code>pData</code>)</strong>
+<strong>Cell information (<code>colData</code>)</strong>
<ul>
<li>
<code>Cell</code> - Unique cell identifier.</li>
@@ -577,7 +487,7 @@
</ul>
</li>
<li>
-<strong>Gene information (<code>fData</code>)</strong>
+<strong>Gene information (<code>rowData</code>)</strong>
<ul>
<li>
<code>Gene</code> - Unique gene identifier.</li>
@@ -594,7 +504,7 @@
</ul>
</li>
<li>
-<strong>Gene by cell information (<code>assayData</code>)</strong>
+<strong>Gene by cell information (<code>assays</code>)</strong>
<ul>
<li>
<code>BaseCellMeans</code> - The expression of genes in each cell adjusted for expected library size.</li>
@@ -615,22 +525,28 @@
<a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
<p>So far we have only simulated a single population of cells but often we are interested in investigating a mixed population of cells and looking to see what cell types are present or what differences there are between them. Splatter is able to simulate these situations by changing the <code>method</code> argument Here we are going to simulate two groups, by specifying the <code>group.prob</code> parameter and setting the <code>method</code> parameter to <code>"groups"</code>:</p>
<p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
-<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
-<a class="sourceLine" id="cb88-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb88-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb101"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb101-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
+<a class="sourceLine" id="cb101-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb101-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim.groups)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<pre><code>## Warning: 'centreSizeFactors' is deprecated.
+## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<pre><code>## Warning: call 'runPCA' explicitly to compute results</code></pre>
<p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
-<p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
+<p>As we have set both the group probabilities to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilities that sum to 1.</p>
</div>
<div id="simulating-paths" class="section level2">
<h2 class="hasAnchor">
<a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
<p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
-<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb91-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
+<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb106-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim.paths)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
+<pre><code>## Warning: 'centreSizeFactors' is deprecated.
+## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
+<pre><code>## Warning: call 'runPCA' explicitly to compute results</code></pre>
<p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here the colours represent the “step†of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
</div>
@@ -638,32 +554,38 @@
<h2 class="hasAnchor">
<a href="#batch-effects" class="anchor"></a>Batch effects</h2>
<p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
-<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb94-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
+<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb111-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim.batches)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
+<pre><code>## Warning: 'centreSizeFactors' is deprecated.
+## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
+<pre><code>## Warning: call 'runPCA' explicitly to compute results</code></pre>
<p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
<p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
-<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
-<a class="sourceLine" id="cb97-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb97-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb116-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb116-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/normalize.html">normalize</a></span>(sim.groups)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<pre><code>## Warning: 'centreSizeFactors' is deprecated.
+## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/scater/man/plot_reddim.html">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<pre><code>## Warning: call 'runPCA' explicitly to compute results</code></pre>
<p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
</div>
<div id="convenience-functions" class="section level2">
<h2 class="hasAnchor">
<a href="#convenience-functions" class="anchor"></a>Convenience functions</h2>
-<p>Each of the Splatter simulation methods has it’s own convenience function. To simulate a single population use <code><a href="../reference/splatSimulate.html">splatSimulateSingle()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "single")</a></code>), to simulate grops use <code><a href="../reference/splatSimulate.html">splatSimulateGroups()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "groups")</a></code>) or to simulate paths use <code><a href="../reference/splatSimulate.html">splatSimulatePaths()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "paths")</a></code>).</p>
+<p>Each of the Splatter simulation methods has it’s own convenience function. To simulate a single population use <code><a href="../reference/splatSimulate.html">splatSimulateSingle()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "single")</a></code>), to simulate groups use <code><a href="../reference/splatSimulate.html">splatSimulateGroups()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "groups")</a></code>) or to simulate paths use <code><a href="../reference/splatSimulate.html">splatSimulatePaths()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "paths")</a></code>).</p>
</div>
</div>
<div id="other-simulations" class="section level1">
<h1 class="hasAnchor">
<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
<p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
-<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
-<pre><code>## Splatter currently contains 13 simulations
+<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
+<pre><code>## Splatter currently contains 14 simulations
##
## Splat (splat)
## DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
@@ -681,6 +603,10 @@
## DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
## The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
##
+## Kersplat (kersplat)
+## DOI: GitHub: Oshlack/splatter
+## The Kersplat simulation extends the Splat model by adding a gene network, more complex cell structure, doublets and empty cells (Experimental).
+##
## Simple (simple)
## DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
## A simple simulation with gamma means and negative binomial counts.
@@ -716,177 +642,65 @@
## SparseDC (sparseDC)
## DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC
## The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</code></pre>
-<p>(or more conveniently for the vignette as a table)</p>
-<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
-<table class="table">
-<thead><tr class="header">
-<th align="left">Name</th>
-<th align="left">Prefix</th>
-<th align="left">DOI</th>
-<th align="left">GitHub</th>
-<th align="left">Description</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td align="left">Splat</td>
-<td align="left">splat</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.</td>
-</tr>
-<tr class="even">
-<td align="left">Splat Single</td>
-<td align="left">splatSingle</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation with a single population.</td>
-</tr>
-<tr class="odd">
-<td align="left">Splat Groups</td>
-<td align="left">splatGroups</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation with multiple groups. Each group can have it’s own differential expression probability and fold change distribution.</td>
-</tr>
-<tr class="even">
-<td align="left">Splat Paths</td>
-<td align="left">splatPaths</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation with differentiation paths. Each path can have it’s own length, skew and probability. Genes can change in non-linear ways.</td>
-</tr>
-<tr class="odd">
-<td align="left">Simple</td>
-<td align="left">simple</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">A simple simulation with gamma means and negative binomial counts.</td>
-</tr>
-<tr class="even">
-<td align="left">Lun</td>
-<td align="left">lun</td>
-<td align="left">10.1186/s13059-016-0947-7</td>
-<td align="left">MarioniLab/Deconvolution2016</td>
-<td align="left">Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.</td>
-</tr>
-<tr class="odd">
-<td align="left">Lun 2</td>
-<td align="left">lun2</td>
-<td align="left">10.1093/biostatistics/kxw055</td>
-<td align="left">MarioniLab/PlateEffects2016</td>
-<td align="left">Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.</td>
-</tr>
-<tr class="even">
-<td align="left">scDD</td>
-<td align="left">scDD</td>
-<td align="left">10.1186/s13059-016-1077-y</td>
-<td align="left">kdkorthauer/scDD</td>
-<td align="left">The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</td>
-</tr>
-<tr class="odd">
-<td align="left">BASiCS</td>
-<td align="left">BASiCS</td>
-<td align="left">10.1371/journal.pcbi.1004333</td>
-<td align="left">catavallejos/BASiCS</td>
-<td align="left">The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects.</td>
-</tr>
-<tr class="even">
-<td align="left">mfa</td>
-<td align="left">mfa</td>
-<td align="left">10.12688/wellcomeopenres.11087.1</td>
-<td align="left">kieranrcampbell/mfa</td>
-<td align="left">The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</td>
-</tr>
-<tr class="odd">
-<td align="left">PhenoPath</td>
-<td align="left">pheno</td>
-<td align="left">10.1101/159913</td>
-<td align="left">kieranrcampbell/phenopath</td>
-<td align="left">The PhenoPath simulation produces a pseudotime trajectory with different types of genes.</td>
-</tr>
-<tr class="even">
-<td align="left">ZINB-WaVE</td>
-<td align="left">zinb</td>
-<td align="left">10.1101/125112</td>
-<td align="left">drisso/zinbwave</td>
-<td align="left">The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</td>
-</tr>
-<tr class="odd">
-<td align="left">SparseDC</td>
-<td align="left">sparseDC</td>
-<td align="left">10.1093/nar/gkx1113</td>
-<td align="left">cran/SparseDC</td>
-<td align="left">The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</td>
-</tr>
-</tbody>
-</table>
<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns a <code>SingleCellExperiment</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">? lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
</div>
<div id="other-expression-values" class="section level1">
<h1 class="hasAnchor">
<a href="#other-expression-values" class="anchor"></a>Other expression values</h1>
<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
-<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb103-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
-<a class="sourceLine" id="cb103-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb123-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
+<a class="sourceLine" id="cb123-3" data-line-number="3"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
-## Gene GeneMean Length
-## <factor> <numeric> <numeric>
-## 1 Gene1 0.0489642776646331 1937
-## 2 Gene2 3.20462567086451 2196
-## 3 Gene3 0.364784855489904 9883
-## 4 Gene4 0.110583350422224 1810
-## 5 Gene5 0.661617770742839 1177
-## 6 Gene6 0.101683292027918 2012</code></pre>
+## Gene GeneMean Length
+## <factor> <numeric> <numeric>
+## Gene1 Gene1 0.0792265397126071 1105
+## Gene2 Gene2 0.0306368911550198 2027
+## Gene3 Gene3 1.75797983978846 5541
+## Gene4 Gene4 0.000969198708564301 2476
+## Gene5 Gene5 0.0554598556966454 2845
+## Gene6 Gene6 2.21278105339233 3607</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
-<a class="sourceLine" id="cb105-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0.0000000 0.000000000 0.00000000 0.000000000 0.000000000
-## Gene2 0.2338332 0.033654084 0.09984799 0.000000000 0.066541011
-## Gene3 0.0000000 0.007477929 0.00000000 0.007379757 0.007392698
-## Gene4 0.0000000 0.000000000 0.04038051 0.000000000 0.000000000
-## Gene5 0.0000000 0.062790457 0.06209748 0.247864539 0.000000000</code></pre>
+<div class="sourceCode" id="cb125"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb125-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/scater/man/calculateTPM.html">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
+<a class="sourceLine" id="cb125-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 0.00000 0.00000 0.00000 0.00000 0.0000
+## Gene2 0.00000 0.00000 0.00000 0.00000 0.0000
+## Gene3 28.33389 58.08241 28.72608 57.73984 112.7174
+## Gene4 0.00000 0.00000 0.00000 0.00000 0.0000
+## Gene5 0.00000 0.00000 0.00000 0.00000 0.0000</code></pre>
<p>The default method used by <code>addGeneLengths</code> to simulate lengths is to generate values from a log-normal distribution which are then rounded to give an integer length. The parameters for this distribution are based on human protein coding genes but can be adjusted if needed (for example for other species). Alternatively lengths can be sampled from a provided vector (see <code><a href="../reference/addGeneLengths.html">?addGeneLengths</a></code> for details and an example).</p>
</div>
<div id="comparing-simulations-and-real-data" class="section level1">
<h1 class="hasAnchor">
<a href="#comparing-simulations-and-real-data" class="anchor"></a>Comparing simulations and real data</h1>
<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
-<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb107-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb107-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
-<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.
-## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
-<pre><code>## [1] "FeatureData" "PhenoData" "Plots"</code></pre>
-<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
+<div class="sourceCode" id="cb127"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb127-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb127-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb127-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a>
+<a class="sourceLine" id="cb127-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb127-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/names.html">names</a></span>(comparison)</a></code></pre></div>
+<pre><code>## [1] "RowData" "ColData" "Plots"</code></pre>
+<div class="sourceCode" id="cb129"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb129-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/names.html">names</a></span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
-## [5] "ZerosGene" "ZerosCell" "MeanZeros"</code></pre>
-<p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+## [5] "ZerosGene" "ZerosCell" "MeanZeros" "VarGeneCor"</code></pre>
+<p>The returned list has three items. The first two are the combined datasets by gene (<code>RowData</code>) and by cell (<code>ColData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
+<div class="sourceCode" id="cb131"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb131-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
-<a class="sourceLine" id="cb114-2" data-line-number="2"><span class="kw"><a href="ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
-<a class="sourceLine" id="cb114-3" data-line-number="3"> <span class="kw"><a href="ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
-<a class="sourceLine" id="cb114-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="ggplot2.tidyverse.org/reference/geom_point.html">geom_point</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb132"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb132-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"ggplot2"</span>)</a>
+<a class="sourceLine" id="cb132-2" data-line-number="2"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(comparison<span class="op">$</span>ColData, <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> sum, <span class="dt">y =</span> detected, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb132-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html">geom_point</a></span>()</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
<div id="comparing-differences" class="section level2">
<h2 class="hasAnchor">
<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a></code></pre></div>
-<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.
-## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb133"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb133-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a>
+<a class="sourceLine" id="cb133-2" data-line-number="2">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb134"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb134-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-qq-1.png" width="576" style="display: block; margin: auto;"></p>
</div>
<div id="making-panels" class="section level2">
@@ -894,22 +708,22 @@
<a href="#making-panels" class="anchor"></a>Making panels</h2>
<p>Each of these comparisons makes several plots which can be a lot to look at. To make this easier, or to produce figures for publications, you can make use of the functions <code>makeCompPanel</code>, <code>makeDiffPanel</code> and <code>makeOverallPanel</code>.</p>
<p>These functions combine the plots into a single panel using the <code>cowplot</code> package. The panels can be quite large and hard to view (for example in RStudio’s plot viewer) so it can be better to output the panels and view them separately. Luckily <code>cowplot</code> provides a convenient function for saving the images. Here are some suggested parameters for outputting each of the panels:</p>
-<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
-<a class="sourceLine" id="cb119-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
-<a class="sourceLine" id="cb119-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb119-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb119-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
-<a class="sourceLine" id="cb119-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
-<a class="sourceLine" id="cb119-7" data-line-number="7"></a>
-<a class="sourceLine" id="cb119-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
-<a class="sourceLine" id="cb119-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb135"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb135-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
+<a class="sourceLine" id="cb135-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
+<a class="sourceLine" id="cb135-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/cowplot/man/save_plot.html">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb135-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb135-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
+<a class="sourceLine" id="cb135-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/cowplot/man/save_plot.html">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
+<a class="sourceLine" id="cb135-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb135-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
+<a class="sourceLine" id="cb135-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/cowplot/man/save_plot.html">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
</div>
</div>
<div id="citing-splatter" class="section level1">
<h1 class="hasAnchor">
<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h1>
<p>If you use Splatter in your work please cite our paper:</p>
-<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb136"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb136-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/citation.html">citation</a></span>(<span class="st">"splatter"</span>)</a></code></pre></div>
<pre><code>##
## Zappia L, Phipson B, Oshlack A. Splatter: Simulation of
## single-cell RNA sequencing data. Genome Biology. 2017;
@@ -929,14 +743,14 @@
<div id="session-information" class="section level1 unnumbered">
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
-<pre><code>## R version 3.5.1 (2018-07-02)
+<div class="sourceCode" id="cb138"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb138-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/sessionInfo.html">sessionInfo</a></span>()</a></code></pre></div>
+<pre><code>## R version 3.6.0 (2019-04-26)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
-## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
-## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
+## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
+## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
@@ -946,73 +760,65 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.8.4 ggplot2_3.0.0
-## [3] splatter_1.4.3 SingleCellExperiment_1.2.0
-## [5] SummarizedExperiment_1.10.1 DelayedArray_0.6.5
-## [7] BiocParallel_1.14.2 matrixStats_0.54.0
-## [9] Biobase_2.40.0 GenomicRanges_1.32.6
-## [11] GenomeInfoDb_1.16.0 IRanges_2.14.11
-## [13] S4Vectors_0.18.3 BiocGenerics_0.26.0
-## [15] BiocStyle_2.8.2
+## [1] scater_1.13.24 ggplot2_3.2.1
+## [3] splatter_1.9.7.9019 SingleCellExperiment_1.7.11
+## [5] SummarizedExperiment_1.15.9 DelayedArray_0.11.8
+## [7] BiocParallel_1.19.3 matrixStats_0.55.0
+## [9] Biobase_2.45.1 GenomicRanges_1.37.16
+## [11] GenomeInfoDb_1.21.2 IRanges_2.19.16
+## [13] S4Vectors_0.23.25 BiocGenerics_0.31.6
+## [15] BiocStyle_2.13.2
##
## loaded via a namespace (and not attached):
-## [1] bitops_1.0-6 fs_1.2.6
-## [3] rprojroot_1.3-2 tools_3.5.1
-## [5] backports_1.1.2 R6_2.2.2
-## [7] vipor_0.4.5 lazyeval_0.2.1
-## [9] colorspace_1.3-2 sp_1.3-1
-## [11] withr_2.1.2 tidyselect_0.2.4
-## [13] gridExtra_2.3 compiler_3.5.1
-## [15] xml2_1.2.0 desc_1.2.0
-## [17] labeling_0.3 bookdown_0.7
-## [19] scales_1.0.0 checkmate_1.8.6
-## [21] pkgdown_1.1.0 commonmark_1.5
-## [23] stringr_1.3.1 digest_0.6.16
-## [25] rmarkdown_1.10 XVector_0.20.0
-## [27] pkgconfig_2.0.2 htmltools_0.3.6
-## [29] akima_0.6-2 highr_0.7
-## [31] limma_3.36.3 rlang_0.2.2
-## [33] shiny_1.1.0 DelayedMatrixStats_1.2.0
-## [35] bindr_0.1.1 dplyr_0.7.6
-## [37] RCurl_1.95-4.11 magrittr_1.5
-## [39] GenomeInfoDbData_1.1.0 Matrix_1.2-14
-## [41] Rcpp_0.12.18 ggbeeswarm_0.6.0
-## [43] munsell_0.5.0 Rhdf5lib_1.2.1
-## [45] viridis_0.5.1 stringi_1.2.4
-## [47] yaml_2.2.0 edgeR_3.22.3
-## [49] MASS_7.3-51 zlibbioc_1.26.0
-## [51] rhdf5_2.24.0 plyr_1.8.4
-## [53] grid_3.5.1 promises_1.0.1
-## [55] shinydashboard_0.7.0 crayon_1.3.4
-## [57] lattice_0.20-35 cowplot_0.9.3
-## [59] splines_3.5.1 locfit_1.5-9.1
-## [61] knitr_1.20 pillar_1.3.0
-## [63] rjson_0.2.20 reshape2_1.4.3
-## [65] glue_1.3.0 evaluate_0.11
-## [67] data.table_1.11.4 httpuv_1.4.5
-## [69] gtable_0.2.0 purrr_0.2.5
-## [71] assertthat_0.2.0 xfun_0.3
-## [73] mime_0.5 xtable_1.8-3
-## [75] roxygen2_6.1.0 later_0.7.4
-## [77] survival_2.42-6 viridisLite_0.3.0
-## [79] tibble_1.4.2 beeswarm_0.2.3
-## [81] memoise_1.1.0 tximport_1.8.0
-## [83] bindrcpp_0.2.2 fitdistrplus_1.0-9</code></pre>
+## [1] viridis_0.5.1 edgeR_3.27.13
+## [3] BiocSingular_1.1.7 viridisLite_0.3.0
+## [5] splines_3.6.0 lsei_1.2-0
+## [7] DelayedMatrixStats_1.7.2 assertthat_0.2.1
+## [9] sp_1.3-1 BiocManager_1.30.7
+## [11] GenomeInfoDbData_1.2.1 vipor_0.4.5
+## [13] yaml_2.2.0 pillar_1.4.2
+## [15] backports_1.1.5 lattice_0.20-38
+## [17] limma_3.41.17 glue_1.3.1
+## [19] digest_0.6.21 RColorBrewer_1.1-2
+## [21] XVector_0.25.0 checkmate_1.9.4
+## [23] colorspace_1.4-1 cowplot_1.0.0
+## [25] htmltools_0.4.0 Matrix_1.2-17
+## [27] pkgconfig_2.0.3 bookdown_0.14
+## [29] zlibbioc_1.31.0 purrr_0.3.2
+## [31] scales_1.0.0 tibble_2.1.3
+## [33] withr_2.1.2 lazyeval_0.2.2
+## [35] survival_2.44-1.1 magrittr_1.5
+## [37] crayon_1.3.4 memoise_1.1.0
+## [39] evaluate_0.14 fs_1.3.1
+## [41] MASS_7.3-51.4 beeswarm_0.2.3
+## [43] tools_3.6.0 fitdistrplus_1.0-14
+## [45] stringr_1.4.0 munsell_0.5.0
+## [47] locfit_1.5-9.1 irlba_2.3.3
+## [49] akima_0.6-2 compiler_3.6.0
+## [51] pkgdown_1.4.1 rsvd_1.0.2
+## [53] rlang_0.4.0.9000 grid_3.6.0
+## [55] RCurl_1.95-4.12 BiocNeighbors_1.3.5
+## [57] rstudioapi_0.10 labeling_0.3
+## [59] bitops_1.0-6 rmarkdown_1.16
+## [61] npsurv_0.4-0 gtable_0.3.0
+## [63] R6_2.4.0 gridExtra_2.3
+## [65] knitr_1.25 dplyr_0.8.3
+## [67] rprojroot_1.3-2 desc_1.2.0
+## [69] stringi_1.4.3 ggbeeswarm_0.6.0
+## [71] Rcpp_1.0.2 tidyselect_0.2.5
+## [73] xfun_0.10</code></pre>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+
<div id="tocnav">
<h2 class="hasAnchor">
<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#installation">Installation</a></li>
<li><a href="#quickstart">Quickstart</a></li>
- <li>
-<a href="#the-splat-simulation">The Splat simulation</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#parameters">Parameters</a></li>
- </ul>
-</li>
+ <li><a href="#the-splat-simulation">The Splat simulation</a></li>
<li>
<a href="#the-splatparams-object">The <code>SplatParams</code> object</a><ul class="nav nav-pills nav-stacked">
<li><a href="#getting-and-setting">Getting and setting</a></li>
@@ -1044,12 +850,13 @@
</div>
+
<footer><div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -1057,5 +864,6 @@
+
</body>
</html>
diff --git a/docs/articles/splatter_files/figure-html/batch-groups-1.png b/docs/articles/splatter_files/figure-html/batch-groups-1.png
index 6f5dbefb6034625d0a75323781c103d5a32333f9..3921a513f2f0196e5deb78b6f65d39505ede04f6 100644
Binary files a/docs/articles/splatter_files/figure-html/batch-groups-1.png and b/docs/articles/splatter_files/figure-html/batch-groups-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/batches-1.png b/docs/articles/splatter_files/figure-html/batches-1.png
index 74e352bb54d442cde648e06fd23c6dfc6793f858..654ef860d46f27d04c411df69721ceaead88192f 100644
Binary files a/docs/articles/splatter_files/figure-html/batches-1.png and b/docs/articles/splatter_files/figure-html/batches-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png b/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png
index c3977b1927b48de5ce6c5ccee747a3e44df97ffb..47cb468191eb4b4dcd5e651db6a9e8a75e2227f5 100644
Binary files a/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png and b/docs/articles/splatter_files/figure-html/comparison-libsize-features-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/comparison-means-1.png b/docs/articles/splatter_files/figure-html/comparison-means-1.png
index a69f5b7e662dec784e77187dde626b57dc0aebd0..d8428503c87d873ccdbacf41e1d125c548221d86 100644
Binary files a/docs/articles/splatter_files/figure-html/comparison-means-1.png and b/docs/articles/splatter_files/figure-html/comparison-means-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/difference-1.png b/docs/articles/splatter_files/figure-html/difference-1.png
index aca16705da3e6d24986f7a97457764f442530a87..313446c9728fa1ff19a1435ab78db566086fb801 100644
Binary files a/docs/articles/splatter_files/figure-html/difference-1.png and b/docs/articles/splatter_files/figure-html/difference-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/difference-qq-1.png b/docs/articles/splatter_files/figure-html/difference-qq-1.png
index 274eae987bfa3b74dba5154fce7f1872b3b48b0f..b4fd23ec8e53f1c566930e530fa70f2572b74bf9 100644
Binary files a/docs/articles/splatter_files/figure-html/difference-qq-1.png and b/docs/articles/splatter_files/figure-html/difference-qq-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/groups-1.png b/docs/articles/splatter_files/figure-html/groups-1.png
index c985872ba0a762ef0a11eceae64ac608e37f59e3..bbd2d385cf991ea0e7d448c6db5dc5063f9788c3 100644
Binary files a/docs/articles/splatter_files/figure-html/groups-1.png and b/docs/articles/splatter_files/figure-html/groups-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/paths-1.png b/docs/articles/splatter_files/figure-html/paths-1.png
index d13dc6196bd0ba01be8f4539abc0074daa75b87a..ecf24cf59835725ec9a345298985c0912f4722be 100644
Binary files a/docs/articles/splatter_files/figure-html/paths-1.png and b/docs/articles/splatter_files/figure-html/paths-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/pca-1.png b/docs/articles/splatter_files/figure-html/pca-1.png
index bf92e106b921a619c42b1a9a18a891ff0291ded4..c30dd42f8399e4e55f4dbebe17678e14eacbcbf1 100644
Binary files a/docs/articles/splatter_files/figure-html/pca-1.png and b/docs/articles/splatter_files/figure-html/pca-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
index a68dcbd91dcb470f657823f1bab9c8f3a062ceae..c82dbfac63c52b121e10c20091625b7a19a095b8 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Citation and Authors • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
@@ -32,12 +36,15 @@
<link href="extra.css" rel="stylesheet">
+
<meta property="og:title" content="Citation and Authors" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -55,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -63,14 +71,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -78,7 +87,7 @@
<ul class="nav navbar-nav">
<li>
<a href="index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -88,15 +97,26 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -107,18 +127,20 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Citation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
</div>
<p>Zappia L, Phipson B, Oshlack A (2017).
“Splatter: simulation of single-cell RNA sequencing data.”
<em>Genome Biology</em>.
-doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-0</a>, <a href="http://dx.doi.org/10.1186/s13059-017-1305-0">http://dx.doi.org/10.1186/s13059-017-1305-0</a>.
+doi: <a href="https://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-0</a>, <a href="http://dx.doi.org/10.1186/s13059-017-1305-0">http://dx.doi.org/10.1186/s13059-017-1305-0</a>.
</p>
<pre>@Article{,
author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
@@ -128,21 +150,22 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
url = {http://dx.doi.org/10.1186/s13059-017-1305-0},
doi = {10.1186/s13059-017-1305-0},
}</pre>
+
<div class="page-header">
<h1>Authors</h1>
</div>
<ul class="list-unstyled">
<li>
- <p><strong>Luke Zappia</strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7744-8565' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Luke Zappia</strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7744-8565' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
- <p><strong>Belinda Phipson</strong>. Author. <a href='https://orcid.org/0000-0002-1711-7454' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Belinda Phipson</strong>. Author. <a href='https://orcid.org/0000-0002-1711-7454' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
- <p><strong>Alicia Oshlack</strong>. Author. <a href='https://orcid.org/0000-0001-9788-5690' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Alicia Oshlack</strong>. Author. <a href='https://orcid.org/0000-0001-9788-5690' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
</ul>
@@ -152,13 +175,14 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -166,6 +190,8 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
+
</body>
</html>
+
diff --git a/docs/index.html b/docs/index.html
index d9fecf4a9ef3948c843b7f170aac62de6255b4cf..f4802b9a8926d565ca3f2b47bf80581e197f7d79 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,14 +1,15 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Simple Simulation of Single-cell RNA Sequencing Data • Splatter</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
<meta property="og:title" content="Simple Simulation of Single-cell RNA Sequencing Data">
<meta property="og:description" content="Splatter is a package for the simulation of single-cell RNA
@@ -17,7 +18,7 @@
estimated from real data and functions are provided for comparing real and
simulated datasets.">
<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script><script>
@@ -33,14 +34,15 @@
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -48,7 +50,7 @@
<ul class="nav navbar-nav">
<li>
<a href="index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -58,6 +60,18 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+<li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
@@ -65,7 +79,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -78,11 +92,12 @@
<!--/.navbar -->
+
</header><div class="row">
<div class="contents col-md-9">
-
-<p><img src="https://s16.postimg.org/xc6u52b0l/splatter_logo_small.png" alt="Splatter logo"></p>
+
+<p><img src="https://github.com/Oshlack/splatter/raw/master/vignettes/splatter-logo-small.png" alt="Splatter logo"></p>
<p>Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:</p>
<ul>
<li>Functions for estimating simulation parameters</li>
@@ -104,26 +119,26 @@
install.packages("BiocManager")
BiocManager::install("splatter")</code></pre>
<p>If you wish to build a local version of the vignette use:</p>
-<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">BiocManager::install("splatter", build_vignettes=TRUE)</a></code></pre>
+<pre class="{r}"><code><a href="https://rdrr.io/pkg/BiocManager/man/install.html">BiocManager::install("splatter", build_vignettes=TRUE)</a></code></pre>
<p>This will also build the vignette and install all suggested dependencies (which aren’t required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.</p>
</div>
<div id="development-version" class="section level3">
<h3 class="hasAnchor">
<a href="#development-version" class="anchor"></a>Development version</h3>
<p>If you want to try the <a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html">development version</a> this can also be installed from Bioconductor:</p>
-<pre class="{r}"><code>library(BiocManager)
+<pre class="{r}"><code><a href="https://rdrr.io/r/base/library.html">library(BiocManager)
valid() # checks for out of date packages
BiocManager::install() # (optional) updates out of date packages
-BiocManager::install("splatter")</code></pre>
+BiocManager::install("splatter")</a></code></pre>
<p>Depending on the current release cycle you may also need to install the development version of R. See <a href="https://www.bioconductor.org/developers/how-to/useDevel/">here</a> for more details.</p>
<p>Alternatively the development version can be installed directly from <a href="https://github.com/Oshlack/splatter">Github</a>:</p>
-<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/devtools/topics/install">devtools::install("Oshlack/splatter")</a></code></pre>
+<pre class="{r}"><code><a href="https://rdrr.io/pkg/devtools/man/install.html">devtools::install("Oshlack/splatter")</a></code></pre>
</div>
</div>
</div>
- <div class="col-md-3" id="sidebar">
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<div class="links">
<h2>Links</h2>
<ul class="list-unstyled">
@@ -152,9 +167,9 @@ BiocManager::install("splatter")</code></pre>
<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
-<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7744-8565" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
-<li>Belinda Phipson <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-1711-7454" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
-<li>Alicia Oshlack <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-9788-5690" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
+<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7744-8565" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
+<li>Belinda Phipson <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-1711-7454" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
+<li>Alicia Oshlack <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-9788-5690" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
</ul>
</div>
@@ -178,7 +193,7 @@ BiocManager::install("splatter")</code></pre>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -186,5 +201,6 @@ BiocManager::install("splatter")</code></pre>
+
</body>
</html>
diff --git a/docs/news/index.html b/docs/news/index.html
index 711ca5fe7e5f3513da3b67bb68bb4bafcee3af9e..00bcbe240a59842ecfcad2e330778bb4ef1d39df 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Changelog • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,12 +36,15 @@
<link href="../extra.css" rel="stylesheet">
+
<meta property="og:title" content="Changelog" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -55,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -63,14 +71,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -78,7 +87,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -88,15 +97,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -107,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -116,15 +137,71 @@
<small>Source: <a href='https://github.com/Oshlack/splatter/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
- <div id="version-1-7-0-2018-11-01" class="section level2">
+ <div id="version-1-8-0-2019-05-03" class="section level1">
+<h1 class="page-header">
+<a href="#version-1-8-0-2019-05-03" class="anchor"></a>Version 1.8.0 (2019-05-03)</h1>
+<ul>
+<li>Bioconductor 3.9 release</li>
+</ul>
+<div id="version-1-7-5-2018-04-18" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-5-2018-04-18" class="anchor"></a>Version 1.7.5 (2018-04-18)</h2>
+<ul>
+<li>Add Splat parameters vignette</li>
+<li>Fix spelling</li>
+</ul>
+</div>
+<div id="version-1-7-4-2018-04-17" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-4-2018-04-17" class="anchor"></a>Version 1.7.4 (2018-04-17)</h2>
+<ul>
+<li>Allow SplatParams parameters to be set in any order</li>
+</ul>
+</div>
+<div id="version-1-7-3-2018-04-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-3-2018-04-15" class="anchor"></a>Version 1.7.3 (2018-04-15)</h2>
+<ul>
+<li>Minor changes to documentation</li>
+<li>Protect against integer overflow in simulation functions</li>
+<li>Fix order of groups in splatSimulate</li>
+</ul>
+</div>
+<div id="version-1-7-2-2018-12-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-2-2018-12-06" class="anchor"></a>Version 1.7.2 (2018-12-06)</h2>
+<ul>
+<li>Add ImmunoOncology biocViews tag at request of Bioconductor team</li>
+</ul>
+</div>
+<div id="version-1-7-1-2018-11-17" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-1-2018-11-17" class="anchor"></a>Version 1.7.1 (2018-11-17)</h2>
+<ul>
+<li>Fix bugs in vignette</li>
+</ul>
+</div>
+<div id="version-1-7-0-2018-11-01" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-7-0-2018-11-01" class="anchor"></a>Version 1.7.0 (2018-11-01)</h2>
-<p>Bioconductor 3.9 devel</p>
+<ul>
+<li>Bioconductor 3.9 devel</li>
+</ul>
+</div>
+<div id="version-1-6-1-2018-12-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-6-1-2018-12-06" class="anchor"></a>Version 1.6.1 (2018-12-06)</h2>
+<ul>
+<li>Add ImmunoOncology biocViews tag at request of Bioconductor team</li>
+</ul>
+</div>
</div>
<div id="version-1-6-0-2018-11-01" class="section level1">
<h1 class="page-header">
<a href="#version-1-6-0-2018-11-01" class="anchor"></a>Version 1.6.0 (2018-11-01)</h1>
-<p>Bioconductor 3.8 release</p>
+<ul>
+<li>Bioconductor 3.8 release</li>
+</ul>
<div id="version-1-5-8-2018-10-22" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-8-2018-10-22" class="anchor"></a>Version 1.5.8 (2018-10-22)</h2>
@@ -167,7 +244,7 @@
<ul>
<li>Fix bug in getLNormFactors when reversing factors less than one</li>
<li>Update documentation to new Roxygen version (6.1.0)</li>
-<li>Change varible name in vignette for compatibility with scater</li>
+<li>Change variable name in vignette for compatibility with scater</li>
<li>Add suggested package checks to tests</li>
</ul>
</div>
@@ -448,7 +525,7 @@
<h2 class="hasAnchor">
<a href="#version-0-99-13-2017-03-25" class="anchor"></a>Version 0.99.13 (2017-03-25)</h2>
<ul>
-<li>Modify how Lun2Params stores gene paramters to use data.frame</li>
+<li>Modify how Lun2Params stores gene parameters to use data.frame</li>
<li>Move sampling of genes/cells to lun2Simulate</li>
<li>Return to old Lun2 nGenes estimate</li>
</ul>
@@ -461,7 +538,7 @@
<li>Update compareSCESets plots</li>
<li>Modify Lun2 nGenes estimate</li>
<li>Modify how addFeatureStats names columns</li>
-<li>Add infinte bcv.df warning to splatSimulate</li>
+<li>Add infinite bcv.df warning to splatSimulate</li>
</ul>
</div>
<div id="version-0-99-11-2017-03-20" class="section level2">
@@ -626,7 +703,7 @@
<ul>
<li>Redesign how parameters are stored</li>
<li>Each simulation now has it’s own S4 Params class</li>
-<li>Modify exisiting simulations to use new parameter objects</li>
+<li>Modify existing simulations to use new parameter objects</li>
</ul>
</div>
<div id="version-0-6-0-2016-10-12" class="section level2">
@@ -674,7 +751,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#version-1-7-0-2018-11-01">1.7.0</a></li>
+ <li><a href="#version-1-8-0-2019-05-03">1.8.0</a></li>
<li><a href="#version-1-6-0-2018-11-01">1.6.0</a></li>
<li><a href="#version-1-4-0-2018-05-02">1.4.0</a></li>
<li><a href="#version-1-2-0-2017-10-30">1.2.0</a></li>
@@ -686,13 +763,14 @@
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -700,6 +778,8 @@
+
</body>
</html>
+
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 6ca2f37ab4f657e9f79e79032b2e34e0e13397d5..9145958100221f2aa0772a573f7847ce6e60ad5b 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -21,8 +21,6 @@ body > .container {
display: flex;
height: 100%;
flex-direction: column;
-
- padding-top: 60px;
}
body > .container .row {
@@ -58,9 +56,14 @@ img {
max-width: 100%;
}
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
/* Typographic tweaking ---------------------------------*/
-.contents h1.page-header {
+.contents .page-header {
margin-top: calc(-60px + 1em);
}
@@ -97,21 +100,13 @@ a.anchor {
margin-top: -40px;
}
-/* Static header placement on mobile devices */
-@media (max-width: 767px) {
- .navbar-fixed-top {
- position: absolute;
- }
- .navbar {
- padding: 0;
- }
-}
-
-
/* Sidebar --------------------------*/
#sidebar {
margin-top: 30px;
+ position: -webkit-sticky;
+ position: sticky;
+ top: 70px;
}
#sidebar h2 {
font-size: 1.5em;
@@ -128,6 +123,9 @@ a.anchor {
.orcid {
height: 16px;
+ /* margins are required by official ORCID trademark and display guidelines */
+ margin-left:4px;
+ margin-right:4px;
vertical-align: middle;
}
@@ -136,10 +134,9 @@ a.anchor {
.ref-index th {font-weight: normal;}
.ref-index td {vertical-align: top;}
+.ref-index .icon {width: 40px;}
.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
-
-.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
.ref-index .title {width: 60%;}
.ref-arguments th {text-align: right; padding-right: 10px;}
@@ -218,6 +215,19 @@ a.sourceLine:hover {
visibility: visible;
}
+/* headroom.js ------------------------ */
+
+.headroom {
+ will-change: transform;
+ transition: transform 200ms linear;
+}
+.headroom--pinned {
+ transform: translateY(0%);
+}
+.headroom--unpinned {
+ transform: translateY(-100%);
+}
+
/* mark.js ----------------------------*/
mark {
@@ -230,3 +240,17 @@ mark {
.html-widget {
margin-bottom: 10px;
}
+
+/* fontawesome ------------------------ */
+
+.fab {
+ font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+ code a:link:after, code a:visited:after {
+ content: "";
+ }
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index de9bd7247cf858fdc66d64631f9b67f06b170f5a..087a76227251d084449b3512dfe9ff20b680c371 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -2,14 +2,12 @@
(function($) {
$(function() {
- $("#sidebar")
- .stick_in_parent({offset_top: 40})
- .on('sticky_kit:bottom', function(e) {
- $(this).parent().css('position', 'static');
- })
- .on('sticky_kit:unbottom', function(e) {
- $(this).parent().css('position', 'relative');
- });
+ $('.navbar-fixed-top').headroom();
+
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ $(window).resize(function(){
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ });
$('body').scrollspy({
target: '#sidebar',
@@ -25,9 +23,13 @@
for (var i = 0; i < links.length; i++) {
if (links[i].getAttribute("href") === "#")
continue;
- var path = paths(links[i].pathname);
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
- var length = prefix_length(cur_path, path);
+ var length = prefix_length(nav_path, cur_path);
if (length > max_length) {
max_length = length;
pos = i;
@@ -52,13 +54,14 @@
return(pieces);
}
+ // Returns -1 if not found
function prefix_length(needle, haystack) {
if (needle.length > haystack.length)
- return(0);
+ return(-1);
// Special case for length-0 haystack, since for loop won't run
if (haystack.length === 0) {
- return(needle.length === 0 ? 1 : 0);
+ return(needle.length === 0 ? 0 : -1);
}
for (var i = 0; i < haystack.length; i++) {
@@ -78,9 +81,9 @@
element.setAttribute('data-original-title', tooltipOriginalTitle);
}
- if(Clipboard.isSupported()) {
+ if(ClipboardJS.isSupported()) {
$(document).ready(function() {
- var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+ var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
$(".examples, div.sourceCode").addClass("hasCopyButton");
@@ -91,7 +94,7 @@
$('.btn-copy-ex').tooltip({container: 'body'});
// Initialize clipboard:
- var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+ var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
text: function(trigger) {
return trigger.parentNode.textContent;
}
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 62c46f74eabe7b994e85a9559cb62cb7af13968e..fac2f364b8e75a30a0afa9db214fda7a4581062f 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,7 +1,8 @@
-pandoc: 2.1.1
-pkgdown: 1.1.0
+pandoc: 2.3.1
+pkgdown: 1.4.1
pkgdown_sha: ~
articles:
+ splat_params: splat_params.html
splatter: splatter.html
urls:
reference: http://oshlack.github.io/splatter/reference
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index 51890b3232712fd57200b120e9e76ff119dca730..8ec7b27267316abb222682ee88011444372db1ab 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate BASiCS simulation parameters — BASiCSEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate BASiCS simulation parameters — BASiCSEstimate" />
+<meta property="og:title" content="Estimate BASiCS simulation parameters — BASiCSEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the BASiCS simulation from a real dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,9 +141,7 @@
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the BASiCS simulation from a real dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>,
@@ -141,7 +159,7 @@
<span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>,
<span class='kw'>regression</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -154,7 +172,7 @@ containing count data to estimate parameters from.</p></td>
<th>spike.info</th>
<td><p>data.frame describing spike-ins with two columns: "Name"
giving the names of the spike-in features (must match
-<code>rownames(counts)</code>) and "Input" giving the number of input
+<code><a href='https://rdrr.io/r/base/colnames.html'>rownames(counts)</a></code>) and "Input" giving the number of input
molecules.</p></td>
</tr>
<tr>
@@ -178,7 +196,7 @@ a multiple of <code>thin</code>.</p></td>
<tr>
<th>regression</th>
<td><p>logical. Whether to use regression to identify
-over-dispersion. See <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p></td>
+over-dispersion. See <code><a href='https://rdrr.io/pkg/BASiCS/man/BASiCS_MCMC.html'>BASiCS_MCMC</a></code> for details.</p></td>
</tr>
<tr>
<th>params</th>
@@ -195,59 +213,55 @@ messages.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Optional parameters passed to <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code>.</p></td>
+ <td><p>Optional parameters passed to <code><a href='https://rdrr.io/pkg/BASiCS/man/BASiCS_MCMC.html'>BASiCS_MCMC</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>BASiCSParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://rdrr.io/pkg/BASiCS/man/BASiCS_MCMC.html'>BASiCS_MCMC</a></code> that
takes the output and converts it to a BASiCSParams object. Either a set of
spike-ins or batch information (or both) must be supplied. If only batch
information is provided there must be at least two batches. See
-<code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p>
-
+<code><a href='https://rdrr.io/pkg/BASiCS/man/BASiCS_MCMC.html'>BASiCS_MCMC</a></code> for details.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
-<span class='no'>spike.info</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'>rownames</span>(<span class='no'>sc_example_counts</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
- <span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'>rnorm</span>(<span class='fl'>10</span>, <span class='fl'>500</span>, <span class='fl'>200</span>),
+<span class='no'>spike.info</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>sce</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
+ <span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span>(<span class='fl'>10</span>, <span class='fl'>500</span>, <span class='fl'>200</span>),
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>BASiCSEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>100</span>, <span class='fl'>1</span>:<span class='fl'>30</span>],
- <span class='no'>spike.info</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>BASiCSEstimate</span>(<span class='no'>sce</span>[<span class='fl'>1</span>:<span class='fl'>100</span>, <span class='fl'>1</span>:<span class='fl'>30</span>], <span class='no'>spike.info</span>)
<span class='no'>params</span>
-<span class='co'># }</span></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -255,6 +269,8 @@ information is provided there must be at least two batches. See
+
</body>
</html>
+
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
index 9c2a7b92ce80c4a7964edc3940bc085270f5ace1..ec28ffb4e19feb659f9261f8af4a0072c9849490 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The BASiCSParams class — BASiCSParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The BASiCSParams class — BASiCSParams" />
+<meta property="og:title" content="The BASiCSParams class — BASiCSParams" />
<meta property="og:description" content="S4 class that holds parameters for the BASiCS simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,67 +141,64 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the BASiCS simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The BASiCS simulation uses the following parameters:</p><dl class='dl-horizontal'>
+
+
+<p>The BASiCS simulation uses the following parameters:</p><dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
<dt><em>Batch parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>nBatches</code></dt><dd><p>Number of batches to simulate.</p></dd>
- <dt><code>batchCells</code></dt><dd><p>Number of cells in each batch.</p></dd>
- </dl></p></dd>
+ <dt><code>batchCells</code></dt><dd><p>Number of cells in each batch.</p></dd></dl></p></dd>
<dt><em>Gene parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>gene.params</code></dt><dd><p>A <code>data.frame</code> containing gene
- parameters with two coloumns: <code>Mean</code> (mean expression for
+ parameters with two columns: <code>Mean</code> (mean expression for
each biological gene) and <code>Delta</code> (cell-to-cell
- heterogeneity for each biological gene).</p></dd>
- </dl></p></dd>
+ heterogeneity for each biological gene).</p></dd></dl></p></dd>
<dt><em>Spike-in parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>nSpikes</code></dt><dd><p>The number of spike-ins to simulate.</p></dd>
- <dt><code>spike.means</code></dt><dd><p>Input molecules for each spike-in.</p></dd>
- </dl></p></dd>
+ <dt><code>spike.means</code></dt><dd><p>Input molecules for each spike-in.</p></dd></dl></p></dd>
<dt><em>Cell parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>cell.params</code></dt><dd><p>A <code>data.frame</code> containing gene
- parameters with two coloumns: <code>Phi</code> (mRNA content factor for
+ parameters with two columns: <code>Phi</code> (mRNA content factor for
each cell, scaled to sum to the number of cells in each batch)
- and <code>S</code> (capture efficient for each cell).</p></dd>
- </dl></p></dd>
+ and <code>S</code> (capture efficient for each cell).</p></dd></dl></p></dd>
<dt><em>Variability parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>theta</code></dt><dd><p>Technical variability parameter for each
- batch.</p></dd>
- </dl></p></dd>
+ batch.</p></dd></dl></p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
+
+<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='BASiCSEstimate.html'>BASiCSEstimate</a></code>. For details of the BASiCS simulation see
<code><a href='BASiCSSimulate.html'>BASiCSSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -189,6 +206,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index c0992a6a4d5524a6cbbc47d6ae0c2457c3ff3cff..4eb147902de7d32dcf60911a3ab80149942aca3d 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>BASiCS simulation — BASiCSSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="BASiCS simulation — BASiCSSimulate" />
+<meta property="og:title" content="BASiCS simulation — BASiCSSimulate" />
<meta property="og:description" content="Simulate counts using the BASiCS method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Simulate counts using the BASiCS method.</p>
-
</div>
<pre class="usage"><span class='fu'>BASiCSSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -145,54 +163,50 @@
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://rdrr.io/pkg/BASiCS/man/BASiCS_Sim.html'>BASiCS_Sim</a></code> that
takes a <code><a href='BASiCSParams.html'>BASiCSParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> for more details of how the simulation
+output to a <code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object.
+See <code><a href='https://rdrr.io/pkg/BASiCS/man/BASiCS_Sim.html'>BASiCS_Sim</a></code> for more details of how the simulation
works.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
-Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
+Single-Cell Sequencing data. PLoS Computational Biology (2015).</p>
<p>Paper: <a href='10.1371/journal.pcbi.1004333'>10.1371/journal.pcbi.1004333</a></p>
<p>Code: <a href='https://github.com/catavallejos/BASiCS'>https://github.com/catavallejos/BASiCS</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>BASiCSSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='warning'>Warning: Number of gene.params not equal to nGenes, gene.params will be sampled.</span></div><div class='output co'>#> <span class='warning'>Warning: Number of cell.params not equal to nCells, cell.params will be sampled.</span></div><div class='output co'>#> <span class='message'>Simulating counts with BASiCS...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"BASiCS"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>BASiCSSimulate</span>()
+}</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='warning'>Warning: Number of gene.params not equal to nGenes, gene.params will be sampled.</span></div><div class='output co'>#> <span class='warning'>Warning: Number of cell.params not equal to nCells, cell.params will be sampled.</span></div><div class='output co'>#> <span class='message'>Simulating counts with BASiCS...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -200,6 +214,8 @@ Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
+
</body>
</html>
+
diff --git a/docs/reference/KersplatParams.html b/docs/reference/KersplatParams.html
new file mode 100644
index 0000000000000000000000000000000000000000..336f318626e6ca0a157fe1d62fd620d947b62c51
--- /dev/null
+++ b/docs/reference/KersplatParams.html
@@ -0,0 +1,250 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>The KersplatParams class — KersplatParams • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="The KersplatParams class — KersplatParams" />
+<meta property="og:description" content="S4 class that holds parameters for the Kersplat simulation." />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>The KersplatParams class</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllClasses.R'><code>R/AllClasses.R</code></a></small>
+ <div class="hidden name"><code>KersplatParams.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>S4 class that holds parameters for the Kersplat simulation.</p>
+ </div>
+
+
+
+ <h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
+
+
+
+
+<p>The Kersplat simulation uses the following parameters:</p>
+<dl class='dl-horizontal'>
+ <dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
+ <dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
+ <dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+ <dt><em>Mean parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>mean.shape</code></dt><dd><p>Shape parameter for the mean gamma
+ distribution.</p></dd>
+ <dt><code>mean.rate</code></dt><dd><p>Rate parameter for the mean gamma
+ distribution.</p></dd>
+ <dt><code>mean.outProb</code></dt><dd><p>Probability that a gene is an
+ expression outlier.</p></dd>
+ <dt><code>mean.outFacLoc</code></dt><dd><p>Location (meanlog) parameter for
+ the expression outlier factor log-normal distribution.</p></dd>
+ <dt><code>mean.outFacScale</code></dt><dd><p>Scale (sdlog) parameter for the
+ expression outlier factor log-normal distribution.</p></dd>
+ <dt><code>mean.dens</code></dt><dd><p><code><a href='https://rdrr.io/r/stats/density.html'>density</a></code> object describing
+ the log gene mean density.</p></dd>
+ <dt><code>[mean.method]</code></dt><dd><p>Method to use for simulating gene
+ means. Either "fit" to sample from a gamma distribution (with
+ expression outliers) or "density" to sample from the provided
+ density object.</p></dd>
+ <dt><code>[mean.values]</code></dt><dd><p>Vector of means for each gene.</p></dd></dl></p></dd>
+ <dt><em>Biological Coefficient of Variation parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>bcv.common</code></dt><dd><p>Underlying common dispersion across all
+ genes.</p></dd>
+ <dt><code>[bcv.df]</code></dt><dd><p>Degrees of Freedom for the BCV inverse
+ chi-squared distribution.</p></dd></dl></p></dd>
+ <dt><em>Network parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[network.graph]</code></dt><dd><p>Graph containing the gene network.</p></dd>
+ <dt><code>[network.nRegs]</code></dt><dd><p>Number of regulators in the
+ network.</p></dd></dl></p></dd>
+ <dt><em>Paths parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[paths.programs]</code></dt><dd><p>Number of expression programs.</p></dd>
+ <dt><code>[paths.design]</code></dt><dd><p>data.frame describing path
+ structure. See <code><a href='kersplatSimPaths.html'>kersplatSimPaths</a></code> for details.</p></dd></dl></p></dd>
+ <dt><em>Library size parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>lib.loc</code></dt><dd><p>Location (meanlog) parameter for the
+ library size log-normal distribution, or mean parameter if a
+ normal distribution is used.</p></dd>
+ <dt><code>lib.scale</code></dt><dd><p>Scale (sdlog) parameter for the library
+ size log-normal distribution, or sd parameter if a normal
+ distribution is used.</p></dd>
+ <dt><code>lib.dens</code></dt><dd><p><code><a href='https://rdrr.io/r/stats/density.html'>density</a></code> object describing
+ the library size density.</p></dd>
+ <dt><code>[lib.method]</code></dt><dd><p>Method to use for simulating library
+ sizes. Either "fit" to sample from a log-normal distribution or
+ "density" to sample from the provided density object.</p></dd></dl></p></dd>
+ <dt><em>Design parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[cells.design]</code></dt><dd><p>data.frame describing cell
+ structure. See <code><a href='kersplatSimCellMeans.html'>kersplatSimCellMeans</a></code> for details.</p></dd></dl></p></dd>
+ <dt><em>Doublet parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[doublet.prop]</code></dt><dd><p>Proportion of cells that are
+ doublets.</p></dd></dl></p></dd>
+ <dt><em>Ambient parameters</em></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>[ambient.scale]</code></dt><dd><p>Scaling factor for the library
+ size log-normal distribution when generating ambient library
+ sizes.</p></dd>
+ <dt><code>[ambient.nEmpty]</code></dt><dd><p>Number of empty cells to
+ simulate.</p></dd></dl></p></dd>
+
+</dl>
+
+<p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='kersplatEstimate.html'>kersplatEstimate</a></code>. For details of the Kersplat simulation
+see <code><a href='kersplatSimulate.html'>kersplatSimulate</a></code>.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#parameters">Parameters</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index 92ffb513141ff6c55356fa1d50dd67e06d1dc2f0..8f1973eeb17beb3dcaca45c0fa901366540f7636 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The Lun2Params class — Lun2Params • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The Lun2Params class — Lun2Params" />
+<meta property="og:title" content="The Lun2Params class — Lun2Params" />
<meta property="og:description" content="S4 class that holds parameters for the Lun2 simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,74 +141,72 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the Lun2 simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Lun2 simulation uses the following parameters:</p>
+
+
+<p>The Lun2 simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
<dt><em>Gene parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>gene.params</code></dt><dd><p>A <code>data.frame</code> containing gene
- parameters with two coloumns: <code>Mean</code> (mean expression for
+ parameters with two columns: <code>Mean</code> (mean expression for
each gene) and <code>Disp</code> (dispersion for each gene).</p></dd>
<dt><code>zi.params</code></dt><dd><p>A <code>data.frame</code> containing
- zero-inflated gene parameters with three coloumns: <code>Mean</code>
+ zero-inflated gene parameters with three columns: <code>Mean</code>
(mean expression for each gene), <code>Disp</code> (dispersion for
- each, gene), and <code>Prop</code> (zero proportion for each gene).</p></dd>
- </dl></p></dd>
+ each, gene), and <code>Prop</code> (zero proportion for each gene).</p></dd></dl></p></dd>
<dt><code>[nPlates]</code></dt><dd><p>The number of plates to simulate.</p></dd>
<dt><em>Plate parameters</em></dt><dd><p><dl class='dl-horizontal'>
- <dt><code>plate.ingroup</code></dt><dd><p>Character vecotor giving the plates
+ <dt><code>plate.ingroup</code></dt><dd><p>Character vector giving the plates
considered to be part of the "ingroup".</p></dd>
<dt><code>plate.mod</code></dt><dd><p>Plate effect modifier factor. The plate
effect variance is divided by this value.</p></dd>
- <dt><code>plate.var</code></dt><dd><p>Plate effect variance.</p></dd>
- </dl></p></dd>
+ <dt><code>plate.var</code></dt><dd><p>Plate effect variance.</p></dd></dl></p></dd>
<dt><em>Cell parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>cell.plates</code></dt><dd><p>Factor giving the plate that each cell
comes from.</p></dd>
<dt><code>cell.libSizes</code></dt><dd><p>Library size for each cell.</p></dd>
<dt><code>cell.libMod</code></dt><dd><p>Modifier factor for library sizes.
- The library sizes are multiplied by this value.</p></dd>
- </dl></p></dd>
+ The library sizes are multiplied by this value.</p></dd></dl></p></dd>
<dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>de.nGenes</code></dt><dd><p>Number of differentially expressed
genes.</p></dd>
<dt><code>de.fc</code></dt><dd><p>Fold change for differentially expressed
- genes.</p></dd>
- </dl></p></dd>
+ genes.</p></dd></dl></p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
+
+<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='lun2Estimate.html'>lun2Estimate</a></code>. For details of the Lun2 simulation see
<code><a href='lun2Simulate.html'>lun2Simulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -196,6 +214,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
index 67a076289bf4b4877c782ff37df868fe23e2dfa6..66fd9f86366f09fe62d0f88b33260e3b3bf1ba87 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The LunParams class — LunParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The LunParams class — LunParams" />
+<meta property="og:title" content="The LunParams class — LunParams" />
<meta property="og:description" content="S4 class that holds parameters for the Lun simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,17 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the Lun simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Lun simulation uses the following parameters:</p>
+
+
+<p>The Lun simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
@@ -142,12 +163,10 @@
<dt><code>[mean.shape]</code></dt><dd><p>Shape parameter for the mean gamma
distribution.</p></dd>
<dt><code>[mean.rate]</code></dt><dd><p>Rate parameter for the mean gamma
- distribution.</p></dd>
- </dl></p></dd>
+ distribution.</p></dd></dl></p></dd>
<dt><em>Counts parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>[count.disp]</code></dt><dd><p>The dispersion parameter for the
- counts negative binomial distribution.</p></dd>
- </dl></p></dd>
+ counts negative binomial distribution.</p></dd></dl></p></dd>
<dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>[de.nGenes]</code></dt><dd><p>The number of genes that are
differentially expressed in each group</p></dd>
@@ -155,32 +174,32 @@
expressed genes that are up-regulated in each group</p></dd>
<dt><code>[de.upFC]</code></dt><dd><p>The fold change for up-regulated genes</p></dd>
<dt><code>[de.downFC]</code></dt><dd><p>The fold change for down-regulated
- genes</p></dd>
- </dl></p></dd>
+ genes</p></dd></dl></p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
+
+<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='lunEstimate.html'>lunEstimate</a></code>. For details of the Lun simulation see
<code><a href='lunSimulate.html'>lunSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -188,6 +207,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/MFAParams.html b/docs/reference/MFAParams.html
index 2e5f571d4f40137f799f78a92fb688e9cd338bd4..226b26290637e137cb5919388ae5580535f511b4 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The MFAParams class — MFAParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The MFAParams class — MFAParams" />
+<meta property="og:title" content="The MFAParams class — MFAParams" />
<meta property="og:description" content="S4 class that holds parameters for the mfa simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,17 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the mfa simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The mfa simulation uses the following parameters:</p><dl class='dl-horizontal'>
+
+
+<p>The mfa simulation uses the following parameters:</p><dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
@@ -142,31 +163,32 @@
<dt><code>[dropout.present]</code></dt><dd><p>Logical. Whether to simulate dropout.</p></dd>
<dt><code>dropout.lambda</code></dt><dd><p>Lambda parameter for the exponential
dropout function.</p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
-<code><a href='mfaEstimate.html'>mfaEstimate</a></code>. See <code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code> for more
+
+<p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='mfaEstimate.html'>mfaEstimate</a></code>. See <code><a href='https://rdrr.io/pkg/mfa/man/create_synthetic.html'>create_synthetic</a></code> for more
details about the parameters. For details of the Splatter implementation of
the mfa simulation see <code><a href='mfaSimulate.html'>mfaSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -174,6 +196,8 @@ the mfa simulation see <code><a href='mfaSimulate.html'>mfaSimulate</a></code>.<
+
</body>
</html>
+
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
index 25b222320b6d26f969b59a15a863e3a25bbe29a6..3ecf3aba1a3907c269f8ebc20cd730cc159d1924 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The Params virtual class — Params • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The Params virtual class — Params" />
+<meta property="og:title" content="The Params virtual class — Params" />
<meta property="og:description" content="Virtual S4 class that all other Params classes inherit from." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,42 +141,44 @@
</div>
<div class="ref-description">
-
<p>Virtual S4 class that all other Params classes inherit from.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Params class defines the following parameters:</p>
+
+
+<p>The Params class defines the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data.</p>
-
+
+<p>The parameters not shown in brackets can be estimated from real data.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -164,6 +186,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
index 449a50746511957f332d6d30dee340fd13e56690..d6fb682ffbc19b0c160342b35eb6ef76145fb2e9 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The PhenoParams class — PhenoParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The PhenoParams class — PhenoParams" />
+<meta property="og:title" content="The PhenoParams class — PhenoParams" />
<meta property="og:description" content="S4 class that holds parameters for the PhenoPath simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,17 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the PhenoPath simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The PhenoPath simulation uses the following parameters:</p>
+
+
+<p>The PhenoPath simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
@@ -143,30 +164,31 @@
pseudotime + beta interactions regime</p></dd>
<dt><code>[n.de.pst.beta]</code></dt><dd><p>Number of genes to simulate from the
differential expression + pseudotime + interactions regime</p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
+
+<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='phenoEstimate.html'>phenoEstimate</a></code>. For details of the PhenoPath simulation
see <code><a href='phenoSimulate.html'>phenoSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -174,6 +196,8 @@ see <code><a href='phenoSimulate.html'>phenoSimulate</a></code>.</p>
+
</body>
</html>
+
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
index de57312ca7a08092ec5f74a3ade2b170ae1f06e9..4433e4790281a7cf48c30608d7ac57f1f657feb3 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The SCDDParams class — SCDDParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The SCDDParams class — SCDDParams" />
+<meta property="og:title" content="The SCDDParams class — SCDDParams" />
<meta property="og:description" content="S4 class that holds parameters for the scDD simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,21 +141,22 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the scDD simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The SCDD simulation uses the following parameters:</p>
+
+
+<p>The SCDD simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate (not used).</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate in each condition.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
- <dt><code>SCdat</code></dt><dd><p><code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> containing real
+ <dt><code>SCdat</code></dt><dd><p><code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> containing real
data.</p></dd>
<dt><code>nDE</code></dt><dd><p>Number of DE genes to simulate.</p></dd>
<dt><code>nDP</code></dt><dd><p>Number of DP genes to simulate.</p></dd>
@@ -149,31 +170,32 @@
condition. If all equal to 1 will be set to <code>NULL</code> (default).</p></dd>
<dt><code>[condition]</code></dt><dd><p>String giving the column that represents
biological group of interest.</p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
-<code><a href='scDDEstimate.html'>scDDEstimate</a></code>. See <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more
+
+<p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='scDDEstimate.html'>scDDEstimate</a></code>. See <code><a href='https://rdrr.io/pkg/scDD/man/simulateSet.html'>simulateSet</a></code> for more
details about the parameters. For details of the Splatter implementation of
the scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -181,6 +203,8 @@ the scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code
+
</body>
</html>
+
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
index 9d678e46cce9d10f580c68a3b9d8617251f37455..bb2431808a808393990d9ad18ad0ca97db26c74d 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The SimpleParams class — SimpleParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The SimpleParams class — SimpleParams" />
+<meta property="og:title" content="The SimpleParams class — SimpleParams" />
<meta property="og:description" content="S4 class that holds parameters for the simple simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,17 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the simple simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The simple simulation uses the following parameters:</p>
+
+
+<p>The simple simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
@@ -141,30 +162,31 @@
distribution.</p></dd>
<dt><code>[count.disp]</code></dt><dd><p>The dispersion parameter for the counts
negative binomial distribution.</p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
+
+<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='simpleEstimate.html'>simpleEstimate</a></code>. For details of the simple simulation
see <code><a href='simpleSimulate.html'>simpleSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -172,6 +194,8 @@ see <code><a href='simpleSimulate.html'>simpleSimulate</a></code>.</p>
+
</body>
</html>
+
diff --git a/docs/reference/SparseDCParams.html b/docs/reference/SparseDCParams.html
index 819e4e341723e17612cf0d85b20a6087d040dae0..9973c3999b91b651c8f4c7eb94de9c20bc216e30 100644
--- a/docs/reference/SparseDCParams.html
+++ b/docs/reference/SparseDCParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The SparseDCParams class — SparseDCParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The SparseDCParams class — SparseDCParams" />
+<meta property="og:title" content="The SparseDCParams class — SparseDCParams" />
<meta property="og:description" content="S4 class that holds parameters for the SparseDC simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,17 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the SparseDC simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The SparseDC simulation uses the following parameters:</p>
+
+
+<p>The SparseDC simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate in each condition.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
@@ -150,30 +171,31 @@
proportion of cells from that cluster.</p></dd>
<dt><code>[mean.lower]</code></dt><dd><p>Lower bound for cluster gene means.</p></dd>
<dt><code>[mean.upper]</code></dt><dd><p>Upper bound for cluster gene means.</p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
+
+<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='sparseDCEstimate.html'>sparseDCEstimate</a></code>. For details of the SparseDC simulation
see <code><a href='sparseDCSimulate.html'>sparseDCSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -181,6 +203,8 @@ see <code><a href='sparseDCSimulate.html'>sparseDCSimulate</a></code>.</p>
+
</body>
</html>
+
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
index 687e6b5670a5b2088d78c88ab1facd06accd63b8..51feee86ad5041466cc9fd06688ff36c02a33a47 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The SplatParams class — SplatParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The SplatParams class — SplatParams" />
-<meta property="og:description" content="S4 class that holds parameters for the Splatter simulation." />
+<meta property="og:title" content="The SplatParams class — SplatParams" />
+<meta property="og:description" content="S4 class that holds parameters for the Splat simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,17 @@
</div>
<div class="ref-description">
-
- <p>S4 class that holds parameters for the Splatter simulation.</p>
-
+ <p>S4 class that holds parameters for the Splat simulation.</p>
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The Splatter simulation requires the following parameters:</p>
+
+
+<p>The Splat simulation requires the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
@@ -142,14 +163,12 @@
<dt><code>[batch.facLoc]</code></dt><dd><p>Location (meanlog) parameter for the
batch effect factor log-normal distribution. Can be a vector.</p></dd>
<dt><code>[batch.facScale]</code></dt><dd><p>Scale (sdlog) parameter for the
- batch effect factor log-normal distribution. Can be a vector.</p></dd>
- </dl></p></dd>
+ batch effect factor log-normal distribution. Can be a vector.</p></dd></dl></p></dd>
<dt><em>Mean parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>mean.shape</code></dt><dd><p>Shape parameter for the mean gamma
distribution.</p></dd>
<dt><code>mean.rate</code></dt><dd><p>Rate parameter for the mean gamma
- distribution.</p></dd>
- </dl></p></dd>
+ distribution.</p></dd></dl></p></dd>
<dt><em>Library size parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>lib.loc</code></dt><dd><p>Location (meanlog) parameter for the
library size log-normal distribution, or mean parameter if a
@@ -158,40 +177,35 @@
size log-normal distribution, or sd parameter if a normal
distribution is used.</p></dd>
<dt><code>lib.norm</code></dt><dd><p>Logical. Whether to use a normal
- distribution for library sizes instead of a log-normal.</p></dd>
- </dl></p></dd>
+ distribution for library sizes instead of a log-normal.</p></dd></dl></p></dd>
<dt><em>Expression outlier parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>out.prob</code></dt><dd><p>Probability that a gene is an expression
outlier.</p></dd>
<dt><code>out.facLoc</code></dt><dd><p>Location (meanlog) parameter for the
expression outlier factor log-normal distribution.</p></dd>
<dt><code>out.facScale</code></dt><dd><p>Scale (sdlog) parameter for the
- expression outlier factor log-normal distribution.</p></dd>
- </dl></p></dd>
+ expression outlier factor log-normal distribution.</p></dd></dl></p></dd>
<dt><em>Group parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>[nGroups]</code></dt><dd><p>The number of groups or paths to
simulate.</p></dd>
<dt><code>[group.prob]</code></dt><dd><p>Probability that a cell comes from a
- group.</p></dd>
- </dl></p></dd>
+ group.</p></dd></dl></p></dd>
<dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>[de.prob]</code></dt><dd><p>Probability that a gene is differentially
expressed in a group. Can be a vector.</p></dd>
- <dt><code>[de.loProb]</code></dt><dd><p>Probability that a differentially
+ <dt><code>[de.downProb]</code></dt><dd><p>Probability that a differentially
expressed gene is down-regulated. Can be a vector.</p></dd>
<dt><code>[de.facLoc]</code></dt><dd><p>Location (meanlog) parameter for the
differential expression factor log-normal distribution. Can be a
vector.</p></dd>
<dt><code>[de.facScale]</code></dt><dd><p>Scale (sdlog) parameter for the
differential expression factor log-normal distribution. Can be a
- vector.</p></dd>
- </dl></p></dd>
+ vector.</p></dd></dl></p></dd>
<dt><em>Biological Coefficient of Variation parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>bcv.common</code></dt><dd><p>Underlying common dispersion across all
genes.</p></dd>
<dt><code>bcv.df</code></dt><dd><p>Degrees of Freedom for the BCV inverse
- chi-squared distribution.</p></dd>
- </dl></p></dd>
+ chi-squared distribution.</p></dd></dl></p></dd>
<dt><em>Dropout parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>dropout.type</code></dt><dd><p>The type of dropout to simulate.
"none" indicates no dropout, "experiment" is global dropout using
@@ -202,8 +216,7 @@
<dt><code>dropout.mid</code></dt><dd><p>Midpoint parameter for the dropout
logistic function.</p></dd>
<dt><code>dropout.shape</code></dt><dd><p>Shape parameter for the dropout
- logistic function.</p></dd>
- </dl></p></dd>
+ logistic function.</p></dd></dl></p></dd>
<dt><em>Differentiation path parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>[path.from]</code></dt><dd><p>Vector giving the originating point of
each path. This allows path structure such as a cell type which
@@ -212,9 +225,10 @@
this form would have a "from" parameter of c(0, 1, 1) (where 0 is
the origin). If no vector is given all paths will start at the
origin.</p></dd>
- <dt><code>[path.length]</code></dt><dd><p>Vector giving the number of steps to
+ <dt><code>[path.nSteps]</code></dt><dd><p>Vector giving the number of steps to
simulate along each path. If a single value is given it will be
- applied to all paths.</p></dd>
+ applied to all paths. This parameter was previously called
+ <code>path.length</code>.</p></dd>
<dt><code>[path.skew]</code></dt><dd><p>Vector giving the skew of each path.
Values closer to 1 will give more cells towards the starting
population, values closer to 0 will give more cells towards the
@@ -227,32 +241,32 @@
in the middle.</p></dd>
<dt><code>[path.sigmaFac]</code></dt><dd><p>Sigma factor for non-linear gene
paths. A higher value will result in more extreme non-linear
- variations along a path.</p></dd>
- </dl></p></dd>
+ variations along a path.</p></dd></dl></p></dd>
+
</dl>
- <p>The parameters not shown in brackets can be estimated from real data using
-<code><a href='splatEstimate.html'>splatEstimate</a></code>. For details of the Splatter simulation
+
+<p>The parameters not shown in brackets can be estimated from real data using
+<code><a href='splatEstimate.html'>splatEstimate</a></code>. For details of the Splat simulation
see <code><a href='splatSimulate.html'>splatSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -260,6 +274,8 @@ see <code><a href='splatSimulate.html'>splatSimulate</a></code>.</p>
+
</body>
</html>
+
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
index 9783ea87d183a03d0fa81e523017e87c3d9b1e19..a8ab04f4ee9274421020465e917bf640f8e63193 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>The ZINBParams class — ZINBParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="The ZINBParams class — ZINBParams" />
+<meta property="og:title" content="The ZINBParams class — ZINBParams" />
<meta property="og:description" content="S4 class that holds parameters for the ZINB-WaVE simulation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,49 +141,51 @@
</div>
<div class="ref-description">
-
<p>S4 class that holds parameters for the ZINB-WaVE simulation.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="parameters"><a class="anchor" href="#parameters"></a>Parameters</h2>
- <p>The ZINB-WaVE simulation uses the following parameters:</p>
+
+
+<p>The ZINB-WaVE simulation uses the following parameters:</p>
<dl class='dl-horizontal'>
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate.</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
<dt><code>model</code></dt><dd><p>Object describing a ZINB model.</p></dd>
+
</dl>
- <p>The majority of the parameters for this simulation are stored in a
-<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/ZinbModel-class'>ZinbModel</a></code> object. Please refer to the documentation
-for this class and its constructor(<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbModel'>zinbModel</a></code>) for
+
+<p>The majority of the parameters for this simulation are stored in a
+<code><a href='https://rdrr.io/pkg/zinbwave/man/ZinbModel-class.html'>ZinbModel</a></code> object. Please refer to the documentation
+for this class and its constructor(<code><a href='https://rdrr.io/pkg/zinbwave/man/zinbModel.html'>zinbModel</a></code>) for
details about all the parameters.</p>
<p>The parameters not shown in brackets can be estimated from real data using
<code><a href='zinbEstimate.html'>zinbEstimate</a></code>. For details of the ZINB-WaVE simulation
see <code><a href='zinbSimulate.html'>zinbSimulate</a></code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#parameters">Parameters</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -171,6 +193,8 @@ see <code><a href='zinbSimulate.html'>zinbSimulate</a></code>.</p>
+
</body>
</html>
+
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index d60618c426830800a40af5beeee3375fc350e462..95c9dfa0edd828130686d6ed2442e2f6722167ca 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Add feature statistics — addFeatureStats • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Add feature statistics — addFeatureStats" />
+<meta property="og:title" content="Add feature statistics — addFeatureStats" />
<meta property="og:description" content="Add additional feature statistics to a SingleCellExperiment object" />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,14 +141,12 @@
</div>
<div class="ref-description">
-
<p>Add additional feature statistics to a SingleCellExperiment object</p>
-
</div>
- <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>),
+ <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>),
<span class='kw'>log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>offset</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>no.zeros</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -156,11 +174,10 @@ given SingleCellExperiment.</p></td>
calculating statistics.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with additional feature statistics</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Currently adds the following statistics: mean, variance, coefficient of
@@ -169,29 +186,27 @@ the <code>rowData</code> slot and are named <code>Stat[Log]Value[No0]</code> whe
<code>Log</code> and <code>No0</code> are added if those arguments are true.
UpperCamelCase is used to differentiate these columns from those added by
analysis packages.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -199,6 +214,8 @@ analysis packages.</p>
+
</body>
</html>
+
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 8e234151c5347cabc79e4a5bb966c1fae7006836..149092850384742bebcd9bd16fe2dc34b5436d0b 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Add gene lengths — addGeneLengths • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Add gene lengths — addGeneLengths" />
+<meta property="og:title" content="Add gene lengths — addGeneLengths" />
<meta property="og:description" content="Add gene lengths to an SingleCellExperiment object" />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,14 +141,12 @@
</div>
<div class="ref-description">
-
<p>Add gene lengths to an SingleCellExperiment object</p>
-
</div>
- <pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"generate"</span>, <span class='st'>"sample"</span>), <span class='kw'>loc</span> <span class='kw'>=</span> <span class='fl'>7.9</span>,
+ <pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"generate"</span>, <span class='st'>"sample"</span>), <span class='kw'>loc</span> <span class='kw'>=</span> <span class='fl'>7.9</span>,
<span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>lengths</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -153,68 +171,64 @@
<td><p>Vector of lengths for the sample method.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with added gene lengths</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function adds simulated gene lengths to the
<code>rowData</code> slot of a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that can be
+<code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object that can be
used for calculating length normalised expression values such as TPM or FPKM.
The <code>generate</code> method simulates lengths using a (rounded) log-normal
distribution, with the default <code>loc</code> and <code>scale</code> parameters based
on human protein-coding genes. Alternatively the <code>sample</code> method can be
used which randomly samples lengths (with replacement) from a supplied
vector.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Default generate method</span>
<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
-<span class='fu'>head</span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> DataFrame with 6 rows and 3 columns
-#> Gene GeneMean Length
-#> <factor> <numeric> <numeric>
-#> 1 Gene1 0.197443857880758 1235
-#> 2 Gene2 5.46465220002874 2081
-#> 3 Gene3 0.707714763953083 2387
-#> 4 Gene4 0.15575800464631 995
-#> 5 Gene5 0.0181238728394951 2635
-#> 6 Gene6 1.30100599611438 2357</div><div class='input'># Sample method (human coding genes)
-</div><span class='co'># NOT RUN {</span>
-<span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
-<span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
+<span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> DataFrame with 6 rows and 3 columns
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> Gene1 Gene1 0.0792265397126071 1105
+#> Gene2 Gene2 0.0306368911550198 2027
+#> Gene3 Gene3 1.75797983978846 5541
+#> Gene4 Gene4 0.000969198708564301 2476
+#> Gene5 Gene5 0.0554598556966454 2845
+#> Gene6 Gene6 2.21278105339233 3607</div><div class='input'><span class='co'># Sample method (human coding genes)</span>
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>GenomicFeatures</span>)
<span class='no'>txdb</span> <span class='kw'><-</span> <span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>
<span class='no'>tx.lens</span> <span class='kw'><-</span> <span class='fu'>transcriptLengths</span>(<span class='no'>txdb</span>, <span class='kw'>with.cds_len</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>tx.lens</span> <span class='kw'><-</span> <span class='no'>tx.lens</span>[<span class='no'>tx.lens</span>$<span class='no'>cds_len</span> <span class='kw'>></span> <span class='fl'>0</span>, ]
-<span class='no'>gene.lens</span> <span class='kw'><-</span> <span class='fu'>max</span>(<span class='fu'>splitAsList</span>(<span class='no'>tx.lens</span>$<span class='no'>tx_len</span>, <span class='no'>tx.lens</span>$<span class='no'>gene_id</span>))
+<span class='no'>gene.lens</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fu'>splitAsList</span>(<span class='no'>tx.lens</span>$<span class='no'>tx_len</span>, <span class='no'>tx.lens</span>$<span class='no'>gene_id</span>))
<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"sample"</span>, <span class='kw'>lengths</span> <span class='kw'>=</span> <span class='no'>gene.lens</span>)
-<span class='co'># }</span></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -222,6 +236,8 @@ vector.</p>
+
</body>
</html>
+
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
index 4c3f93eb85573c80f6fa980b4d0316f0f4ad84b5..87493098c21f4a8b410957735d8eeeede3aee5ac 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Brownian bridge — bridge • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Brownian bridge — bridge" />
+<meta property="og:title" content="Brownian bridge — bridge" />
<meta property="og:description" content="Calculate a smoothed Brownian bridge between two points. A Brownian bridge is
a random walk with fixed end points." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ a random walk with fixed end points." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ a random walk with fixed end points." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ a random walk with fixed end points." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ a random walk with fixed end points." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ a random walk with fixed end points." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ a random walk with fixed end points." />
</div>
<div class="ref-description">
-
<p>Calculate a smoothed Brownian bridge between two points. A Brownian bridge is
a random walk with fixed end points.</p>
-
</div>
<pre class="usage"><span class='fu'>bridge</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>sigma.fac</span> <span class='kw'>=</span> <span class='fl'>0.8</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -154,31 +172,30 @@ a random walk with fixed end points.</p>
<td><p>multiplier specifying how extreme each step can be.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Vector of length n following a path from x to y.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -186,6 +203,8 @@ a random walk with fixed end points.</p>
+
</body>
</html>
+
diff --git a/docs/reference/bringItemsForward.html b/docs/reference/bringItemsForward.html
new file mode 100644
index 0000000000000000000000000000000000000000..9c264777850c4b8beeac1c35ae02c590810ca087
--- /dev/null
+++ b/docs/reference/bringItemsForward.html
@@ -0,0 +1,197 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Bring items forward — bringItemsForward • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Bring items forward — bringItemsForward" />
+<meta property="og:description" content="Move selected items to the start of a list." />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Bring items forward</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/utils.R'><code>R/utils.R</code></a></small>
+ <div class="hidden name"><code>bringItemsForward.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Move selected items to the start of a list.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>bringItemsForward</span>(<span class='no'>ll</span>, <span class='no'>items</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>ll</th>
+ <td><p>list to adjust item order.</p></td>
+ </tr>
+ <tr>
+ <th>items</th>
+ <td><p>vector of items to bring to the front. Any not in the list will
+be ignored.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>list with selected items first</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
index 663faca6b09e5a0dd9137d91902566b92386fce1..69284b6990c96eefa88f6f341b0bf5c196dd3381 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Compare SingleCellExperiment objects — compareSCEs • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Compare SingleCellExperiment objects — compareSCEs" />
+<meta property="og:title" content="Compare SingleCellExperiment objects — compareSCEs" />
<meta property="og:description" content="Combine the data from several SingleCellExperiment objects and produce some
basic plots comparing them." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ basic plots comparing them." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ basic plots comparing them." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ basic plots comparing them." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ basic plots comparing them." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ basic plots comparing them." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,15 +142,13 @@ basic plots comparing them." />
</div>
<div class="ref-description">
-
<p>Combine the data from several SingleCellExperiment objects and produce some
basic plots comparing them.</p>
-
</div>
<pre class="usage"><span class='fu'>compareSCEs</span>(<span class='no'>sces</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -156,18 +174,17 @@ compare.</p></td>
<td><p>vector of colours to use for each dataset.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>List containing the combined datasets and plots.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The returned list has three items:</p>
<dl class='dl-horizontal'>
- <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+ <dt><code>RowData</code></dt><dd><p>Combined row data from the provided
SingleCellExperiments.</p></dd>
- <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
+ <dt><code>ColData</code></dt><dd><p>Combined column data from the provided
SingleCellExperiments.</p></dd>
<dt><code>Plots</code></dt><dd><p>Comparison plots
<dl class='dl-horizontal'>
@@ -175,7 +192,7 @@ compare.</p></td>
<dt><code>Variances</code></dt><dd><p>Boxplot of variance distribution.</p></dd>
<dt><code>MeanVar</code></dt><dd><p>Scatter plot with fitted lines showing the
mean-variance relationship.</p></dd>
- <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+ <dt><code>LibrarySizes</code></dt><dd><p>Boxplot of the library size
distribution.</p></dd>
<dt><code>ZerosGene</code></dt><dd><p>Boxplot of the percentage of each gene
that is zero.</p></dd>
@@ -183,43 +200,42 @@ compare.</p></td>
that is zero.</p></dd>
<dt><code>MeanZeros</code></dt><dd><p>Scatter plot with fitted lines showing
the mean-zeros relationship.</p></dd>
- </dl></p></dd>
+ <dt><code>VarGeneCor</code></dt><dd><p>Heatmap of correlation of the 100 most
+ variable genes.</p></dd></dl></p></dd>
+
</dl>
- <p>The plots returned by this function are created using
-<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
+
+<p>The plots returned by this function are created using
+<code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
-
+using <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "FeatureData" "PhenoData" "Plots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
-#> [6] "ZerosCell" "MeanZeros" </div></pre>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "RowData" "ColData" "Plots" </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+#> [6] "ZerosCell" "MeanZeros" "VarGeneCor" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -227,6 +243,8 @@ using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></co
+
</body>
</html>
+
diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
index 30744dc31501007f995b9ff7e1e51735426a61ae..e7bf37cf527a0c77a2fac8b6e09169c7c830a678 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Diff SingleCellExperiment objects — diffSCEs • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Diff SingleCellExperiment objects — diffSCEs" />
+<meta property="og:title" content="Diff SingleCellExperiment objects — diffSCEs" />
<meta property="og:description" content="Combine the data from several SingleCellExperiment objects and produce some
basic plots comparing them to a reference." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ basic plots comparing them to a reference." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ basic plots comparing them to a reference." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ basic plots comparing them to a reference." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ basic plots comparing them to a reference." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ basic plots comparing them to a reference." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,15 +142,13 @@ basic plots comparing them to a reference." />
</div>
<div class="ref-description">
-
<p>Combine the data from several SingleCellExperiment objects and produce some
basic plots comparing them to a reference.</p>
-
</div>
<pre class="usage"><span class='fu'>diffSCEs</span>(<span class='no'>sces</span>, <span class='no'>ref</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -161,11 +179,10 @@ reference</p></td>
<td><p>vector of colours to use for each dataset.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>List containing the combined datasets and plots.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function aims to look at the differences between a reference
@@ -177,9 +194,9 @@ Q-Q plots are also returned.</p>
<p>The returned list has five items:</p>
<dl class='dl-horizontal'>
<dt><code>Reference</code></dt><dd><p>The SingleCellExperiment used as the reference.</p></dd>
- <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+ <dt><code>RowData</code></dt><dd><p>Combined feature data from the provided
SingleCellExperiments.</p></dd>
- <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
+ <dt><code>ColData</code></dt><dd><p>Combined column data from the provided
SingleCellExperiments.</p></dd>
<dt><code>Plots</code></dt><dd><p>Difference plots
<dl class='dl-horizontal'>
@@ -187,15 +204,14 @@ Q-Q plots are also returned.</p>
<dt><code>Variances</code></dt><dd><p>Boxplot of variance differences.</p></dd>
<dt><code>MeanVar</code></dt><dd><p>Scatter plot showing the difference from
the reference variance across expression ranks.</p></dd>
- <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+ <dt><code>LibraeySizes</code></dt><dd><p>Boxplot of the library size
differences.</p></dd>
<dt><code>ZerosGene</code></dt><dd><p>Boxplot of the differences in the
percentage of each gene that is zero.</p></dd>
<dt><code>ZerosCell</code></dt><dd><p>Boxplot of the differences in the
percentage of each cell that is zero.</p></dd>
<dt><code>MeanZeros</code></dt><dd><p>Scatter plot showing the difference from
- the reference percentage of zeros across expression ranks.</p></dd>
- </dl></p></dd>
+ the reference percentage of zeros across expression ranks.</p></dd></dl></p></dd>
<dt><code>QQPlots</code></dt><dd><p>Quantile-Quantile plots
<dl class='dl-horizontal'>
<dt><code>Means</code></dt><dd><p>Q-Q plot of the means.</p></dd>
@@ -204,44 +220,41 @@ Q-Q plots are also returned.</p>
<dt><code>ZerosGene</code></dt><dd><p>Q-Q plot of the percentage of zeros per
gene.</p></dd>
<dt><code>ZerosCell</code></dt><dd><p>Q-Q plot of the percentage of zeros per
- cell.</p></dd>
- </dl></p></dd>
+ cell.</p></dd></dl></p></dd>
+
</dl>
- <p>The plots returned by this function are created using
-<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
+
+<p>The plots returned by this function are created using
+<code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
-
+using <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "FeatureData" "PhenoData" "Plots" "QQPlots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "RowData" "ColData" "Plots" "QQPlots" </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -249,6 +262,8 @@ using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></co
+
</body>
</html>
+
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index 960dcab37dd7426ec29f1ad517edfdef1e80d9f6..d785e1238255e651da0494ce3cbb380ffbee708d 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Expand parameters — expandParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Expand parameters — expandParams" />
+<meta property="og:title" content="Expand parameters — expandParams" />
<meta property="og:description" content="Expand the parameters that can be vectors so that they are the same length as
the number of groups." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ the number of groups." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ the number of groups." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ the number of groups." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ the number of groups." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ the number of groups." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,10 +142,8 @@ the number of groups." />
</div>
<div class="ref-description">
-
<p>Expand the parameters that can be vectors so that they are the same length as
the number of groups.</p>
-
</div>
<pre class="usage"><span class='fu'>expandParams</span>(<span class='no'>object</span>, <span class='no'>...</span>)
@@ -138,7 +156,7 @@ the number of groups.</p>
<span class='co'># S4 method for SplatParams</span>
<span class='fu'>expandParams</span>(<span class='no'>object</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -151,31 +169,30 @@ the number of groups.</p>
<td><p>additional arguments.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Expanded object.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -183,6 +200,8 @@ the number of groups.</p>
+
</body>
</html>
+
diff --git a/docs/reference/getBetaStepProbs.html b/docs/reference/getBetaStepProbs.html
new file mode 100644
index 0000000000000000000000000000000000000000..6340f5b36b673300b61c06c3cb996a54c9c56c9c
--- /dev/null
+++ b/docs/reference/getBetaStepProbs.html
@@ -0,0 +1,206 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get Beta step probabilities — getBetaStepProbs • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Get Beta step probabilities — getBetaStepProbs" />
+<meta property="og:description" content="Use a Beta distribution for set probabilities along a path" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Get Beta step probabilities</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>getBetaStepProbs.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Use a Beta distribution for set probabilities along a path</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>getBetaStepProbs</span>(<span class='no'>steps</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>steps</th>
+ <td><p>Number of steps</p></td>
+ </tr>
+ <tr>
+ <th>alpha</th>
+ <td><p>Alpha parameter</p></td>
+ </tr>
+ <tr>
+ <th>beta</th>
+ <td><p>Beta parameter</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Vector of probabilities</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The density is sampled from a Beta distribution between 0 and 1. Infinite
+densities at edges are adjusted and then the values are scaled to give
+probabilities.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
index 0eae1399a1620b3bf8dc864e242701b0efa77161..7169316eb8fc7ee5105a3234afc0cd2021cd13d6 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Get log-normal factors — getLNormFactors • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Get log-normal factors — getLNormFactors" />
+<meta property="og:title" content="Get log-normal factors — getLNormFactors" />
<meta property="og:description" content="Randomly generate multiplication factors from a log-normal distribution." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Randomly generate multiplication factors from a log-normal distribution.</p>
-
</div>
<pre class="usage"><span class='fu'>getLNormFactors</span>(<span class='no'>n.facs</span>, <span class='no'>sel.prob</span>, <span class='no'>neg.prob</span>, <span class='no'>fac.loc</span>, <span class='no'>fac.scale</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -153,31 +171,30 @@ from 1.</p></td>
<td><p>Scale factor for the log-normal distribution.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Vector containing generated factors.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -185,6 +202,8 @@ from 1.</p></td>
+
</body>
</html>
+
diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
index c2c7a3877a4c677283f4b9a1dcfb5ebd9973db57..5edeb06de31cc5e7ca2a4e62ff76ce16f957ace3 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Get a parameter — getParam • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Get a parameter — getParam" />
+<meta property="og:title" content="Get a parameter — getParam" />
<meta property="og:description" content="Accessor function for getting parameter values." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,14 @@
</div>
<div class="ref-description">
-
<p>Accessor function for getting parameter values.</p>
-
</div>
<pre class="usage"><span class='fu'>getParam</span>(<span class='no'>object</span>, <span class='no'>name</span>)
<span class='co'># S4 method for Params</span>
<span class='fu'>getParam</span>(<span class='no'>object</span>, <span class='no'>name</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -143,11 +161,10 @@
<td><p>name of the parameter to get.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The extracted parameter value</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
@@ -158,22 +175,21 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -181,6 +197,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
index 8c2f7bc0769398cf372ecb1fb7b076693eed859a..8f35f1ef8f644bf20f9cfc6682a8c62d7b357512 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Get parameters — getParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Get parameters — getParams" />
+<meta property="og:title" content="Get parameters — getParams" />
<meta property="og:description" content="Get multiple parameter values from a Params object." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Get multiple parameter values from a Params object.</p>
-
</div>
<pre class="usage"><span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='no'>names</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -140,15 +158,14 @@
<td><p>vector of names of the parameters to get.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>List with the values of the selected parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
-<span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='fu'>c</span>(<span class='st'>"nGenes"</span>, <span class='st'>"nCells"</span>, <span class='st'>"mean.rate"</span>))</div><div class='output co'>#> $nGenes
+<span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"nGenes"</span>, <span class='st'>"nCells"</span>, <span class='st'>"mean.rate"</span>))</div><div class='output co'>#> $nGenes
#> [1] 10000
#>
#> $nCells
@@ -162,22 +179,21 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -185,6 +201,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
index 3b14391f0f30718d863e20e8a01e2d50bc76d74e..cf81c50dbb5e67a3aa642b7f9953d885c45b6259 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Get path order — getPathOrder • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Get path order — getPathOrder" />
+<meta property="og:title" content="Get path order — getPathOrder" />
<meta property="og:description" content="Identify the correct order to process paths so that preceding paths have
already been simulated." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ already been simulated." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ already been simulated." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ already been simulated." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ already been simulated." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ already been simulated." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,48 +142,45 @@ already been simulated." />
</div>
<div class="ref-description">
-
<p>Identify the correct order to process paths so that preceding paths have
already been simulated.</p>
-
</div>
<pre class="usage"><span class='fu'>getPathOrder</span>(<span class='no'>path.from</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>path.from</th>
- <td><p>vector giving the path endpoints that each path orginates
+ <td><p>vector giving the path endpoints that each path originates
from.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Vector giving the order to process paths in.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -171,6 +188,8 @@ from.</p></td>
+
</body>
</html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 494a3e562a804eff203df6fa980117ff0273678a..f40865b21772d16a71597b7b7b51378704376d18 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Function reference • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,12 +36,15 @@
<link href="../extra.css" rel="stylesheet">
+
<meta property="og:title" content="Function reference" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -55,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -63,14 +71,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -78,7 +87,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -88,15 +97,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -107,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -133,7 +154,7 @@
<tr>
<td>
- <p><code><a href="newParams.html">newBASiCSParams()</a></code> <code><a href="newParams.html">newLun2Params()</a></code> <code><a href="newParams.html">newLunParams()</a></code> <code><a href="newParams.html">newMFAParams()</a></code> <code><a href="newParams.html">newPhenoParams()</a></code> <code><a href="newParams.html">newSCDDParams()</a></code> <code><a href="newParams.html">newSimpleParams()</a></code> <code><a href="newParams.html">newSparseDCParams()</a></code> <code><a href="newParams.html">newSplatParams()</a></code> <code><a href="newParams.html">newZINBParams()</a></code> </p>
+ <p><code><a href="newParams.html">newBASiCSParams()</a></code> <code><a href="newParams.html">newKersplatParams()</a></code> <code><a href="newParams.html">newLun2Params()</a></code> <code><a href="newParams.html">newLunParams()</a></code> <code><a href="newParams.html">newMFAParams()</a></code> <code><a href="newParams.html">newPhenoParams()</a></code> <code><a href="newParams.html">newSCDDParams()</a></code> <code><a href="newParams.html">newSimpleParams()</a></code> <code><a href="newParams.html">newSparseDCParams()</a></code> <code><a href="newParams.html">newSplatParams()</a></code> <code><a href="newParams.html">newZINBParams()</a></code> </p>
</td>
<td><p>New Params</p></td>
</tr><tr>
@@ -168,6 +189,12 @@
<td><p>The BASiCSParams class</p></td>
</tr><tr>
+ <td>
+ <p><code><a href="KersplatParams.html">KersplatParams</a></code> </p>
+ </td>
+ <td><p>The KersplatParams class</p></td>
+ </tr><tr>
+
<td>
<p><code><a href="Lun2Params.html">Lun2Params</a></code> </p>
</td>
@@ -242,6 +269,12 @@
<td><p>Estimate BASiCS simulation parameters</p></td>
</tr><tr>
+ <td>
+ <p><code><a href="kersplatEstimate.html">kersplatEstimate()</a></code> </p>
+ </td>
+ <td><p>Estimate Kersplat simulation parameters</p></td>
+ </tr><tr>
+
<td>
<p><code><a href="lun2Estimate.html">lun2Estimate()</a></code> </p>
</td>
@@ -340,6 +373,12 @@
<td><p>BASiCS simulation</p></td>
</tr><tr>
+ <td>
+ <p><code><a href="kersplatSimulate.html">kersplatSimulate()</a></code> </p>
+ </td>
+ <td><p>Kersplat simulation</p></td>
+ </tr><tr>
+
<td>
<p><code><a href="lun2Simulate.html">lun2Simulate()</a></code> </p>
</td>
@@ -489,7 +528,7 @@
<td>
<p><code><a href="summariseDiff.html">summariseDiff()</a></code> </p>
</td>
- <td><p>Summarise diffSCESs</p></td>
+ <td><p>Summarise diffSCEs</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -589,7 +628,7 @@
<td>
<p><code><a href="showValues.html">showValues()</a></code> </p>
</td>
- <td><p>Show vales</p></td>
+ <td><p>Show values</p></td>
</tr><tr>
<td>
@@ -614,13 +653,14 @@
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -628,6 +668,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/kersplatEstBCV.html b/docs/reference/kersplatEstBCV.html
new file mode 100644
index 0000000000000000000000000000000000000000..1c5e791ebe57b18bd5bae61b1e7c91cd18f6f052
--- /dev/null
+++ b/docs/reference/kersplatEstBCV.html
@@ -0,0 +1,210 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Kersplat BCV parameters — kersplatEstBCV • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Estimate Kersplat BCV parameters — kersplatEstBCV" />
+<meta property="og:description" content="Estimate Biological Coefficient of Variation (BCV) parameters for the
+Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Kersplat BCV parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-estimate.R'><code>R/kersplat-estimate.R</code></a></small>
+ <div class="hidden name"><code>kersplatEstBCV.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Estimate Biological Coefficient of Variation (BCV) parameters for the
+Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatEstBCV</span>(<span class='no'>counts</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>counts matrix.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with estimated BCV parameters</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The <code><a href='https://rdrr.io/pkg/edgeR/man/estimateDisp.html'>estimateDisp</a></code> function is used to estimate the common
+dispersion across the dataset. An exponential correction is applied based on
+fitting an exponential relationship between simulated and estimated values.
+If this results in a negative dispersion a simpler linear correction is
+applied instead.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatEstLib.html b/docs/reference/kersplatEstLib.html
new file mode 100644
index 0000000000000000000000000000000000000000..2bb0d4b0827e930e2a12a830ecfd9141de9360ec
--- /dev/null
+++ b/docs/reference/kersplatEstLib.html
@@ -0,0 +1,208 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Kersplat library size parameters — kersplatEstLib • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Estimate Kersplat library size parameters — kersplatEstLib" />
+<meta property="og:description" content="Estimate the library size parameters for the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Kersplat library size parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-estimate.R'><code>R/kersplat-estimate.R</code></a></small>
+ <div class="hidden name"><code>kersplatEstLib.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Estimate the library size parameters for the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatEstLib</span>(<span class='no'>counts</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>counts matrix.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with library size parameters</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Parameters for the log-normal distribution are estimated by fitting the
+library sizes using <code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code>. All the fitting
+methods are tried and the fit with the best Cramer-von Mises statistic is
+selected. The density of the library sizes is also estimated using
+<code><a href='https://rdrr.io/r/stats/density.html'>density</a></code>.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatEstMean.html b/docs/reference/kersplatEstMean.html
new file mode 100644
index 0000000000000000000000000000000000000000..dc6b93b1f202b92967f35b3291e1516be6fb56ef
--- /dev/null
+++ b/docs/reference/kersplatEstMean.html
@@ -0,0 +1,216 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Kersplat means — kersplatEstMean • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Estimate Kersplat means — kersplatEstMean" />
+<meta property="og:description" content="Estimate mean parameters for the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Kersplat means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-estimate.R'><code>R/kersplat-estimate.R</code></a></small>
+ <div class="hidden name"><code>kersplatEstMean.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Estimate mean parameters for the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatEstMean</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>norm.counts</th>
+ <td><p>library size normalised counts matrix.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with estimated means</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Parameters for the gamma distribution are estimated by fitting the mean
+normalised counts using <code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code>. All the fitting
+methods are tried and the fit with the best Cramer-von Mises statistic is
+selected. The density of the means is also estimated using
+<code><a href='https://rdrr.io/r/stats/density.html'>density</a></code>.</p>
+<p>Expression outlier genes are detected using the Median Absolute Deviation
+(MAD) from median method. If the log2 mean expression of a gene is greater
+than two MADs above the median log2 mean expression it is designated as an
+outlier. The proportion of outlier genes is used to estimate the outlier
+probability. Factors for each outlier gene are calculated by dividing mean
+expression by the median mean expression. A log-normal distribution is then
+fitted to these factors in order to estimate the outlier factor location and
+scale parameters using the <code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code> MLE method.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatEstimate.html b/docs/reference/kersplatEstimate.html
new file mode 100644
index 0000000000000000000000000000000000000000..6a29eef47861c47109ec911e0bd4e7e3f5e8baef
--- /dev/null
+++ b/docs/reference/kersplatEstimate.html
@@ -0,0 +1,283 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Estimate Kersplat simulation parameters — kersplatEstimate • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Estimate Kersplat simulation parameters — kersplatEstimate" />
+<meta property="og:description" content="Estimate simulation parameters for the Kersplat simulation from a real
+dataset. See the individual estimation functions for more details on how this
+is done." />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Estimate Kersplat simulation parameters</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-estimate.R'><code>R/kersplat-estimate.R</code></a></small>
+ <div class="hidden name"><code>kersplatEstimate.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Estimate simulation parameters for the Kersplat simulation from a real
+dataset. See the individual estimation functions for more details on how this
+is done.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newKersplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>kersplatEstimate</span>(<span class='no'>counts</span>,
+ <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newKersplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
+<span class='co'># S3 method for matrix</span>
+<span class='fu'>kersplatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newKersplatParams</a></span>(),
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>counts</th>
+ <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object to store estimated values in.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object containing the estimated parameters.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='kersplatEstMean.html'>kersplatEstMean</a></code>, <code><a href='kersplatEstBCV.html'>kersplatEstBCV</a></code>,
+<code><a href='kersplatEstLib.html'>kersplatEstLib</a></code></p></div>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Load example data</span>
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)</div><div class='output co'>#> <span class='warning'>Warning: package ‘scater’ was built under R version 3.6.1</span></div><div class='output co'>#> <span class='message'>Loading required package: ggplot2</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
+
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>kersplatEstimate</span>(<span class='no'>sce</span>)</div><div class='output co'>#> <span class='message'>Registered S3 method overwritten by 'R.oo':</span>
+#> <span class='message'> method from </span>
+#> <span class='message'> throw.default R.methodsS3</span></div><div class='output co'>#> <span class='warning'>Warning: The Kersplat simulation is still experimental and may produce unreliable results. Please try it and report any issues to https://github.com/Oshlack/splatter/issues. The development version may have improved features.</span>
+#> <span class='warning'>This warning is displayed once per session.</span></div><div class='output co'>#> <span class='message'>Estimating mean parameters...</span></div><div class='output co'>#> <span class='message'>Selected MGE (CvM) fit</span></div><div class='output co'>#> <span class='message'>Estimating expression outlier parameters...</span></div><div class='output co'>#> <span class='message'>Estimating BCV parameters...</span></div><div class='output co'>#> <span class='message'>Raw: 2.60817370717138 A: 8.12109336156054 B: 1.31905414419672 C: -8.4603750374735 Y: 1.36293824634938</span></div><div class='output co'>#> <span class='message'>Estimating library size parameters...</span></div><div class='output co'>#> <span class='message'>Selected MGE (CvM) fit</span></div><div class='input'><span class='no'>params</span></div><div class='output co'>#> A Params object of class KersplatParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 200 955861
+#>
+#> 24 additional parameters
+#>
+#> Mean:
+#> (RATE) (SHAPE) (OUT PROB)
+#> 0.00272354467142995 0.475100032448728 0
+#> (Out Location) (Out Scale) (DENSITY)
+#> 4 0.5 Object of class density
+#> [Method] [Values]
+#> fit Not set
+#>
+#> BCV:
+#> (COMMON DISP) [DoF]
+#> 1.11818764383748 60
+#>
+#> Network:
+#> [Graph] [nRegs] [regsSet]
+#> Not set 100 FALSE
+#>
+#> Paths:
+#> [nPrograms] [Means]
+#> 10 Not set
+#>
+#> [Design]
+#> data.frame (1 x 3) with columns: Path, From, Steps
+#> Path From Steps
+#> 1 1 0 100
+#>
+#> Library size:
+#> (LOCATION) (SCALE) (DENSITY)
+#> 12.7854772402738 0.0327578186101294 Object of class density
+#> [Method]
+#> fit
+#>
+#> Cells:
+#>
+#> [Design]
+#> data.frame (1 x 4) with columns: Path, Probability, Alpha, Beta
+#> Path Probability Alpha Beta
+#> 1 1 1 1 0
+#>
+#> Doublets:
+#> [Prop]
+#> 0
+#>
+#> Ambient:
+#> [Scale] [Empty]
+#> 0.05 0
+#> </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#see-also">See also</a></li>
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatGenNetwork.html b/docs/reference/kersplatGenNetwork.html
new file mode 100644
index 0000000000000000000000000000000000000000..3a95bb92dfbb8f25c13aaf705f16d6f45147978c
--- /dev/null
+++ b/docs/reference/kersplatGenNetwork.html
@@ -0,0 +1,202 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Generate Kersplat gene network — kersplatGenNetwork • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Generate Kersplat gene network — kersplatGenNetwork" />
+<meta property="og:description" content="Generate a gene network for the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Generate Kersplat gene network</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatGenNetwork.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Generate a gene network for the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatGenNetwork</span>(<span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with gene network</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Currently a very simple approach is used which needs to be improved. A
+network is generated using the <code><a href='https://rdrr.io/pkg/igraph/man/sample_forestfire.html'>sample_forestfire</a></code>
+function and edge weights are sampled from a standard normal distribution.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSample.html b/docs/reference/kersplatSample.html
new file mode 100644
index 0000000000000000000000000000000000000000..19b8f8ac322e85efe0cae14635985d4bdda296fc
--- /dev/null
+++ b/docs/reference/kersplatSample.html
@@ -0,0 +1,261 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Kersplat sample — kersplatSample • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Kersplat sample — kersplatSample" />
+<meta property="og:description" content="Sample cells for the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Kersplat sample</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSample.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Sample cells for the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSample</span>(<span class='no'>params</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment object containing the simulated counts and
+intermediate values.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The second stage is a two-step Kersplat simulation is to generate cells based
+on a complete <code><a href='KersplatParams.html'>KersplatParams</a></code> object.
+intermediate parameters.</p>
+<p>The sampling process involves the following steps:</p><ol>
+<li><p>Simulate library sizes for each cell</p></li>
+<li><p>Simulate means for each cell</p></li>
+<li><p>Simulate endogenous counts for each cell</p></li>
+<li><p>Simulate ambient counts for each cell</p></li>
+<li><p>Simulate final counts for each cell</p></li>
+</ol>
+
+<p>The final output is a
+<code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object that
+contains the simulated counts but also the values for various intermediate
+steps. These are stored in the <code>colData</code> (for cell specific
+information), <code>rowData</code> (for gene specific information) or
+<code>assays</code> (for gene by cell matrices) slots. This additional
+information includes:</p><dl class='dl-horizontal'>
+ <dt><code>colData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>Cell</dt><dd><p>Unique cell identifier.</p></dd>
+ <dt>Type</dt><dd><p>Whether the cell is a Cell, Doublet or Empty.</p></dd>
+ <dt>CellLibSize</dt><dd><p>The expected number of endogenous counts for
+ that cell.</p></dd>
+ <dt>AmbientLibSize</dt><dd><p>The expected number of ambient counts for
+ that cell.</p></dd>
+ <dt>Path</dt><dd><p>The path the cell belongs to.</p></dd>
+ <dt>Step</dt><dd><p>How far along the path each cell is.</p></dd>
+ <dt>Path1</dt><dd><p>For doublets the path of the first partner in the
+ doublet (otherwise <code>NA</code>).</p></dd>
+ <dt>Step1</dt><dd><p>For doublets the step of the first partner in the
+ doublet (otherwise <code>NA</code>).</p></dd>
+ <dt>Path2</dt><dd><p>For doublets the path of the second partner in the
+ doublet (otherwise <code>NA</code>).</p></dd>
+ <dt>Step2</dt><dd><p>For doublets the step of the second partner in the
+ doublet (otherwise <code>NA</code>).</p></dd></dl></p></dd>
+ <dt><code>rowData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>Gene</dt><dd><p>Unique gene identifier.</p></dd>
+ <dt>BaseMean</dt><dd><p>The base expression level for that gene.</p></dd>
+ <dt>AmbientMean</dt><dd><p>The ambient expression level for that gene.</p></dd></dl></p></dd>
+ <dt><code>assays</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>CellMeans</dt><dd><p>The mean expression of genes in each cell
+ after any differential expression and adjusted for expected
+ library size.</p></dd>
+ <dt>CellCounts</dt><dd><p>Endogenous count matrix.</p></dd>
+ <dt>AmbientCounts</dt><dd><p>Ambient count matrix.</p></dd>
+ <dt>counts</dt><dd><p>Final count matrix.</p></dd></dl></p></dd>
+
+</dl>
+
+<p>Values that have been added by Splatter are named using <code>UpperCamelCase</code>
+in order to differentiate them from the values added by analysis packages
+which typically use <code>underscore_naming</code>.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='kersplatSimLibSizes.html'>kersplatSimLibSizes</a></code>, <code><a href='kersplatSimCellMeans.html'>kersplatSimCellMeans</a></code>,
+<code><a href='kersplatSimCellCounts.html'>kersplatSimCellCounts</a></code>, <code><a href='kersplatSimAmbientCounts.html'>kersplatSimAmbientCounts</a></code>,
+<code><a href='kersplatSimCounts.html'>kersplatSimCounts</a></code></p></div>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='kersplatSetup.html'>kersplatSetup</a></span>()</div><div class='output co'>#> <span class='message'>Setting up parameters...</span></div><div class='output co'>#> <span class='message'>Generating gene network...</span></div><div class='output co'>#> <span class='message'>Selecting regulators...</span></div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Sampling from gamma distribution...</span></div><div class='output co'>#> <span class='message'>Simulating paths...</span></div><div class='output co'>#> <span class='message'>Simulating path 1...</span></div><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>kersplatSample</span>(<span class='no'>params</span>)</div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Sampling from log-normal distribution...</span></div><div class='output co'>#> <span class='message'>Assigning cells to paths...</span></div><div class='output co'>#> <span class='message'>Assigning cells to steps...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Applying BCV adjustment...</span></div><div class='output co'>#> <span class='message'>Simulating cell counts...</span></div><div class='output co'>#> <span class='message'>Simulating ambient counts...</span></div><div class='output co'>#> <span class='message'>Simulating final counts...</span></div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ <li><a href="#see-also">See also</a></li>
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSelectRegs.html b/docs/reference/kersplatSelectRegs.html
new file mode 100644
index 0000000000000000000000000000000000000000..7696a43a4a3c2a15ed955903ced9dbb80b3ede98
--- /dev/null
+++ b/docs/reference/kersplatSelectRegs.html
@@ -0,0 +1,202 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Select Kersplat regulators — kersplatSelectRegs • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Select Kersplat regulators — kersplatSelectRegs" />
+<meta property="og:description" content="Select regulator genes in the gene network for a Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Select Kersplat regulators</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSelectRegs.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Select regulator genes in the gene network for a Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSelectRegs</span>(<span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with gene regulators</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Regulators are randomly selected, weighted according to the difference
+between their out degree and in degree. This is an arbitrary weighting and
+may be improved or replace in the future.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSetup.html b/docs/reference/kersplatSetup.html
new file mode 100644
index 0000000000000000000000000000000000000000..b0689f7e197c09232c8c031fd717727f957f701d
--- /dev/null
+++ b/docs/reference/kersplatSetup.html
@@ -0,0 +1,236 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Kersplat setup — kersplatSetup • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Kersplat setup — kersplatSetup" />
+<meta property="og:description" content="Setup the parameters required for the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Kersplat setup</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSetup.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Setup the parameters required for the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSetup</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newKersplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A complete KersplatParams object</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The first stage is a two-step Kersplat simulation is to generate some of the
+intermediate parameters. The resulting parameters allow multiple simulated
+datasets to be generated from the same biological structure (using
+<code><a href='kersplatSample.html'>kersplatSample</a></code>). As with all the other parameters these values
+can be manually overwritten if desired.</p>
+<p>The setup involves the following steps:</p><ol>
+<li><p>Generate a gene network (if not already present)</p></li>
+<li><p>Select regulator genes (if not already present)</p></li>
+<li><p>Simulate gene means (if not already present)</p></li>
+<li><p>Simulate cell paths</p></li>
+</ol>
+
+<p>The resulting <code><a href='KersplatParams.html'>KersplatParams</a></code> object will have the following
+parameters set (if they weren't already).</p>
+<ul>
+<li><p><code>mean.values</code></p></li>
+<li><p><code>network.graph</code></p></li>
+<li><p><code>network.regsSet</code></p></li>
+<li><p><code>paths.means</code></p></li>
+</ul>
+
+<p>See <code><a href='KersplatParams.html'>KersplatParams</a></code> for more details about these parameters and
+the functions for the individual steps for more details about the process.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='kersplatGenNetwork.html'>kersplatGenNetwork</a></code>, <code><a href='kersplatSelectRegs.html'>kersplatSelectRegs</a></code>,
+<code><a href='kersplatSimGeneMeans.html'>kersplatSimGeneMeans</a></code>, <code><a href='kersplatSimPaths.html'>kersplatSimPaths</a></code>,
+<code><a href='KersplatParams.html'>KersplatParams</a></code></p></div>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>kersplatSetup</span>()</div><div class='output co'>#> <span class='message'>Setting up parameters...</span></div><div class='output co'>#> <span class='message'>Generating gene network...</span></div><div class='output co'>#> <span class='message'>Selecting regulators...</span></div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Sampling from gamma distribution...</span></div><div class='output co'>#> <span class='message'>Simulating paths...</span></div><div class='output co'>#> <span class='message'>Simulating path 1...</span></div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ <li><a href="#see-also">See also</a></li>
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimAmbientCounts.html b/docs/reference/kersplatSimAmbientCounts.html
new file mode 100644
index 0000000000000000000000000000000000000000..df8928bbcd97a12735805afc3b7145f3ba41befc
--- /dev/null
+++ b/docs/reference/kersplatSimAmbientCounts.html
@@ -0,0 +1,207 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat ambient counts — kersplatSimAmbientCounts • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat ambient counts — kersplatSimAmbientCounts" />
+<meta property="og:description" content="Simulate Kersplat ambient counts" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat ambient counts</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimAmbientCounts.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate Kersplat ambient counts</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimAmbientCounts</span>(<span class='no'>sim</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SingleCellExperiment containing simulation.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object with simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment with ambient counts</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The overall expression profile to calculated by averaging the cell counts
+of the (non-empty) cells. This is then multiplied by the ambient library
+sizes to get a mean for each cell. Counts are then sampled from a Poisson
+distribution using these means.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimCellCounts.html b/docs/reference/kersplatSimCellCounts.html
new file mode 100644
index 0000000000000000000000000000000000000000..4e08c86bf5ba082d14108784064db51b3cdd5cc2
--- /dev/null
+++ b/docs/reference/kersplatSimCellCounts.html
@@ -0,0 +1,205 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat cell counts — kersplatSimCellCounts • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat cell counts — kersplatSimCellCounts" />
+<meta property="og:description" content="Simulate cell counts for the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat cell counts</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimCellCounts.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate cell counts for the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimCellCounts</span>(<span class='no'>sim</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SingleCellExperiment containing simulation.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object with simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment with cell counts</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Counts are sampled from a Poisson distribution with lambda equal to the
+cell means matrix.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimCellMeans.html b/docs/reference/kersplatSimCellMeans.html
new file mode 100644
index 0000000000000000000000000000000000000000..8472592b783f3c50be13cbb3c1c4fd58e638e1e4
--- /dev/null
+++ b/docs/reference/kersplatSimCellMeans.html
@@ -0,0 +1,243 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat cell means — kersplatSimCellMeans • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat cell means — kersplatSimCellMeans" />
+<meta property="og:description" content="Simulate endogenous counts for each cell in a Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat cell means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimCellMeans.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate endogenous counts for each cell in a Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SingleCellExperiment containing simulation.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object with simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment with cell means</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Cells are first assigned to a path and a step along that path. This is
+controlled by the <code>cells.design</code> parameter which is a <code>data.frame</code>
+with the columns "Path", "Probability", "Alpha" and "Beta". The Path field
+is an ID for each path and the Probability field is the probability that a
+cell will come from that path (must sum to 1). The Alpha and Beta parameters
+control the density of cells along the path. After they are assigned to paths
+the step for each cell is sampled from a Beta distribution with parameters
+shape1 equals Alpha and shape2 equals beta. This approach is very flexible
+and allows almost any distribution of cells along a path. The distribution
+can be viewed using <code><a href='https://rdrr.io/r/graphics/hist.html'>hist(rbeta(10000, Alpha, Beta), breaks = 100)</a></code>.
+Some useful combinations of parameters are:</p>
+<dl class='dl-horizontal'>
+ <dt><code>Alpha = 1</code>, <code>Beta = 1</code></dt><dd><p>Uniform distribution along the
+ path</p></dd>
+ <dt><code>Alpha = 0</code>, <code>Beta = 1</code></dt><dd><p>All cells at the start of the
+ path.</p></dd>
+ <dt><code>Alpha = 1</code>, <code>Beta = 0</code></dt><dd><p>All cells at the end of the
+ path.</p></dd>
+ <dt><code>Alpha = 0</code>, <code>Beta = 0</code></dt><dd><p>Cells only at each end of the
+ path.</p></dd>
+ <dt><code>Alpha = 1</code>, <code>Beta = 2</code></dt><dd><p>Linear skew towards the start
+ of the path</p></dd>
+ <dt><code>Alpha = 0.5</code>, <code>Beta = 1</code></dt><dd><p>Curved skew towards the start
+ of the path</p></dd>
+ <dt><code>Alpha = 2</code>, <code>Beta = 1</code></dt><dd><p>Linear skew towards the end
+ of the path</p></dd>
+ <dt><code>Alpha = 1</code>, <code>Beta = 0.5</code></dt><dd><p>Curved skew towards the end
+ of the path</p></dd>
+ <dt><code>Alpha = 0.5</code>, <code>Beta = 0.5</code></dt><dd><p>Curved skew towards both
+ ends of the path</p></dd>
+ <dt><code>Alpha = 0.5</code>, <code>Beta = 0.5</code></dt><dd><p>Curved skew away from both
+ ends of the path</p></dd>
+
+</dl>
+
+<p>Once cells are assigned to paths and steps the correct means are extracted
+from the <code>paths.means</code> parameter and adjusted based on each cell's
+library size. An adjustment for BCV is then applied. Doublets are also
+simulated at this stage by selecting two path/step combinations and averaging
+the means.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimCounts.html b/docs/reference/kersplatSimCounts.html
new file mode 100644
index 0000000000000000000000000000000000000000..5c7ad9a679c9ca5b6c13629f2b377c2f94f4f042
--- /dev/null
+++ b/docs/reference/kersplatSimCounts.html
@@ -0,0 +1,211 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat final counts — kersplatSimCounts • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat final counts — kersplatSimCounts" />
+<meta property="og:description" content="Simulate the final counts matrix for a Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat final counts</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimCounts.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate the final counts matrix for a Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimCounts</span>(<span class='no'>sim</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SingleCellExperiment containing simulation.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object with simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment with counts matrix</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The cell counts matrix and ambient counts matrix are added together. The
+result is then downsampled to the cell library size (for cells and doublets)
+or the ambient library size (for empty cells) using the
+<code><a href='https://rdrr.io/pkg/DropletUtils/man/downsampleMatrix.html'>downsampleMatrix</a></code> function.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='https://rdrr.io/pkg/DropletUtils/man/downsampleMatrix.html'>downsampleMatrix</a></code></p></div>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ <li><a href="#see-also">See also</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimGeneMeans.html b/docs/reference/kersplatSimGeneMeans.html
new file mode 100644
index 0000000000000000000000000000000000000000..288f18c43cad1d43380c2e111ebb4c02b804e907
--- /dev/null
+++ b/docs/reference/kersplatSimGeneMeans.html
@@ -0,0 +1,210 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat gene means — kersplatSimGeneMeans • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat gene means — kersplatSimGeneMeans" />
+<meta property="og:description" content="Simulate Kersplat gene means" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat gene means</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimGeneMeans.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate Kersplat gene means</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimGeneMeans</span>(<span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with gene means</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Gene means are simulated in one of two ways depending on the value of the
+<code>mean.method</code> parameter.</p>
+<p>If <code>mean.method</code> is "fit" (default) then means are sampled from a Gamma
+distribution with shape equals <code>mean.shape</code> and rate equals
+<code>mean.rate</code>. Expression outliers are then added by replacing some
+values with the median multiplied by a factor from a log-normal distribution.
+This is the same process used for the Splat simulation.</p>
+<p>If <code>mean.method</code> is "density" then means are sampled from the
+density object in the <code>mean.density</code> parameter using a rejection
+sampling method. This approach is more flexible but may violate some
+statistical assumptions.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimLibSizes.html b/docs/reference/kersplatSimLibSizes.html
new file mode 100644
index 0000000000000000000000000000000000000000..2ccf3711d84ddeb98bf75f46e86dae09c2a0cd83
--- /dev/null
+++ b/docs/reference/kersplatSimLibSizes.html
@@ -0,0 +1,215 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat library sizes — kersplatSimLibSizes • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat library sizes — kersplatSimLibSizes" />
+<meta property="og:description" content="Generate library sizes for cells in the Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat library sizes</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimLibSizes.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Generate library sizes for cells in the Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimLibSizes</span>(<span class='no'>sim</span>, <span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>sim</th>
+ <td><p>SingleCellExperiment containing simulation.</p></td>
+ </tr>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object with simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment with library sizes</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Library sizes are simulated in one of two ways depending on the value of the
+<code>lib.method</code> parameter.</p>
+<p>If <code>lib.method</code> is "fit" (default) then means are sampled from a
+log-normal distribution with meanlog equals <code>lib.loc</code> and sdlog equals
+<code>lib.scale</code>.</p>
+<p>If <code>mean.method</code> is "density" then library sizes are sampled from the
+density object in the <code>lib.density</code> parameter using a rejection
+sampling method. This approach is more flexible but may violate some
+statistical assumptions.</p>
+<p>Ambient library sizes are also generated from a log-normal distribution based
+on the parameters for the cell library size and adjusted using the
+<code>ambient.scale</code> parameter.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimPaths.html b/docs/reference/kersplatSimPaths.html
new file mode 100644
index 0000000000000000000000000000000000000000..66103d52608a6342003d20e37d26206d94d50f32
--- /dev/null
+++ b/docs/reference/kersplatSimPaths.html
@@ -0,0 +1,225 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Simulate Kersplat paths — kersplatSimPaths • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Simulate Kersplat paths — kersplatSimPaths" />
+<meta property="og:description" content="Simulate gene means for each step along each path of a Kersplat simulation" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Simulate Kersplat paths</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimPaths.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate gene means for each step along each path of a Kersplat simulation</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimPaths</span>(<span class='no'>params</span>, <span class='no'>verbose</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>KersplatParams object with path means</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The method of simulating paths is inspired by the method used in the PROSSTT
+simulation. Changes in expression are controlled by <code>paths.nPrograms</code>
+regulatory programs. Each of the regulatory genes in the gene network has
+some association with each program. This is analogous to there being changes
+in the environment (the programs) which are sensed by receptors (regulatory
+genes) and cause changes in expression downstream. For each path a random
+walk is generated for each program and the changes passed on to the
+regulatory genes. At each step the changes propagate through the network
+according to the weights on edges between genes. This algorithm is fairly
+simple but should result in correlation relationships between genes. However
+it is likely to be improved and adjusted in the future.</p>
+<p>The path structure itself is specified by the <code>paths.design</code> parameter.
+This is a <code>data.frame</code> with three columns: "Path", "From", and "Steps".
+The Path field is an ID for each path while the Steps field controls the
+length of each path. Increasing the number of steps will increase the
+difference in expression between the ends of the paths. The From field sets
+the originating point of each path. For example a From of <code>0, 0, 0</code>
+would indicate three paths from the origin while a From of <code>0, 1, 1</code>
+would give a branching structure with Path 1 beginning at the origin and
+Path 2 and Path 3 beginning at the end of Path 1.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Papadopoulos N, Parra RG, Söding J. PROSSTT: probabilistic simulation of
+single-cell RNA-seq data for complex differentiation processes.
+Bioinformatics (2019). <a href='https://doi.org/10.1093/bioinformatics/btz078'>https://doi.org/10.1093/bioinformatics/btz078</a>.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ <li><a href="#references">References</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/kersplatSimulate.html b/docs/reference/kersplatSimulate.html
new file mode 100644
index 0000000000000000000000000000000000000000..86bf3c334b73eaf3b7952c9129551551d3b3bc0f
--- /dev/null
+++ b/docs/reference/kersplatSimulate.html
@@ -0,0 +1,217 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Kersplat simulation — kersplatSimulate • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Kersplat simulation — kersplatSimulate" />
+<meta property="og:description" content="Simulate scRNA-seq count data using the Kersplat model" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Kersplat simulation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>kersplatSimulate.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Simulate scRNA-seq count data using the Kersplat model</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>kersplatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newKersplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>params</th>
+ <td><p>KersplatParams object containing simulation parameters.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>any additional parameter settings to override what is provided in
+<code>params</code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>SingleCellExperiment containing simulated counts and intermediate
+values</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This functions is for simulating data in a single step. It consists of a
+call to <code><a href='kersplatSetup.html'>kersplatSetup</a></code> followed by a call to
+<code><a href='kersplatSample.html'>kersplatSample</a></code>. Please see the documentation for those
+functions for more details of the individual steps.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='kersplatSetup.html'>kersplatSetup</a></code>, <code><a href='kersplatSample.html'>kersplatSample</a></code></p></div>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>kersplatSimulate</span>()</div><div class='output co'>#> <span class='message'>Setting up parameters...</span></div><div class='output co'>#> <span class='message'>Generating gene network...</span></div><div class='output co'>#> <span class='message'>Selecting regulators...</span></div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Sampling from gamma distribution...</span></div><div class='output co'>#> <span class='message'>Simulating paths...</span></div><div class='output co'>#> <span class='message'>Simulating path 1...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Sampling from log-normal distribution...</span></div><div class='output co'>#> <span class='message'>Assigning cells to paths...</span></div><div class='output co'>#> <span class='message'>Assigning cells to steps...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Applying BCV adjustment...</span></div><div class='output co'>#> <span class='message'>Simulating cell counts...</span></div><div class='output co'>#> <span class='message'>Simulating ambient counts...</span></div><div class='output co'>#> <span class='message'>Simulating final counts...</span></div><div class='input'>
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ <li><a href="#see-also">See also</a></li>
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index 10d46c20e5a00beb47fbb18633a69a92fea548ed..a3402c2c634156803bbe7658e8360085dc3c8038 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>List simulations — listSims • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="List simulations — listSims" />
+<meta property="og:title" content="List simulations — listSims" />
<meta property="og:description" content="List all the simulations that are currently available in Splatter with a
brief description." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ brief description." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ brief description." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ brief description." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ brief description." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ brief description." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ brief description." />
</div>
<div class="ref-description">
-
<p>List all the simulations that are currently available in Splatter with a
brief description.</p>
-
</div>
<pre class="usage"><span class='fu'>listSims</span>(<span class='kw'>print</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -138,15 +156,14 @@ brief description.</p>
<td><p>logical. Whether to print to the console.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Invisibly returns a data.frame containing the information that is
displayed.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 13 simulations
+ <pre class="examples"><div class='input'><span class='fu'>listSims</span>()</div><div class='output co'>#> Splatter currently contains 14 simulations
#>
#> Splat (splat)
#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
@@ -164,6 +181,10 @@ displayed.</p>
#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
#>
+#> Kersplat (kersplat)
+#> DOI: GitHub: Oshlack/splatter
+#> The Kersplat simulation extends the Splat model by adding a gene network, more complex cell structure, doublets and empty cells (Experimental).
+#>
#> Simple (simple)
#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> A simple simulation with gamma means and negative binomial counts.
@@ -205,22 +226,21 @@ displayed.</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -228,6 +248,8 @@ displayed.</p>
+
</body>
</html>
+
diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
index b940b0ad1d050f8aef52c509492d852018706767..b4dd4d529e1277350763377ea0c4637161ca004a 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Logistic function — logistic • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Logistic function — logistic" />
+<meta property="og:title" content="Logistic function — logistic" />
<meta property="og:description" content="Implementation of the logistic function" />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Implementation of the logistic function</p>
-
</div>
<pre class="usage"><span class='fu'>logistic</span>(<span class='no'>x</span>, <span class='no'>x0</span>, <span class='no'>k</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -144,31 +162,30 @@
<td><p>shape parameter. Gives the slope of the function.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>Value of logistic funciton with given parameters</p>
-
+ <p>Value of logistic function with given parameters</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -176,6 +193,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 8ece3e84a66ec7851c2849975e614551a4a85ef9..0ce51e6f0bf044edc00e269bcbd9f40c08804022 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Lun2 simulation parameters — lun2Estimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Lun2 simulation parameters — lun2Estimate" />
+<meta property="og:title" content="Estimate Lun2 simulation parameters — lun2Estimate" />
<meta property="og:description" content="Estimate simulation parameters for the Lun2 simulation from a real dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,9 +141,7 @@
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the Lun2 simulation from a real dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>,
@@ -137,7 +155,7 @@
<span class='co'># S3 method for matrix</span>
<span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(),
<span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -170,50 +188,46 @@ back-end to be used. Default is <code>SerialParam</code> which uses a
single core.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>LunParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>See <code><a href='Lun2Params.html'>Lun2Params</a></code> for more details on the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_cell_info"</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
-<span class='no'>plates</span> <span class='kw'><-</span> <span class='fu'>factor</span>(<span class='no'>sc_example_cell_info</span>$<span class='no'>Mutation_Status</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lun2Estimate</span>(<span class='no'>sc_example_counts</span>, <span class='no'>plates</span>, <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>20</span>)
+<span class='no'>plates</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>as.numeric</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/factor.html'>factor</a></span>(<span class='fu'>colData</span>(<span class='no'>sce</span>)$<span class='no'>Mutation_Status</span>))
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lun2Estimate</span>(<span class='no'>sce</span>, <span class='no'>plates</span>, <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>params</span>
-<span class='co'># }</span></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -221,6 +235,8 @@ single core.</p></td>
+
</body>
</html>
+
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index a2c680d0218402dffd85bf5cb983b21b64d83fab..d88e808d38f02d6818d3cae14beb55d4c3d6c394 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Lun2 simulation — lun2Simulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Lun2 simulation — lun2Simulate" />
+<meta property="og:title" content="Lun2 simulation — lun2Simulate" />
<meta property="og:description" content="Simulate single-cell RNA-seq count data using the method described in Lun
and Marioni "Overcoming confounding plate effects in differential expression
analyses of single-cell RNA-seq data"." />
@@ -41,8 +45,10 @@ analyses of single-cell RNA-seq data"." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ analyses of single-cell RNA-seq data"." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ analyses of single-cell RNA-seq data"." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ analyses of single-cell RNA-seq data"." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ analyses of single-cell RNA-seq data"." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ analyses of single-cell RNA-seq data"." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,16 +143,14 @@ analyses of single-cell RNA-seq data"." />
</div>
<div class="ref-description">
-
<p>Simulate single-cell RNA-seq count data using the method described in Lun
and Marioni "Overcoming confounding plate effects in differential expression
analyses of single-cell RNA-seq data".</p>
-
</div>
<pre class="usage"><span class='fu'>lun2Simulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>zinb</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -154,11 +172,10 @@ analyses of single-cell RNA-seq data".</p>
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The Lun2 simulation uses a negative-binomial distribution where the means and
@@ -168,48 +185,43 @@ simulation is the addition of plate effects. Differential expression can be
added between two groups of plates (an "ingroup" and all other plates).
Library size factors are also applied and optionally a zero-inflated
negative-binomial can be used.</p>
-<p>If the number of genes to simulate differs from the number of provied gene
+<p>If the number of genes to simulate differs from the number of provided gene
parameters or the number of cells to simulate differs from the number of
-library sizes the relevant paramters will be sampled with a warning. This
+library sizes the relevant parameters will be sampled with a warning. This
allows any number of genes or cells to be simulated regardless of the
number in the dataset used in the estimation step but has the downside that
some genes or cells may be simulated multiple times.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Lun ATL, Marioni JC. Overcoming confounding plate effects in differential
expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
<p>Paper: <a href='dx.doi.org/10.1093/biostatistics/kxw055'>dx.doi.org/10.1093/biostatistics/kxw055</a></p>
<p>Code: <a href='https://github.com/MarioniLab/PlateEffects2016'>https://github.com/MarioniLab/PlateEffects2016</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating plate means...</span></div><div class='output co'>#> <span class='message'>Simulating libray size factors...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating plate means...</span></div><div class='output co'>#> <span class='message'>Simulating library size factors...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -217,6 +229,8 @@ expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
+
</body>
</html>
+
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 2844626c1c9c1211985343333010c284cf89a35e..af1332c58340c460150a99da553cf4cb5b9545b2 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Lun simulation parameters — lunEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Lun simulation parameters — lunEstimate" />
+<meta property="og:title" content="Estimate Lun simulation parameters — lunEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the Lun simulation from a real dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,9 +141,7 @@
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the Lun simulation from a real dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
@@ -134,7 +152,7 @@
<span class='co'># S3 method for matrix</span>
<span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -148,34 +166,30 @@ containing count data to estimate parameters from.</p></td>
<td><p>LunParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>LunParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. No other parameters are estimated. See <code><a href='LunParams.html'>LunParams</a></code>
for more details on the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)</div><div class='output co'>#> <span class='message'>Loading required package: ggplot2</span></div><div class='output co'>#> <span class='message'></span>
-#> <span class='message'>Attaching package: ‘scater’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:S4Vectors’:</span>
-#> <span class='message'></span>
-#> <span class='message'> rename</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:stats’:</span>
-#> <span class='message'></span>
-#> <span class='message'> filter</span></div><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lunEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
+
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lunEstimate</span>(<span class='no'>sce</span>)
<span class='no'>params</span></div><div class='output co'>#> A Params object of class LunParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> 2000 200 955861
#>
#> 9 additional parameters
#>
@@ -189,7 +203,7 @@ for more details on the parameters.</p>
#>
#> Groups:
#> [GROUPS] [GROUP CELLS]
-#> 1 40
+#> 1 200
#>
#> Diff expr:
#> [Genes] [Up Prop] [Up FC] [Down FC]
@@ -200,24 +214,22 @@ for more details on the parameters.</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -225,6 +237,8 @@ for more details on the parameters.</p>
+
</body>
</html>
+
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index f23ba51fdad42d89815464e25612d5d867e9613b..6d853e5e3569fb0b4d2ccd4a94c7e782999353da 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Lun simulation — lunSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Lun simulation — lunSimulate" />
+<meta property="og:title" content="Lun simulation — lunSimulate" />
<meta property="og:description" content="Simulate single-cell RNA-seq count data using the method described in Lun,
Bach and Marioni "Pooling across cells to normalize single-cell RNA
sequencing data with many zero counts"." />
@@ -41,8 +45,10 @@ sequencing data with many zero counts"." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ sequencing data with many zero counts"." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ sequencing data with many zero counts"." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ sequencing data with many zero counts"." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ sequencing data with many zero counts"." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ sequencing data with many zero counts"." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,15 +143,13 @@ sequencing data with many zero counts"." />
</div>
<div class="ref-description">
-
<p>Simulate single-cell RNA-seq count data using the method described in Lun,
Bach and Marioni "Pooling across cells to normalize single-cell RNA
sequencing data with many zero counts".</p>
-
</div>
<pre class="usage"><span class='fu'>lunSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -149,12 +167,11 @@ sequencing data with many zero counts".</p>
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment object containing the simulated counts and
intermediate values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The Lun simulation generates gene mean expression levels from a gamma
@@ -164,14 +181,12 @@ Counts are then simulated from a negative binomial distribution with
given a size factor (<code>2 ^ rnorm(nCells, mean = 0, sd = 0.5)</code>) and
differential expression can be simulated with fixed fold changes.</p>
<p>See <code><a href='LunParams.html'>LunParams</a></code> for details of the parameters.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
RNA sequencing data with many zero counts. Genome Biology (2016).</p>
<p>Paper: <a href='dx.doi.org/10.1186/s13059-016-0947-7'>dx.doi.org/10.1186/s13059-016-0947-7</a></p>
<p>Code: <a href='https://github.com/MarioniLab/Deconvolution2016'>https://github.com/MarioniLab/Deconvolution2016</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lunSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'>
@@ -181,26 +196,23 @@ RNA sequencing data with many zero counts. Genome Biology (2016).</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -208,6 +220,8 @@ RNA sequencing data with many zero counts. Genome Biology (2016).</p>
+
</body>
</html>
+
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index 5955b69981b7927caba9fb1f2815e96a9dd1c43c..161820ff9c0c967b5e0b8856d4645577849576a6 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Make comparison panel — makeCompPanel • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Make comparison panel — makeCompPanel" />
+<meta property="og:title" content="Make comparison panel — makeCompPanel" />
<meta property="og:description" content="Combine the plots from compareSCEs into a single panel." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,15 +141,13 @@
</div>
<div class="ref-description">
-
<p>Combine the plots from <code>compareSCEs</code> into a single panel.</p>
-
</div>
- <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>,
+ <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Means"</span>,
<span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>, <span class='st'>"Library size"</span>,
<span class='st'>"Zeros per gene"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Mean-zeros relationship"</span>))</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -146,41 +164,38 @@
<td><p>vector of labels for each of the seven plots.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Combined panel plot</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
<span class='no'>panel</span> <span class='kw'><-</span> <span class='fu'>makeCompPanel</span>(<span class='no'>comparison</span>)
-<span class='co'># }</span><div class='input'>
-</div></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -188,6 +203,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index 8d139fa6ede801d3e682bd7ff9b9107f8dc7a9f5..52fcbf45142b6b7523b424ed249b168f9455b9b6 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Make difference panel — makeDiffPanel • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Make difference panel — makeDiffPanel" />
+<meta property="og:title" content="Make difference panel — makeDiffPanel" />
<meta property="og:description" content="Combine the plots from diffSCEs into a single panel." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,16 +141,14 @@
</div>
<div class="ref-description">
-
<p>Combine the plots from <code>diffSCEs</code> into a single panel.</p>
-
</div>
<pre class="usage"><span class='fu'>makeDiffPanel</span>(<span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Difference comparison"</span>,
- <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>,
+ <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>,
<span class='st'>"Zeros per gene"</span>, <span class='st'>"Mean-variance relationship"</span>,
<span class='st'>"Mean-zeros relationship"</span>))</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -147,41 +165,38 @@
<td><p>vector of labels for each of the seven sections.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Combined panel plot</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
<span class='no'>panel</span> <span class='kw'><-</span> <span class='fu'>makeDiffPanel</span>(<span class='no'>difference</span>)
-<span class='co'># }</span><div class='input'>
-</div></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -189,6 +204,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index 62731232a3782c8214f6a476dc8d666467bc913b..48b6801a5a787ef9e02b8afa40a94f48fe34b205 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Make overall panel — makeOverallPanel • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Make overall panel — makeOverallPanel" />
+<meta property="og:title" content="Make overall panel — makeOverallPanel" />
<meta property="og:description" content="Combine the plots from compSCEs and diffSCEs into a
single panel." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ single panel." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ single panel." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ single panel." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ single panel." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ single panel." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,17 +142,15 @@ single panel." />
</div>
<div class="ref-description">
-
<p>Combine the plots from <code>compSCEs</code> and <code>diffSCEs</code> into a
single panel.</p>
-
</div>
<pre class="usage"><span class='fu'>makeOverallPanel</span>(<span class='no'>comp</span>, <span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Overall comparison"</span>,
- <span class='kw'>row.labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>,
+ <span class='kw'>row.labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>,
<span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>, <span class='st'>"Zeros per gene"</span>,
<span class='st'>"Mean-zeros relationship"</span>))</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -153,42 +171,39 @@ single panel.</p>
<td><p>vector of labels for each of the seven rows.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Combined panel plot</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
-<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
<span class='no'>panel</span> <span class='kw'><-</span> <span class='fu'>makeOverallPanel</span>(<span class='no'>comparison</span>, <span class='no'>difference</span>)
-<span class='co'># }</span><div class='input'>
-</div></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -196,6 +211,8 @@ single panel.</p>
+
</body>
</html>
+
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 3384d70b7a62445b836b6153995157be88e81ffd..cb1e210d8f4ff5d29c5d36d4ccce36c9cb8bd256 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate mfa simulation parameters — mfaEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate mfa simulation parameters — mfaEstimate" />
+<meta property="og:title" content="Estimate mfa simulation parameters — mfaEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the mfa simulation from a real dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,9 +141,7 @@
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the mfa simulation from a real dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())
@@ -134,7 +152,7 @@
<span class='co'># S3 method for matrix</span>
<span class='fu'>mfaEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -148,31 +166,33 @@ containing count data to estimate parameters from.</p></td>
<td><p>MFAParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>MFAParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The dropout lambda parameter is estimate using
-<code><a href='http://www.rdocumentation.org/packages/mfa/topics/empirical_lambda'>empirical_lambda</a></code>. See <code><a href='MFAParams.html'>MFAParams</a></code> for more
+<code><a href='https://rdrr.io/pkg/mfa/man/empirical_lambda.html'>empirical_lambda</a></code>. See <code><a href='MFAParams.html'>MFAParams</a></code> for more
details on the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>mfaEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class MFAParams
+<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"mfa"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>mfa</span>)
+ <span class='no'>synth</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/mfa/man/create_synthetic.html'>create_synthetic</a></span>(<span class='kw'>C</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>G</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>zero_negative</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>model_dropout</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
+ <span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>mfaEstimate</span>(<span class='no'>synth</span>$<span class='no'>X</span>)
+ <span class='no'>params</span>
+}</div><div class='output co'>#> A Params object of class MFAParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> 20 5 955861
#>
#> 4 additional parameters
#>
@@ -185,32 +205,30 @@ details on the parameters.</p>
#> TRUE
#>
#> Dropout:
-#> [Present] (LAMBDA)
-#> FALSE 0.00352186231063193
+#> [Present] (LAMBDA)
+#> FALSE 0.264691247771788
#> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -218,6 +236,8 @@ details on the parameters.</p>
+
</body>
</html>
+
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index 4da15e2a8e8706a37645b7f837c742f14ff37172..e30ea343590d72e82a6d0c263f95be3fe3edcb60 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>MFA simulation — mfaSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="MFA simulation — mfaSimulate" />
+<meta property="og:title" content="MFA simulation — mfaSimulate" />
<meta property="og:description" content="Simulate a bifurcating pseudotime path using the mfa method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Simulate a bifurcating pseudotime path using the mfa method.</p>
-
</div>
<pre class="usage"><span class='fu'>mfaSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newMFAParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -145,20 +163,18 @@
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code>
+ <p>This function is just a wrapper around <code><a href='https://rdrr.io/pkg/mfa/man/create_synthetic.html'>create_synthetic</a></code>
that takes a <code><a href='MFAParams.html'>MFAParams</a></code>, runs the simulation then converts the
output from log-expression to counts and returns a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. See
-<code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code> and the mfa paper for more details about
+<code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object. See
+<code><a href='https://rdrr.io/pkg/mfa/man/create_synthetic.html'>create_synthetic</a></code> and the mfa paper for more details about
how the simulation works.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell
@@ -166,35 +182,33 @@ gene expression data using a Bayesian mixture of factor analyzers. Wellcome
Open Research (2017).</p>
<p>Paper: <a href='10.12688/wellcomeopenres.11087.1'>10.12688/wellcomeopenres.11087.1</a></p>
<p>Code: <a href='https://github.com/kieranrcampbell/mfa'>https://github.com/kieranrcampbell/mfa</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>mfaSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div></pre>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"mfa"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>mfaSimulate</span>()
+}</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -202,6 +216,8 @@ Open Research (2017).</p>
+
</body>
</html>
+
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 1cdcfed260cac0419053e9d968b822fb992091a8..46b75adb265674a5e7286472e8cfe484a3b2b19c 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>New Params — newParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="New Params — newParams" />
+<meta property="og:title" content="New Params — newParams" />
<meta property="og:description" content="Create a new Params object. Functions exist for each of the different
Params subtypes." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ Params subtypes." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ Params subtypes." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ Params subtypes." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ Params subtypes." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,25 +130,26 @@ Params subtypes." />
</div><!--/.navbar -->
+
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>New Params</h1>
- <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Lun2Params-methods.R'><code>R/Lun2Params-methods.R</code></a>, and 9 more</small>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/KersplatParams-methods.R'><code>R/KersplatParams-methods.R</code></a>, and 10 more</small>
<div class="hidden name"><code>newParams.Rd</code></div>
</div>
<div class="ref-description">
-
<p>Create a new Params object. Functions exist for each of the different
Params subtypes.</p>
-
</div>
<pre class="usage"><span class='fu'>newBASiCSParams</span>(<span class='no'>...</span>)
+<span class='fu'>newKersplatParams</span>(<span class='no'>...</span>)
+
<span class='fu'>newLun2Params</span>(<span class='no'>...</span>)
<span class='fu'>newLunParams</span>(<span class='no'>...</span>)
@@ -147,7 +167,7 @@ Params subtypes.</p>
<span class='fu'>newSplatParams</span>(<span class='no'>...</span>)
<span class='fu'>newZINBParams</span>(<span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -156,11 +176,10 @@ Params subtypes.</p>
<td><p>additional parameters passed to <code><a href='setParams.html'>setParams</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>New Params object.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>newSimpleParams</span>()
@@ -170,22 +189,21 @@ Params subtypes.</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -193,6 +211,8 @@ Params subtypes.</p>
+
</body>
</html>
+
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 639dde8f40616f51eba9c1c16d55024213e6fb32..c9b2b839d20eaf118bbb8c95623df43c498a3e13 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate PhenoPath simulation parameters — phenoEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate PhenoPath simulation parameters — phenoEstimate" />
+<meta property="og:title" content="Estimate PhenoPath simulation parameters — phenoEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the PhenoPath simulation from a real
dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ dataset." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ dataset." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ dataset." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ dataset." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ dataset." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,10 +142,8 @@ dataset." />
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the PhenoPath simulation from a real
dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>phenoEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newPhenoParams</a></span>())
@@ -136,7 +154,7 @@ dataset.</p>
<span class='co'># S3 method for matrix</span>
<span class='fu'>phenoEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newPhenoParams</a></span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -150,30 +168,32 @@ containing count data to estimate parameters from.</p></td>
<td><p>PhenoParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>PhenoParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The total number of genes is evenly divided into the four types.
See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>phenoEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class PhenoParams
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"phenopath"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='co'># Load example data</span>
+ <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+ <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+ <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
+
+ <span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>phenoEstimate</span>(<span class='no'>sce</span>)
+ <span class='no'>params</span>
+}</div><div class='output co'>#> A Params object of class PhenoParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> 2000 200 955861
#>
#> 4 additional parameters
#>
@@ -186,24 +206,22 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -211,6 +229,8 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
+
</body>
</html>
+
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
index 5920e71a08341d65964d7db0ae062e7cde98da9e..88e0ca80648b6693cf5881bf39305a7c41f30f9f 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>PhenoPath simulation — phenoSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="PhenoPath simulation — phenoSimulate" />
+<meta property="og:title" content="PhenoPath simulation — phenoSimulate" />
<meta property="og:description" content="Simulate counts from a pseudotime trajectory using the PhenoPath method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Simulate counts from a pseudotime trajectory using the PhenoPath method.</p>
-
</div>
<pre class="usage"><span class='fu'>phenoSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newPhenoParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -145,22 +163,20 @@
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is just a wrapper around
-<code><a href='http://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> that takes a
+<code><a href='https://rdrr.io/pkg/phenopath/man/simulate_phenopath.html'>simulate_phenopath</a></code> that takes a
<code><a href='PhenoParams.html'>PhenoParams</a></code>, runs the simulation then converts the
output from log-expression to counts and returns a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
+<code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object. The original
simulated log-expression values are returned in the <code>LogExprs</code> assay.
-See <code><a href='http://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> and the PhenoPath paper for
+See <code><a href='https://rdrr.io/pkg/phenopath/man/simulate_phenopath.html'>simulate_phenopath</a></code> and the PhenoPath paper for
more details about how the simulation works.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
@@ -168,36 +184,33 @@ and environmental backgrounds across single-cells and populations. bioRxiv
(2017).</p>
<p>Paper: <a href='10.1101/159913'>10.1101/159913</a></p>
<p>Code: <a href='https://github.com/kieranrcampbell/phenopath'>https://github.com/kieranrcampbell/phenopath</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>phenoSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'>
-</div></pre>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"phenopath"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>phenoSimulate</span>()
+}</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -205,6 +218,8 @@ and environmental backgrounds across single-cells and populations. bioRxiv
+
</body>
</html>
+
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
index 0545cb0bee3caa0878198f42c608b64956e9e641..417a97337e1ca52b4673d216b2b07ff0af5619b1 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Bind rows (matched) — rbindMatched • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Bind rows (matched) — rbindMatched" />
+<meta property="og:title" content="Bind rows (matched) — rbindMatched" />
<meta property="og:description" content="Bind the rows of two data frames, keeping only the columns that are common
to both." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ to both." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ to both." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ to both." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ to both." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ to both." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ to both." />
</div>
<div class="ref-description">
-
<p>Bind the rows of two data frames, keeping only the columns that are common
to both.</p>
-
</div>
<pre class="usage"><span class='fu'>rbindMatched</span>(<span class='no'>df1</span>, <span class='no'>df2</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -142,32 +160,31 @@ to both.</p>
<td><p>second data.frame to bind.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>data.frame containing rows from <code>df1</code> and <code>df2</code> but only
common columns.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -175,6 +192,8 @@ to both.</p>
+
</body>
</html>
+
diff --git a/docs/reference/sampleDensity.html b/docs/reference/sampleDensity.html
new file mode 100644
index 0000000000000000000000000000000000000000..a6fdbc2c33b13ab4c7061d42b6ecc11cfde93517
--- /dev/null
+++ b/docs/reference/sampleDensity.html
@@ -0,0 +1,207 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Sample density — sampleDensity • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Sample density — sampleDensity" />
+<meta property="og:description" content="Sample from a density object using rejection sampling" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Sample density</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-simulate.R'><code>R/kersplat-simulate.R</code></a></small>
+ <div class="hidden name"><code>sampleDensity.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Sample from a density object using rejection sampling</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>sampleDensity</span>(<span class='no'>n</span>, <span class='no'>dens</span>, <span class='kw'>lower</span> <span class='kw'>=</span> <span class='fl'>0</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>n</th>
+ <td><p>Number of values to sample</p></td>
+ </tr>
+ <tr>
+ <th>dens</th>
+ <td><p>Density object to sample from</p></td>
+ </tr>
+ <tr>
+ <th>lower</th>
+ <td><p>Lower x-axis bound on sampled values</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Vector of sampled values</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Random points (x and y) are generated inside the range of the density object.
+If they value is less than the density for that x value (and x is greater
+than <code>lower</code>) then that x value is retained. Ten thousand points are
+generated at a time until enough valid values have been sampled.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index 3bc5c0891dccbd2f5b7a0e0d801c625ce72bd26a..f7939e3dc74e0ce1ab1d242f8a449da795737f7d 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate scDD simulation parameters — scDDEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate scDD simulation parameters — scDDEstimate" />
+<meta property="og:title" content="Estimate scDD simulation parameters — scDDEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the scDD simulation from a real dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,9 +141,7 @@
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the scDD simulation from a real dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@@ -141,7 +159,7 @@
<span class='co'># S3 method for default</span>
<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>condition</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -179,52 +197,80 @@ Conditions can be 1 or 2.</p></td>
interest.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SCDDParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function applies <code><a href='http://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> to the counts then uses
-<code><a href='http://www.rdocumentation.org/packages/scDD/topics/scDD'>scDD</a></code> to estimate the numbers of each gene type to
+ <p>This function applies <code><a href='https://rdrr.io/pkg/scDD/man/preprocess.html'>preprocess</a></code> to the counts then uses
+<code><a href='https://rdrr.io/pkg/scDD/man/scDD.html'>scDD</a></code> to estimate the numbers of each gene type to
simulate. The output is then converted to a SCDDParams object. See
-<code><a href='http://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> and <code><a href='http://www.rdocumentation.org/packages/scDD/topics/scDD'>scDD</a></code> for details.</p>
-
+<code><a href='https://rdrr.io/pkg/scDD/man/preprocess.html'>preprocess</a></code> and <code><a href='https://rdrr.io/pkg/scDD/man/scDD.html'>scDD</a></code> for details.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-
-<span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>scDDEstimate</span>(<span class='no'>sc_example_counts</span>, <span class='kw'>conditions</span> <span class='kw'>=</span> <span class='no'>conditions</span>)
-<span class='no'>params</span>
-<span class='co'># }</span></pre>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"scDD"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+ <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+ <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>(<span class='kw'>ncells</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>ngenes</span> <span class='kw'>=</span> <span class='fl'>100</span>)
+
+ <span class='fu'>colData</span>(<span class='no'>sce</span>)$<span class='no'>condition</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>sce</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>scDDEstimate</span>(<span class='no'>sce</span>, <span class='kw'>condition</span> <span class='kw'>=</span> <span class='st'>"condition"</span>)
+ <span class='no'>params</span>
+}</div><div class='output co'>#> <span class='message'>Performing Median Normalization</span></div><div class='output co'>#> <span class='message'>Notice: 10 genes have less than 3 nonzero cells per condition. Skipping these genes.</span></div><div class='output co'>#> <span class='message'>Setting up parallel back-end using FALSE cores</span></div><div class='output co'>#> <span class='message'>Clustering observed expression data for each gene</span></div><div class='output co'>#> <span class='message'>Notice: Number of permutations is set to zero; using </span>
+#> <span class='message'> Kolmogorov-Smirnov to test for differences in distributions</span>
+#> <span class='message'> instead of the Bayes Factor permutation test</span></div><div class='output co'>#> <span class='message'>Classifying significant genes into patterns</span></div><div class='output co'>#> A Params object of class SCDDParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
+#>
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 100 10 955861
+#>
+#> 11 additional parameters
+#>
+#> Data:
+#> (SCdat)
+#> SingleCellExperiment with 95 features and 20 cells
+#>
+#> Genes:
+#> (NDE) (NDP) (NDM) (NDP) (NEE) (NEP)
+#> 0 0 0 0 95 5
+#>
+#> Fold change:
+#> [SD Range] [Mode FC]
+#> 1, 3 2, 3, 4
+#>
+#> Variance:
+#> [Inflation]
+#> 1, 1
+#>
+#> Condition:
+#> [Condition]
+#> condition
+#> </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -232,6 +278,8 @@ simulate. The output is then converted to a SCDDParams object. See
+
</body>
</html>
+
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index aa65f8fce98f98b5de6e568eb14995fccbfc4ae3..cbbb965c30be97ec0712180939c4b0d456cae15a 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>scDD simulation — scDDSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="scDD simulation — scDDSimulate" />
+<meta property="og:title" content="scDD simulation — scDDSimulate" />
<meta property="og:description" content="Simulate counts using the scDD method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,14 +141,12 @@
</div>
<div class="ref-description">
-
<p>Simulate counts using the scDD method.</p>
-
</div>
<pre class="usage"><span class='fu'>scDDSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>plots</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>plot.file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -161,19 +179,17 @@ single core.</p></td>
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://rdrr.io/pkg/scDD/man/simulateSet.html'>simulateSet</a></code> that
takes a <code><a href='SCDDParams.html'>SCDDParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more details about how the simulation
+output to a <code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object.
+See <code><a href='https://rdrr.io/pkg/scDD/man/simulateSet.html'>simulateSet</a></code> for more details about how the simulation
works.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Korthauer KD, Chu L-F, Newton MA, Li Y, Thomson J, Stewart R, et al. A
@@ -181,37 +197,33 @@ statistical approach for identifying differential distributions in
single-cell RNA-seq experiments. Genome Biology (2016).</p>
<p>Paper: <a href='10.1186/s13059-016-1077-y'>10.1186/s13059-016-1077-y</a></p>
<p>Code: <a href='https://github.com/kdkorthauer/scDD'>https://github.com/kdkorthauer/scDD</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>scDDSimulate</span>()
-<span class='co'># }</span></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -219,6 +231,8 @@ single-cell RNA-seq experiments. Genome Biology (2016).</p>
+
</body>
</html>
+
diff --git a/docs/reference/selectFit.html b/docs/reference/selectFit.html
new file mode 100644
index 0000000000000000000000000000000000000000..ce93fd9ed2d78978d30713879165216e27065f39
--- /dev/null
+++ b/docs/reference/selectFit.html
@@ -0,0 +1,210 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Select fit — selectFit • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Select fit — selectFit" />
+<meta property="og:description" content="Try a variety of fitting methods and select the best one" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Select fit</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/kersplat-estimate.R'><code>R/kersplat-estimate.R</code></a></small>
+ <div class="hidden name"><code>selectFit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Try a variety of fitting methods and select the best one</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>selectFit</span>(<span class='no'>data</span>, <span class='no'>distr</span>, <span class='kw'>weights</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>data</th>
+ <td><p>The data to fit</p></td>
+ </tr>
+ <tr>
+ <th>distr</th>
+ <td><p>Name of the distribution to fit</p></td>
+ </tr>
+ <tr>
+ <th>weights</th>
+ <td><p>Optional vector of weights</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>logical. Whether to print progress messages</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The selected fit object</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The distribution is fitted to the data using each of the
+<code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code> fitting methods. The fit with the
+smallest Cramer-von Mises statistic is selected.</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index c238ca25c5b9b13e93b8854a375f932d1425844f..8d3283b24e3265b0ffd2de2311c3d24fe51f20b0 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Set a parameter — setParam • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Set a parameter — setParam" />
+<meta property="og:title" content="Set a parameter — setParam" />
<meta property="og:description" content="Function for setting parameter values." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,20 +129,19 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set a parameter</h1>
- <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Lun2Params-methods.R'><code>R/Lun2Params-methods.R</code></a>, and 7 more</small>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/BASiCSParams-methods.R'><code>R/BASiCSParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/KersplatParams-methods.R'><code>R/KersplatParams-methods.R</code></a>, and 8 more</small>
<div class="hidden name"><code>setParam.Rd</code></div>
</div>
<div class="ref-description">
-
<p>Function for setting parameter values.</p>
-
</div>
<pre class="usage"><span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
@@ -131,6 +149,9 @@
<span class='co'># S4 method for BASiCSParams</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+<span class='co'># S4 method for KersplatParams</span>
+<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
+
<span class='co'># S4 method for Lun2Params</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
@@ -151,7 +172,7 @@
<span class='co'># S4 method for ZINBParams</span>
<span class='fu'>setParam</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -165,23 +186,23 @@
</tr>
<tr>
<th>value</th>
- <td><p>value to set the paramter to.</p></td>
+ <td><p>value to set the parameter to.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Object with new parameter value.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
<span class='fu'>setParam</span>(<span class='no'>params</span>, <span class='st'>"nGenes"</span>, <span class='fl'>100</span>)</div><div class='output co'>#> A Params object of class SimpleParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 667401
+#> 100 100 955861
#>
#> 3 additional parameters
#>
@@ -199,22 +220,21 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -222,6 +242,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index 39253e00a8f26475b635a1774a98e2ef781034ba..4e5f5ac87b438b86346153d139ecea153888cab4 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Set a parameter UNCHECKED — setParamUnchecked • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Set a parameter UNCHECKED — setParamUnchecked" />
+<meta property="og:title" content="Set a parameter UNCHECKED — setParamUnchecked" />
<meta property="og:description" content="Function for setting parameter values. THE OUTPUT IS NOT CHECKED FOR
VALIDITY!" />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ VALIDITY!" />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ VALIDITY!" />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ VALIDITY!" />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ VALIDITY!" />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ VALIDITY!" />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,17 +142,15 @@ VALIDITY!" />
</div>
<div class="ref-description">
-
<p>Function for setting parameter values. THE OUTPUT IS NOT CHECKED FOR
VALIDITY!</p>
-
</div>
<pre class="usage"><span class='fu'>setParamUnchecked</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)
<span class='co'># S4 method for Params</span>
<span class='fu'>setParamUnchecked</span>(<span class='no'>object</span>, <span class='no'>name</span>, <span class='no'>value</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -146,34 +164,33 @@ VALIDITY!</p>
</tr>
<tr>
<th>value</th>
- <td><p>value to set the paramter to.</p></td>
+ <td><p>value to set the parameter to.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Object with new parameter value.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -181,6 +198,8 @@ VALIDITY!</p>
+
</body>
</html>
+
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 55aec388f6e6732640c8a8e78b7e3280cba6d8d3..343a2428a7465ddcc16ff0f494ab753e382b4a7e 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Set parameters — setParams • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Set parameters — setParams" />
+<meta property="og:title" content="Set parameters — setParams" />
<meta property="og:description" content="Set multiple parameters in a Params object." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,34 +129,42 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set parameters</h1>
- <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/KersplatParams-methods.R'><code>R/KersplatParams-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Params-methods.R'><code>R/Params-methods.R</code></a>, and 2 more</small>
<div class="hidden name"><code>setParams.Rd</code></div>
</div>
<div class="ref-description">
-
<p>Set multiple parameters in a Params object.</p>
-
</div>
- <pre class="usage"><span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-
+ <pre class="usage"><span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
+
+<span class='co'># S4 method for KersplatParams</span>
+<span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
+
+<span class='co'># S4 method for Params</span>
+<span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
+
+<span class='co'># S4 method for SplatParams</span>
+<span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
- <th>params</th>
+ <th>object</th>
<td><p>Params object to set parameters in.</p></td>
</tr>
<tr>
<th>update</th>
- <td><p>list of parameters to set where <code>names(update)</code> are the
+ <td><p>list of parameters to set where <code><a href='https://rdrr.io/r/base/names.html'>names(update)</a></code> are the
names of the parameters to set and the items in the list are values.</p></td>
</tr>
<tr>
@@ -146,11 +173,10 @@ names of the parameters to set and the items in the list are values.</p></td>
parameters specified in <code>update</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Params object with updated values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Each parameter is set by a call to <code><a href='setParam.html'>setParam</a></code>. If the same
@@ -158,16 +184,16 @@ parameter is specified multiple times it will be set multiple times.
Parameters can be specified using a list via <code>update</code> (useful when
collecting parameter values in some way) or individually (useful when setting
them manually), see examples.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (Genes) (Cells) [Seed]
-#> 10000 100 667401
+#> 10000 100 955861
#>
#> 3 additional parameters
#>
@@ -182,10 +208,11 @@ them manually), see examples.</p>
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>50</span>)
<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 667401
+#> 1000 50 955861
#>
#> 3 additional parameters
#>
@@ -197,13 +224,14 @@ them manually), see examples.</p>
#> [Dispersion]
#> 0.1
#> </div><div class='input'><span class='co'># Set via update list</span>
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='fu'>list</span>(<span class='kw'>mean.rate</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>mean.shape</span> <span class='kw'>=</span> <span class='fl'>0.8</span>))
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>mean.rate</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>mean.shape</span> <span class='kw'>=</span> <span class='fl'>0.8</span>))
<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 667401
+#> 1000 50 955861
#>
#> 3 additional parameters
#>
@@ -214,30 +242,29 @@ them manually), see examples.</p>
#> Counts:
#> [Dispersion]
#> 0.1
-#> </div></pre>
+#> </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -245,6 +272,8 @@ them manually), see examples.</p>
+
</body>
</html>
+
diff --git a/docs/reference/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
index 44d12b82bc3c4950881445e1564881c713bba0c0..06025321e954ad312c36980d04215bea8a1699cc 100644
--- a/docs/reference/setParamsUnchecked.html
+++ b/docs/reference/setParamsUnchecked.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Set parameters UNCHECKED — setParamsUnchecked • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Set parameters UNCHECKED — setParamsUnchecked" />
+<meta property="og:title" content="Set parameters UNCHECKED — setParamsUnchecked" />
<meta property="og:description" content="Set multiple parameters in a Params object." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Set multiple parameters in a Params object.</p>
-
</div>
<pre class="usage"><span class='fu'>setParamsUnchecked</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -137,7 +155,7 @@
</tr>
<tr>
<th>update</th>
- <td><p>list of parameters to set where <code>names(update)</code> are the
+ <td><p>list of parameters to set where <code><a href='https://rdrr.io/r/base/names.html'>names(update)</a></code> are the
names of the parameters to set and the items in the list are values.</p></td>
</tr>
<tr>
@@ -146,11 +164,10 @@ names of the parameters to set and the items in the list are values.</p></td>
parameters specified in <code>update</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Params object with updated values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Each parameter is set by a call to <code><a href='setParam.html'>setParam</a></code>. If the same
@@ -158,29 +175,27 @@ parameter is specified multiple times it will be set multiple times.
Parameters can be specified using a list via <code>update</code> (useful when
collecting parameter values in some way) or individually (useful when setting
them manually), see examples. THE FINAL OBJECT IS NOT CHECKED FOR VALIDITY!</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -188,6 +203,8 @@ them manually), see examples. THE FINAL OBJECT IS NOT CHECKED FOR VALIDITY!</p>
+
</body>
</html>
+
diff --git a/docs/reference/showDFs.html b/docs/reference/showDFs.html
index f847334ce6629f8b086378be0dee6cbeaefcaaaf..ca9b8f3426dc40300d605767a2d18a46d4606c3b 100644
--- a/docs/reference/showDFs.html
+++ b/docs/reference/showDFs.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Show data.frame — showDFs • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Show data.frame — showDFs" />
+<meta property="og:title" content="Show data.frame — showDFs" />
<meta property="og:description" content="Function used for pretty printing data.frame parameters." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Function used for pretty printing data.frame parameters.</p>
-
</div>
<pre class="usage"><span class='fu'>showDFs</span>(<span class='no'>dfs</span>, <span class='no'>not.default</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -140,25 +158,30 @@
<td><p>logical vector giving which have changed from the default.</p></td>
</tr>
</table>
-
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Print data.frame parameters</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
- </ul>
+ <li><a href="#value">Value</a></li>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -166,6 +189,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
index 33d88d60028bc6fbd0432a75979e2b2c826844fd..0b34baaa40e532f1fbd6daf2f5499ab1e8d9ae97 100644
--- a/docs/reference/showPP.html
+++ b/docs/reference/showPP.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Show pretty print — showPP • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Show pretty print — showPP" />
+<meta property="og:title" content="Show pretty print — showPP" />
<meta property="og:description" content="Function used for pretty printing params object." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Function used for pretty printing params object.</p>
-
</div>
<pre class="usage"><span class='fu'>showPP</span>(<span class='no'>params</span>, <span class='no'>pp</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -140,31 +158,30 @@
<td><p>list specifying how the object should be displayed.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Print params object to console</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -172,6 +189,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/showValues.html b/docs/reference/showValues.html
index cac7b285b98fd7bc8b5a1584c178a8f58d3ef2f7..12794a6f74b4689692a5d6a322fb67cb1adca669 100644
--- a/docs/reference/showValues.html
+++ b/docs/reference/showValues.html
@@ -1,28 +1,32 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Show vales — showValues • Splatter</title>
+<title>Show values — showValues • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Show vales — showValues" />
-<meta property="og:description" content="Function used for pretty printing scale or vector parameters." />
+<meta property="og:title" content="Show values — showValues" />
+<meta property="og:description" content="Function used for pretty printing scalar or vector parameters." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,24 +129,23 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Show vales</h1>
+ <h1>Show values</h1>
<small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
<div class="hidden name"><code>showValues.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>Function used for pretty printing scale or vector parameters.</p>
-
+ <p>Function used for pretty printing scalar or vector parameters.</p>
</div>
<pre class="usage"><span class='fu'>showValues</span>(<span class='no'>values</span>, <span class='no'>not.default</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -140,25 +158,30 @@
<td><p>logical vector giving which have changed from the default.</p></td>
</tr>
</table>
-
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Print values</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
- </ul>
+ <li><a href="#value">Value</a></li>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -166,6 +189,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 9ced2b7f06ba101a450481458917562441deae72..ea36ff15c0b56b6b74490ad6004ad0f197d413b7 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate simple simulation parameters — simpleEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate simple simulation parameters — simpleEstimate" />
+<meta property="og:title" content="Estimate simple simulation parameters — simpleEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the simple simulation from a real dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,9 +141,7 @@
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the simple simulation from a real dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
@@ -134,7 +152,7 @@
<span class='co'># S3 method for matrix</span>
<span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -148,38 +166,38 @@ containing count data to estimate parameters from.</p></td>
<td><p>SimpleParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SimpleParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The mean parameters are estimated by fitting a gamma distribution
to the library size normalised mean expression level using
-<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
+<code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
details on the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>simpleEstimate</span>(<span class='no'>sc_example_counts</span>)
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>simpleEstimate</span>(<span class='no'>sce</span>)
<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> 2000 200 955861
#>
#> 3 additional parameters
#>
#> Mean:
-#> (RATE) (SHAPE)
-#> 0.0008052293183292 0.131835949613878
+#> (RATE) (SHAPE)
+#> 0.00315146081285586 0.562634238245172
#>
#> Counts:
#> [Dispersion]
@@ -190,24 +208,22 @@ details on the parameters.</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -215,6 +231,8 @@ details on the parameters.</p>
+
</body>
</html>
+
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
index 366c133ea5dc92275d84bbb9708bb7e5880b69ab..f24d66a9525703e416eed19872199283b1becec5 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simple simulation — simpleSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simple simulation — simpleSimulate" />
+<meta property="og:title" content="Simple simulation — simpleSimulate" />
<meta property="og:description" content="Simulate counts from a simple negative binomial distribution without
simulated library sizes, differential expression etc." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ simulated library sizes, differential expression etc." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ simulated library sizes, differential expression etc." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ simulated library sizes, differential expression etc." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ simulated library sizes, differential expression etc." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ simulated library sizes, differential expression etc." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ simulated library sizes, differential expression etc." />
</div>
<div class="ref-description">
-
<p>Simulate counts from a simple negative binomial distribution without
simulated library sizes, differential expression etc.</p>
-
</div>
<pre class="usage"><span class='fu'>simpleSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -147,11 +165,10 @@ simulated library sizes, differential expression etc.</p>
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Gene means are simulated from a gamma distribution with
@@ -159,7 +176,6 @@ simulated library sizes, differential expression etc.</p>
simulated from a negative binomial distribution with <code>mu = means</code> and
<code>size = 1 / counts.disp</code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
details of the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>simpleSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='co'># Override default parameters</span>
@@ -169,24 +185,22 @@ details of the parameters.</p>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -194,6 +208,8 @@ details of the parameters.</p>
+
</body>
</html>
+
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index fe37d83eb6e71054ec555e18a50d053c7c171681..3da07e87ab34a681a5e3cc2082127834c6fb53f6 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate SparseDC simulation parameters — sparseDCEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate SparseDC simulation parameters — sparseDCEstimate" />
+<meta property="og:title" content="Estimate SparseDC simulation parameters — sparseDCEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the SparseDC simulation from a real
dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ dataset." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ dataset." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ dataset." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ dataset." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ dataset." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,10 +142,8 @@ dataset." />
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the SparseDC simulation from a real
dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>, <span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@@ -138,7 +156,7 @@ dataset.</p>
<span class='co'># S3 method for matrix</span>
<span class='fu'>sparseDCEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='no'>nclusters</span>,
<span class='kw'>norm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -157,7 +175,7 @@ containing count data to estimate parameters from.</p></td>
</tr>
<tr>
<th>norm</th>
- <td><p>logical, whether to libray size normalise counts before
+ <td><p>logical, whether to library size normalise counts before
estimation. Set this to FALSE if counts is already normalised.</p></td>
</tr>
<tr>
@@ -165,38 +183,38 @@ estimation. Set this to FALSE if counts is already normalised.</p></td>
<td><p>PhenoParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SparseParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The counts are preprocessed using
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/pre_proc_data'>pre_proc_data</a></code> and then parameters are estimated using
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/sparsedc_cluster'>sparsedc_cluster</a></code> using lambda values calculated using
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/lambda1_calculator'>lambda1_calculator</a></code> and
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/lambda2_calculator'>lambda2_calculator</a></code>.</p>
+<code><a href='https://rdrr.io/pkg/SparseDC/man/pre_proc_data.html'>pre_proc_data</a></code> and then parameters are estimated using
+<code><a href='https://rdrr.io/pkg/SparseDC/man/sparsedc_cluster.html'>sparsedc_cluster</a></code> using lambda values calculated using
+<code><a href='https://rdrr.io/pkg/SparseDC/man/lambda1_calculator.html'>lambda1_calculator</a></code> and
+<code><a href='https://rdrr.io/pkg/SparseDC/man/lambda2_calculator.html'>lambda2_calculator</a></code>.</p>
<p>See <code><a href='SparseDCParams.html'>SparseDCParams</a></code> for more details on the parameters.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"SparseDC"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='co'># Load example data</span>
+ <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+ <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+ <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>(<span class='kw'>ncells</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>ngenes</span> <span class='kw'>=</span> <span class='fl'>100</span>)
-<span class='fu'>set.seed</span>(<span class='fl'>1</span>)
-<span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>sce</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>sparseDCEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>500</span>, ], <span class='no'>conditions</span>,
- <span class='kw'>nclusters</span> <span class='kw'>=</span> <span class='fl'>3</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SparseDCParams
+ <span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>sparseDCEstimate</span>(<span class='no'>sce</span>, <span class='no'>conditions</span>, <span class='kw'>nclusters</span> <span class='kw'>=</span> <span class='fl'>3</span>)
+ <span class='no'>params</span>
+}</div><div class='output co'>#> A Params object of class SparseDCParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 500 20 667401
+#> 100 10 955861
#>
#> 7 additional parameters
#>
@@ -206,7 +224,7 @@ input data. The counts are preprocessed using
#>
#> Clusters:
#> (CONDITION 1) (CONDITION 2)
-#> 1, 2, 3 1, 2, 3
+#> 2, 3 1, 2, 3
#>
#> Means:
#> [Lower] [Upper]
@@ -217,24 +235,22 @@ input data. The counts are preprocessed using
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -242,6 +258,8 @@ input data. The counts are preprocessed using
+
</body>
</html>
+
diff --git a/docs/reference/sparseDCSimulate.html b/docs/reference/sparseDCSimulate.html
index f71ca37c6e061ff6fefce7ea9a459a9c2f081f67..e88c3a28ca749f0b70959e1ee29e76cd17059607 100644
--- a/docs/reference/sparseDCSimulate.html
+++ b/docs/reference/sparseDCSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>SparseDC simulation — sparseDCSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="SparseDC simulation — sparseDCSimulate" />
+<meta property="og:title" content="SparseDC simulation — sparseDCSimulate" />
<meta property="og:description" content="Simulate counts from cluster in two conditions using the SparseDC method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Simulate counts from cluster in two conditions using the SparseDC method.</p>
-
</div>
<pre class="usage"><span class='fu'>sparseDCSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSparseDCParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -145,22 +163,20 @@
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is just a wrapper around
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/sim_data'>sim_data</a></code> that takes a
+<code><a href='https://rdrr.io/pkg/SparseDC/man/sim_data.html'>sim_data</a></code> that takes a
<code><a href='SparseDCParams.html'>SparseDCParams</a></code>, runs the simulation then converts the
output from log-expression to counts and returns a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
+<code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object. The original
simulated log-expression values are returned in the <code>LogExprs</code> assay.
-See <code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/sim_data'>sim_data</a></code> and the SparseDC paper for
+See <code><a href='https://rdrr.io/pkg/SparseDC/man/sim_data.html'>sim_data</a></code> and the SparseDC paper for
more details about how the simulation works.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
@@ -170,36 +186,33 @@ and environmental backgrounds across single-cells and populations. bioRxiv
tracing cell type changes via single-cell RNA-sequencing data.
Nucleic Acids Research (2017).</p>
<p>Paper: <a href='10.1093/nar/gkx1113'>10.1093/nar/gkx1113</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>sparseDCSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'>
-</div></pre>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"SparseDC"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>sparseDCSimulate</span>()
+}</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -207,6 +220,8 @@ Nucleic Acids Research (2017).</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
index 6b3ec33b6adf1e96e8ab5f3890dbb86d9213fe9d..e6b74cfad44ff07301b1250bd11f754f637a47e8 100644
--- a/docs/reference/splatEstBCV.html
+++ b/docs/reference/splatEstBCV.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV" />
+<meta property="og:title" content="Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV" />
<meta property="og:description" content="Parameters are estimated using the estimateDisp function
in the edgeR package." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ in the edgeR package." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ in the edgeR package." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ in the edgeR package." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ in the edgeR package." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ in the edgeR package." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ in the edgeR package." />
</div>
<div class="ref-description">
-
- <p>Parameters are estimated using the <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function
+ <p>Parameters are estimated using the <code><a href='https://rdrr.io/pkg/edgeR/man/estimateDisp.html'>estimateDisp</a></code> function
in the <code>edgeR</code> package.</p>
-
</div>
<pre class="usage"><span class='fu'>splatEstBCV</span>(<span class='no'>counts</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -142,42 +160,39 @@ in the <code>edgeR</code> package.</p>
<td><p>SplatParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SplatParams object with estimated values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>The <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function is used to estimate the common
+ <p>The <code><a href='https://rdrr.io/pkg/edgeR/man/estimateDisp.html'>estimateDisp</a></code> function is used to estimate the common
dispersion and prior degrees of freedom. See
-<code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> for details. When estimating parameters on
+<code><a href='https://rdrr.io/pkg/edgeR/man/estimateDisp.html'>estimateDisp</a></code> for details. When estimating parameters on
simulated data we found a broadly linear relationship between the true
underlying common dispersion and the <code>edgR</code> estimate, therefore we
apply a small correction, <code>disp = 0.1 + 0.25 * edgeR.disp</code>.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -185,6 +200,8 @@ apply a small correction, <code>disp = 0.1 + 0.25 * edgeR.disp</code>.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
index 772c473f74b6cb472ee65aadf6de28be637cabbb..f7f7930cbdc79a1cbc1f5fa3dce6a3c7cb8860bd 100644
--- a/docs/reference/splatEstDropout.html
+++ b/docs/reference/splatEstDropout.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Splat dropout parameters — splatEstDropout • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Splat dropout parameters — splatEstDropout" />
+<meta property="og:title" content="Estimate Splat dropout parameters — splatEstDropout" />
<meta property="og:description" content="Estimate the midpoint and shape parameters for the logistic function used
when simulating dropout." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ when simulating dropout." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ when simulating dropout." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ when simulating dropout." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ when simulating dropout." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ when simulating dropout." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ when simulating dropout." />
</div>
<div class="ref-description">
-
<p>Estimate the midpoint and shape parameters for the logistic function used
when simulating dropout.</p>
-
</div>
<pre class="usage"><span class='fu'>splatEstDropout</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -142,41 +160,38 @@ when simulating dropout.</p>
<td><p>SplatParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SplatParams object with estimated values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Logistic function parameters are estimated by fitting a logistic function
to the relationship between log2 mean gene expression and the proportion of
-zeros in each gene. See <code><a href='http://www.rdocumentation.org/packages/stats/topics/nls'>nls</a></code> for details of fitting.
+zeros in each gene. See <code><a href='https://rdrr.io/r/stats/nls.html'>nls</a></code> for details of fitting.
Note this is done on the experiment level, more granular (eg. group or cell)
level dropout is not estimated.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -184,6 +199,8 @@ level dropout is not estimated.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
index 7da2a211bfc7ba006f67c22b630a715ed6357dbf..9bebff74c085f30e42657518744faef88ee69d8a 100644
--- a/docs/reference/splatEstLib.html
+++ b/docs/reference/splatEstLib.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Splat library size parameters — splatEstLib • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Splat library size parameters — splatEstLib" />
+<meta property="og:title" content="Estimate Splat library size parameters — splatEstLib" />
<meta property="og:description" content="The Shapiro-Wilks test is used to determine if the library sizes are
normally distributed. If so a normal distribution is fitted to the library
sizes, if not (most cases) a log-normal distribution is fitted and the
@@ -43,8 +47,10 @@ fitdist for details on the fitting." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -62,6 +68,7 @@ fitdist for details on the fitting." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -70,14 +77,15 @@ fitdist for details on the fitting." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -85,7 +93,7 @@ fitdist for details on the fitting." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -95,15 +103,26 @@ fitdist for details on the fitting." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -114,6 +133,7 @@ fitdist for details on the fitting." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -125,17 +145,15 @@ fitdist for details on the fitting." />
</div>
<div class="ref-description">
-
<p>The Shapiro-Wilks test is used to determine if the library sizes are
normally distributed. If so a normal distribution is fitted to the library
sizes, if not (most cases) a log-normal distribution is fitted and the
estimated parameters are added to the params object. See
-<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code> for details on the fitting.</p>
-
+<code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code> for details on the fitting.</p>
</div>
<pre class="usage"><span class='fu'>splatEstLib</span>(<span class='no'>counts</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -148,31 +166,30 @@ estimated parameters are added to the params object. See
<td><p>splatParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>splatParams object with estimated values.</p>
-
+ <p>SplatParams object with estimated values.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -180,6 +197,8 @@ estimated parameters are added to the params object. See
+
</body>
</html>
+
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
index cad61299ea231e6dda6a281d4e8ce5478ee87c97..f2a15d684104cb94958e3b56560fd9e1a8239480 100644
--- a/docs/reference/splatEstMean.html
+++ b/docs/reference/splatEstMean.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Splat mean parameters — splatEstMean • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Splat mean parameters — splatEstMean" />
+<meta property="og:title" content="Estimate Splat mean parameters — splatEstMean" />
<meta property="og:description" content="Estimate rate and shape parameters for the gamma distribution used to
simulate gene expression means." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ simulate gene expression means." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ simulate gene expression means." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ simulate gene expression means." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ simulate gene expression means." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ simulate gene expression means." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ simulate gene expression means." />
</div>
<div class="ref-description">
-
<p>Estimate rate and shape parameters for the gamma distribution used to
simulate gene expression means.</p>
-
</div>
<pre class="usage"><span class='fu'>splatEstMean</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -142,43 +160,40 @@ simulate gene expression means.</p>
<td><p>SplatParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SplatParams object with estimated values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>Parameter for the gamma distribution are estimated by fitting the mean
-normalised counts using <code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. The 'maximum
+ <p>Parameters for the gamma distribution are estimated by fitting the mean
+normalised counts using <code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code>. The 'maximum
goodness-of-fit estimation' method is used to minimise the Cramer-von Mises
distance. This can fail in some situations, in which case the 'method of
moments estimation' method is used instead. Prior to fitting the means are
winsorized by setting the top and bottom 10 percent of values to the 10th
and 90th percentiles.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -186,6 +201,8 @@ and 90th percentiles.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
index feafe8971935af2b17818e237cbc35144de38e15..c99279fdae4c701d0d2b8876777d6313b8df0b8d 100644
--- a/docs/reference/splatEstOutlier.html
+++ b/docs/reference/splatEstOutlier.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Splat expression outlier parameters — splatEstOutlier • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Splat expression outlier parameters — splatEstOutlier" />
+<meta property="og:title" content="Estimate Splat expression outlier parameters — splatEstOutlier" />
<meta property="og:description" content="Parameters are estimated by comparing means of individual genes to the
median mean expression level." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ median mean expression level." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ median mean expression level." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ median mean expression level." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ median mean expression level." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ median mean expression level." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ median mean expression level." />
</div>
<div class="ref-description">
-
<p>Parameters are estimated by comparing means of individual genes to the
median mean expression level.</p>
-
</div>
<pre class="usage"><span class='fu'>splatEstOutlier</span>(<span class='no'>norm.counts</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -142,11 +160,10 @@ median mean expression level.</p>
<td><p>SplatParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SplatParams object with estimated values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Expression outlier genes are detected using the Median Absolute Deviation
@@ -156,30 +173,28 @@ outlier. The proportion of outlier genes is used to estimate the outlier
probability. Factors for each outlier gene are calculated by dividing mean
expression by the median mean expression. A log-normal distribution is then
fitted to these factors in order to estimate the outlier factor location and
-scale parameters using <code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>.</p>
-
+scale parameters using <code><a href='https://rdrr.io/pkg/fitdistrplus/man/fitdist.html'>fitdist</a></code>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -187,6 +202,8 @@ scale parameters using <code><a href='http://www.rdocumentation.org/packages/fit
+
</body>
</html>
+
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index ab01b87b9c45c1a9ecb3f913b37449c12d48393f..3fab8c36e9ed966d43cb3bc78327ff0008ec1961 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate Splat simulation parameters — splatEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate Splat simulation parameters — splatEstimate" />
+<meta property="og:title" content="Estimate Splat simulation parameters — splatEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the Splat simulation from a real
dataset. See the individual estimation functions for more details on how this
is done." />
@@ -41,8 +45,10 @@ is done." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ is done." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ is done." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ is done." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ is done." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ is done." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,11 +143,9 @@ is done." />
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the Splat simulation from a real
dataset. See the individual estimation functions for more details on how this
is done.</p>
-
</div>
<pre class="usage"><span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
@@ -138,7 +156,7 @@ is done.</p>
<span class='co'># S3 method for matrix</span>
<span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -152,48 +170,47 @@ containing count data to estimate parameters from.</p></td>
<td><p>SplatParams object to store estimated values in.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SplatParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='splatEstMean.html'>splatEstMean</a></code>, <code><a href='splatEstLib.html'>splatEstLib</a></code>,
<code><a href='splatEstOutlier.html'>splatEstOutlier</a></code>, <code><a href='splatEstBCV.html'>splatEstBCV</a></code>,
<code><a href='splatEstDropout.html'>splatEstDropout</a></code></p></div>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>()
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SplatParams
+<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sce</span>)</div><div class='output co'>#> <span class='message'>NOTE: Library sizes have been found to be normally distributed instead of log-normal. You may want to check this is correct.</span></div><div class='input'><span class='no'>params</span></div><div class='output co'>#> A Params object of class SplatParams
#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> 2000 200 955861
#>
#> 28 additional parameters
#>
#> Batches:
#> [BATCHES] [BATCH CELLS] [Location] [Scale]
-#> 1 40 0.1 0.1
+#> 1 200 0.1 0.1
#>
#> Mean:
-#> (RATE) (SHAPE)
-#> 0.0032639148887191 0.419304527025529
+#> (RATE) (SHAPE)
+#> 0.002962686167343 0.496997730070513
#>
#> Library size:
-#> (LOCATION) (SCALE) (Norm)
-#> 12.7053037408488 0.58910919018286 FALSE
+#> (LOCATION) (SCALE) (NORM)
+#> 357331.235 11607.2332293176 TRUE
#>
#> Exprs outliers:
-#> (PROBABILITY) (LOCATION) (SCALE)
-#> 0.00623376623376623 4.22280669039478 0.422108697251885
+#> (PROBABILITY) (Location) (Scale)
+#> 0 4 0.5
#>
#> Groups:
#> [Groups] [Group Probs]
@@ -204,15 +221,15 @@ containing count data to estimate parameters from.</p></td>
#> 0.1 0.5 0.1 0.4
#>
#> BCV:
-#> (COMMON DISP) (DOF)
-#> 3.21969047393022 14.7262017878812
+#> (COMMON DISP) (DOF)
+#> 0.752043426792845 11211.8933424157
#>
#> Dropout:
-#> [Type] (MIDPOINT) (SHAPE)
-#> none 5.00420976858168 -0.652889139821156
+#> [Type] (MIDPOINT) (SHAPE)
+#> none 2.71153535179343 -1.37209356733765
#>
#> Paths:
-#> [From] [Length] [Skew] [Non-linear] [Sigma Factor]
+#> [From] [Steps] [Skew] [Non-linear] [Sigma Factor]
#> 0 100 0.5 0.1 0.8
#> </div></pre>
</div>
@@ -220,24 +237,22 @@ containing count data to estimate parameters from.</p></td>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#see-also">See also</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -245,6 +260,8 @@ containing count data to estimate parameters from.</p></td>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index 328e91bfef28ca7fb15b345d03c6ea8bf3a36602..df9fc4d3a74f952a26e761f70323268c79178248 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate BCV means — splatSimBCVMeans • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate BCV means — splatSimBCVMeans" />
+<meta property="og:title" content="Simulate BCV means — splatSimBCVMeans" />
<meta property="og:description" content="Simulate means for each gene in each cell that are adjusted to follow a
mean-variance trend using Biological Coefficient of Variation taken from
and inverse gamma distribution." />
@@ -41,8 +45,10 @@ and inverse gamma distribution." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ and inverse gamma distribution." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ and inverse gamma distribution." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ and inverse gamma distribution." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ and inverse gamma distribution." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ and inverse gamma distribution." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,15 +143,13 @@ and inverse gamma distribution." />
</div>
<div class="ref-description">
-
<p>Simulate means for each gene in each cell that are adjusted to follow a
mean-variance trend using Biological Coefficient of Variation taken from
and inverse gamma distribution.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimBCVMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -144,31 +162,30 @@ and inverse gamma distribution.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated BCV means.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -176,6 +193,8 @@ and inverse gamma distribution.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index 2dc5f20b39bb28d9bd76a8a19c0a43f62abf4d88..242767dd717b3aa73d69db2481dbcfedef7f67f3 100644
--- a/docs/reference/splatSimBatchCellMeans.html
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate batch means — splatSimBatchCellMeans • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate batch means — splatSimBatchCellMeans" />
+<meta property="og:title" content="Simulate batch means — splatSimBatchCellMeans" />
<meta property="og:description" content="Simulate a mean for each gene in each cell incorporating batch effect
factors." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ factors." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ factors." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ factors." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ factors." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ factors." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,14 +142,12 @@ factors." />
</div>
<div class="ref-description">
-
<p>Simulate a mean for each gene in each cell incorporating batch effect
factors.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimBatchCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -142,31 +160,30 @@ factors.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated batch means.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -174,6 +191,8 @@ factors.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 05ed4c5a81e3b4e31db4bf5c85f295d634fcac53..f62b51a237ff7553b0a03cda40d905c2fdab2764 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate batch effects — splatSimBatchEffects • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate batch effects — splatSimBatchEffects" />
+<meta property="og:title" content="Simulate batch effects — splatSimBatchEffects" />
<meta property="og:description" content="Simulate batch effects. Batch effect factors for each batch are produced
using getLNormFactors and these are added along with updated
means for each batch." />
@@ -41,8 +45,10 @@ means for each batch." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ means for each batch." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ means for each batch." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ means for each batch." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ means for each batch." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ means for each batch." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,15 +143,13 @@ means for each batch." />
</div>
<div class="ref-description">
-
<p>Simulate batch effects. Batch effect factors for each batch are produced
using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added along with updated
means for each batch.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimBatchEffects</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -144,31 +162,30 @@ means for each batch.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated batch effects.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -176,6 +193,8 @@ means for each batch.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index f66e44a91a32aa251955ff3f6f6dc2bb5c5c8b31..b025f346184d7e5d3dc18aa692497c07a9926126 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate cell means — splatSimCellMeans • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate cell means — splatSimCellMeans" />
+<meta property="og:title" content="Simulate cell means — splatSimCellMeans" />
<meta property="og:description" content="Simulate a gene by cell matrix giving the mean expression for each gene in
each cell. Cells start with the mean expression for the group they belong to
(when simulating groups) or cells are assigned the mean expression from a
@@ -43,8 +47,10 @@ means are adjusted for each cell's expected library size." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -62,6 +68,7 @@ means are adjusted for each cell's expected library size." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -70,14 +77,15 @@ means are adjusted for each cell's expected library size." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -85,7 +93,7 @@ means are adjusted for each cell's expected library size." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -95,15 +103,26 @@ means are adjusted for each cell's expected library size." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -114,6 +133,7 @@ means are adjusted for each cell's expected library size." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -125,13 +145,11 @@ means are adjusted for each cell's expected library size." />
</div>
<div class="ref-description">
-
<p>Simulate a gene by cell matrix giving the mean expression for each gene in
each cell. Cells start with the mean expression for the group they belong to
(when simulating groups) or cells are assigned the mean expression from a
random position on the appropriate path (when simulating paths). The selected
means are adjusted for each cell's expected library size.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimSingleCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
@@ -139,7 +157,7 @@ means are adjusted for each cell's expected library size.</p>
<span class='fu'>splatSimGroupCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
<span class='fu'>splatSimPathCellMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -152,31 +170,30 @@ means are adjusted for each cell's expected library size.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with added cell means.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -184,6 +201,8 @@ means are adjusted for each cell's expected library size.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index e394fc9c213b0e743203a7ebc215537f750737a2..72a3889076a6b65f035a3e003435923801f71bd9 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate group differential expression — splatSimDE • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,18 +36,20 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate group differential expression — splatSimDE" />
+<meta property="og:title" content="Simulate group differential expression — splatSimDE" />
<meta property="og:description" content="Simulate differential expression. Differential expression factors for each
group are produced using getLNormFactors and these are added
-along with updated means for each group. For paths care is taked to make sure
+along with updated means for each group. For paths care is taken to make sure
they are simulated in the correct order." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -61,6 +67,7 @@ they are simulated in the correct order." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -69,14 +76,15 @@ they are simulated in the correct order." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -84,7 +92,7 @@ they are simulated in the correct order." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -94,15 +102,26 @@ they are simulated in the correct order." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -113,6 +132,7 @@ they are simulated in the correct order." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -124,18 +144,16 @@ they are simulated in the correct order." />
</div>
<div class="ref-description">
-
<p>Simulate differential expression. Differential expression factors for each
group are produced using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added
-along with updated means for each group. For paths care is taked to make sure
+along with updated means for each group. For paths care is taken to make sure
they are simulated in the correct order.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimGroupDE</span>(<span class='no'>sim</span>, <span class='no'>params</span>)
<span class='fu'>splatSimPathDE</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -148,31 +166,30 @@ they are simulated in the correct order.</p>
<td><p>splatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated differential expression.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -180,6 +197,8 @@ they are simulated in the correct order.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index 81abab016da0b427f4ee9e9db63424783a078f95..c07cd8c6b6a0843bc1cb61a432f511479dcc005d 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate dropout — splatSimDropout • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,9 +36,9 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate dropout — splatSimDropout" />
-<meta property="og:description" content="A logistic function is used to form a relationshop between the expression
+<meta property="og:title" content="Simulate dropout — splatSimDropout" />
+<meta property="og:description" content="A logistic function is used to form a relationship between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped." />
@@ -42,8 +46,10 @@ to decide which counts should be dropped." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -61,6 +67,7 @@ to decide which counts should be dropped." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -69,14 +76,15 @@ to decide which counts should be dropped." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -84,7 +92,7 @@ to decide which counts should be dropped." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -94,15 +102,26 @@ to decide which counts should be dropped." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -113,6 +132,7 @@ to decide which counts should be dropped." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -124,16 +144,14 @@ to decide which counts should be dropped." />
</div>
<div class="ref-description">
-
- <p>A logistic function is used to form a relationshop between the expression
+ <p>A logistic function is used to form a relationship between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimDropout</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -146,31 +164,30 @@ to decide which counts should be dropped.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated dropout and observed counts.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -178,6 +195,8 @@ to decide which counts should be dropped.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index 5375508f309a5af51ecff06d235d48875c8c01cc..afd1d9009617d8b08952d16cb60e35653a6f13d8 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate gene means — splatSimGeneMeans • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate gene means — splatSimGeneMeans" />
+<meta property="og:title" content="Simulate gene means — splatSimGeneMeans" />
<meta property="og:description" content="Simulate gene means from a gamma distribution. Also simulates outlier
expression factors. Genes with an outlier factor not equal to 1 are replaced
with the median mean expression multiplied by the outlier factor." />
@@ -41,8 +45,10 @@ with the median mean expression multiplied by the outlier factor." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ with the median mean expression multiplied by the outlier factor." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ with the median mean expression multiplied by the outlier factor." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ with the median mean expression multiplied by the outlier factor." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ with the median mean expression multiplied by the outlier factor." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ with the median mean expression multiplied by the outlier factor." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,15 +143,13 @@ with the median mean expression multiplied by the outlier factor." />
</div>
<div class="ref-description">
-
<p>Simulate gene means from a gamma distribution. Also simulates outlier
expression factors. Genes with an outlier factor not equal to 1 are replaced
with the median mean expression multiplied by the outlier factor.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimGeneMeans</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -144,31 +162,30 @@ with the median mean expression multiplied by the outlier factor.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated gene means.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -176,6 +193,8 @@ with the median mean expression multiplied by the outlier factor.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index 400123fa1865dec2baba6ec8c2268abfd306c566..56b61da064b03bc76788d9dbcf7cfc22d0f5563b 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate library sizes — splatSimLibSizes • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate library sizes — splatSimLibSizes" />
+<meta property="og:title" content="Simulate library sizes — splatSimLibSizes" />
<meta property="og:description" content="Simulate expected library sizes. Typically a log-normal distribution is used
but there is also the option to use a normal distribution. In this case any
negative values are set to half the minimum non-zero value." />
@@ -41,8 +45,10 @@ negative values are set to half the minimum non-zero value." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ negative values are set to half the minimum non-zero value." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ negative values are set to half the minimum non-zero value." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ negative values are set to half the minimum non-zero value." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ negative values are set to half the minimum non-zero value." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ negative values are set to half the minimum non-zero value." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,15 +143,13 @@ negative values are set to half the minimum non-zero value." />
</div>
<div class="ref-description">
-
<p>Simulate expected library sizes. Typically a log-normal distribution is used
but there is also the option to use a normal distribution. In this case any
negative values are set to half the minimum non-zero value.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimLibSizes</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -144,31 +162,30 @@ negative values are set to half the minimum non-zero value.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated library sizes.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -176,6 +193,8 @@ negative values are set to half the minimum non-zero value.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 1c3b745daa4ee725f977ec948bece64289f320b2..871df99cf8e05bbdc53a9f6c1cb3e987e46a23bb 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Simulate true counts — splatSimTrueCounts • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,8 +36,8 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Simulate true counts — splatSimTrueCounts" />
+<meta property="og:title" content="Simulate true counts — splatSimTrueCounts" />
<meta property="og:description" content="Simulate a true counts matrix. Counts are simulated from a poisson
distribution where Each gene in each cell has it's own mean based on the
group (or path position), expected library size and BCV." />
@@ -41,8 +45,10 @@ group (or path position), expected library size and BCV." />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +66,7 @@ group (or path position), expected library size and BCV." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +75,15 @@ group (or path position), expected library size and BCV." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +91,7 @@ group (or path position), expected library size and BCV." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +101,26 @@ group (or path position), expected library size and BCV." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,6 +131,7 @@ group (or path position), expected library size and BCV." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -123,15 +143,13 @@ group (or path position), expected library size and BCV." />
</div>
<div class="ref-description">
-
<p>Simulate a true counts matrix. Counts are simulated from a poisson
distribution where Each gene in each cell has it's own mean based on the
group (or path position), expected library size and BCV.</p>
-
</div>
<pre class="usage"><span class='fu'>splatSimTrueCounts</span>(<span class='no'>sim</span>, <span class='no'>params</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -144,31 +162,30 @@ group (or path position), expected library size and BCV.</p>
<td><p>SplatParams object with simulation parameters.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment with simulated true counts.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -176,6 +193,8 @@ group (or path position), expected library size and BCV.</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index ae36dcd087ef88a05f08d9cc75ec26dfde751956..511d15c2a8be23997eb91131f38919aaf97edb6e 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Splat simulation — splatSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Splat simulation — splatSimulate" />
+<meta property="og:title" content="Splat simulation — splatSimulate" />
<meta property="og:description" content="Simulate count data from a fictional single-cell RNA-seq experiment using
the Splat method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ the Splat method." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ the Splat method." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ the Splat method." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ the Splat method." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ the Splat method." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,13 +142,11 @@ the Splat method." />
</div>
<div class="ref-description">
-
<p>Simulate count data from a fictional single-cell RNA-seq experiment using
the Splat method.</p>
-
</div>
- <pre class="usage"><span class='fu'>splatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"single"</span>, <span class='st'>"groups"</span>,
+ <pre class="usage"><span class='fu'>splatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"single"</span>, <span class='st'>"groups"</span>,
<span class='st'>"paths"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>splatSimulateSingle</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
@@ -136,7 +154,7 @@ the Splat method.</p>
<span class='fu'>splatSimulateGroups</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>splatSimulatePaths</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -162,12 +180,11 @@ trajectories (eg. differentiation processes).</p></td>
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment object containing the simulated counts and
intermediate values.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Parameters can be set in a variety of ways. If no parameters are provided
@@ -187,20 +204,20 @@ can be used.</p>
<li><p>Simulate dropout</p></li>
<li><p>Create final dataset</p></li>
</ol>
- <p>The final output is a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that
+
+<p>The final output is a
+<code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object that
contains the simulated counts but also the values for various intermediate
steps. These are stored in the <code>colData</code> (for cell specific
information), <code>rowData</code> (for gene specific information) or
<code>assays</code> (for gene by cell matrices) slots. This additional
information includes:</p><dl class='dl-horizontal'>
- <dt><code>phenoData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>colData</code></dt><dd><p><dl class='dl-horizontal'>
<dt>Cell</dt><dd><p>Unique cell identifier.</p></dd>
<dt>Group</dt><dd><p>The group or path the cell belongs to.</p></dd>
<dt>ExpLibSize</dt><dd><p>The expected library size for that cell.</p></dd>
- <dt>Step (paths only)</dt><dd><p>how far along the path each cell is.</p></dd>
- </dl></p></dd>
- <dt><code>featureData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt>Step (paths only)</dt><dd><p>how far along the path each cell is.</p></dd></dl></p></dd>
+ <dt><code>rowData</code></dt><dd><p><dl class='dl-horizontal'>
<dt>Gene</dt><dd><p>Unique gene identifier.</p></dd>
<dt>BaseGeneMean</dt><dd><p>The base expression level for that gene.</p></dd>
<dt>OutlierFactor</dt><dd><p>Expression outlier factor for that gene.
@@ -212,9 +229,8 @@ information includes:</p><dl class='dl-horizontal'>
gene in a particular group. Values of 1 indicate the gene is not
differentially expressed.</p></dd>
<dt>SigmaFac[Path]</dt><dd><p>Factor applied to genes that have
- non-linear changes in expression along a path.</p></dd>
- </dl></p></dd>
- <dt><code>assayData</code></dt><dd><p><dl class='dl-horizontal'>
+ non-linear changes in expression along a path.</p></dd></dl></p></dd>
+ <dt><code>assays</code></dt><dd><p><dl class='dl-horizontal'>
<dt>BatchCellMeans</dt><dd><p>The mean expression of genes in each cell
after adding batch effects.</p></dd>
<dt>BaseCellMeans</dt><dd><p>The mean expression of genes in each cell
@@ -226,20 +242,19 @@ information includes:</p><dl class='dl-horizontal'>
adjusted for BCV.</p></dd>
<dt>TrueCounts</dt><dd><p>The simulated counts before dropout.</p></dd>
<dt>Dropout</dt><dd><p>Logical matrix showing which values have been
- dropped in which cells.</p></dd>
- </dl></p></dd>
+ dropped in which cells.</p></dd></dl></p></dd>
+
</dl>
- <p>Values that have been added by Splatter are named using <code>UpperCamelCase</code>
+
+<p>Values that have been added by Splatter are named using <code>UpperCamelCase</code>
in order to differentiate them from the values added by analysis packages
which typically use <code>underscore_naming</code>.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA
sequencing data. Genome Biology (2017).</p>
<p>Paper: <a href='10.1186/s13059-017-1305-0'>10.1186/s13059-017-1305-0</a></p>
<p>Code: <a href='https://github.com/Oshlack/splatter'>https://github.com/Oshlack/splatter</a></p>
-
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='splatSimLibSizes.html'>splatSimLibSizes</a></code>, <code><a href='splatSimGeneMeans.html'>splatSimGeneMeans</a></code>,
@@ -247,11 +262,10 @@ sequencing data. Genome Biology (2017).</p>
<code><a href='splatSimDE.html'>splatSimDE</a></code>, <code><a href='splatSimCellMeans.html'>splatSimCellMeans</a></code>,
<code><a href='splatSimBCVMeans.html'>splatSimBCVMeans</a></code>, <code><a href='splatSimTrueCounts.html'>splatSimTrueCounts</a></code>,
<code><a href='splatSimDropout.html'>splatSimDropout</a></code></p></div>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Simulation with default parameters</span>
-<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><span class='co'># NOT RUN {</span>
+<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># Simulation with different number of genes</span>
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>)
<span class='co'># Simulation with custom parameters</span>
@@ -263,34 +277,30 @@ sequencing data. Genome Biology (2017).</p>
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"groups"</span>)
<span class='co'># Simulate paths</span>
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"paths"</span>)
-<span class='co'># }</span></pre>
+}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#see-also">See also</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -298,6 +308,8 @@ sequencing data. Genome Biology (2017).</p>
+
</body>
</html>
+
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
index 780d10b216c85c0511b5f8440fd598f93f8ff775..f36ada1d7abf1dbe02bb4b1eec9f777f1fa229b2 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>splatter. — splatter • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="splatter. — splatter" />
+<meta property="og:title" content="splatter. — splatter" />
<meta property="og:description" content="splatter is a package for the well-documented and reproducible
simulation of single-cell RNA-seq count data." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ simulation of single-cell RNA-seq count data." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ simulation of single-cell RNA-seq count data." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ simulation of single-cell RNA-seq count data." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ simulation of single-cell RNA-seq count data." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ simulation of single-cell RNA-seq count data." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,44 +142,40 @@ simulation of single-cell RNA-seq count data." />
</div>
<div class="ref-description">
-
<p><span class="pkg">splatter</span> is a package for the well-documented and reproducible
simulation of single-cell RNA-seq count data.</p>
-
</div>
-
+
+
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>As well as it's own simulation model <span class="pkg">splatter</span> provides functions for
the estimation of model parameters.</p>
-
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA
Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p></div>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#details">Details</a></li>
-
<li><a href="#see-also">See also</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -167,6 +183,8 @@ Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p></div>
+
</body>
</html>
+
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index eec87084e1f4c9a97037ba59bc03b27499e153f1..841f0d7628b386b25342c5c833e77deaa3a0511a 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -1,28 +1,32 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Summarise diffSCESs — summariseDiff • Splatter</title>
+<title>Summarise diffSCEs — summariseDiff • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,17 +36,20 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Summarise diffSCESs — summariseDiff" />
+<meta property="og:title" content="Summarise diffSCEs — summariseDiff" />
<meta property="og:description" content="Summarise the results of diffSCEs. Calculates the Median
-Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
-Error (RMSE) for the various properties and ranks them." />
+Absolute Deviation (MAD), Mean Absolute Error (MAE), Root Mean Squared
+Error (RMSE) and Kolmogorov-Smirnov (KS) statistics for the various
+properties and ranks them." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -60,6 +67,7 @@ Error (RMSE) for the various properties and ranks them." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -68,14 +76,15 @@ Error (RMSE) for the various properties and ranks them." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -83,7 +92,7 @@ Error (RMSE) for the various properties and ranks them." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -93,15 +102,26 @@ Error (RMSE) for the various properties and ranks them." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -112,26 +132,26 @@ Error (RMSE) for the various properties and ranks them." />
</div><!--/.navbar -->
+
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Summarise diffSCESs</h1>
+ <h1>Summarise diffSCEs</h1>
<small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
<div class="hidden name"><code>summariseDiff.Rd</code></div>
</div>
<div class="ref-description">
-
<p>Summarise the results of <code><a href='diffSCEs.html'>diffSCEs</a></code>. Calculates the Median
-Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
-Error (RMSE) for the various properties and ranks them.</p>
-
+Absolute Deviation (MAD), Mean Absolute Error (MAE), Root Mean Squared
+Error (RMSE) and Kolmogorov-Smirnov (KS) statistics for the various
+properties and ranks them.</p>
</div>
<pre class="usage"><span class='fu'>summariseDiff</span>(<span class='no'>diff</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -140,51 +160,48 @@ Error (RMSE) for the various properties and ranks them.</p>
<td><p>Output from <code><a href='diffSCEs.html'>diffSCEs</a></code></p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>data.frame with MADs, MAEs, RMSEs, scaled statistics and ranks</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
-<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
-#> 1 Splat Mean 2.623408 NaN 1 2.659195 NaN
-#> 2 Splat Variance 11.848783 NaN 1 10.505147 NaN
-#> 3 Splat ZerosGene 40.000000 NaN 1 44.110000 NaN
-#> 4 Splat MeanVar 11.400920 NaN 1 12.415584 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 43.945000 NaN
-#> 6 Splat LibSize 55997.500000 NaN 1 56484.550000 NaN
-#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.21666 NaN 1
-#> 2 1 13.21816 NaN 1
-#> 3 1 47.71111 NaN 1
-#> 4 1 15.39405 NaN 1
-#> 5 1 53.33878 NaN 1
-#> 6 1 57530.14610 NaN 1</div></pre>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
+<span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
+#> 1 Splat Mean 2.599964 NaN 1 2.584928 NaN
+#> 2 Splat Variance 11.322961 NaN 1 10.470554 NaN
+#> 3 Splat ZerosGene 40.000000 NaN 1 44.310000 NaN
+#> 4 Splat MeanVar 11.115835 NaN 1 12.455595 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 43.525000 NaN
+#> 6 Splat LibSize 57856.500000 NaN 1 59396.950000 NaN
+#> MAERank RMSE RMSEScaled RMSERank KS KSPVal KSRank
+#> 1 1 3.128422 NaN 1 0.361 0.000000e+00 1
+#> 2 1 13.481762 NaN 1 0.557 0.000000e+00 1
+#> 3 1 48.107692 NaN 1 0.574 0.000000e+00 1
+#> 4 1 15.692918 NaN 1 NA NA NA
+#> 5 1 53.139674 NaN 1 NA NA NA
+#> 6 1 60130.247902 NaN 1 1.000 1.450928e-11 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -192,6 +209,8 @@ Error (RMSE) for the various properties and ranks them.</p>
+
</body>
</html>
+
diff --git a/docs/reference/summariseKS.html b/docs/reference/summariseKS.html
new file mode 100644
index 0000000000000000000000000000000000000000..9aab82fc877b85f2e9f51f24feb9d2cd07efdfd0
--- /dev/null
+++ b/docs/reference/summariseKS.html
@@ -0,0 +1,205 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Summarise KS — summariseKS • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Summarise KS — summariseKS" />
+<meta property="og:description" content="Summarise columns of a data.frame compared to a reference using the KS test." />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Summarise KS</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>summariseKS.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Summarise columns of a data.frame compared to a reference using the KS test.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>summariseKS</span>(<span class='no'>data</span>, <span class='no'>ref</span>, <span class='no'>split.col</span>, <span class='no'>stat.cols</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>data</th>
+ <td><p>The data.frame to summarise</p></td>
+ </tr>
+ <tr>
+ <th>ref</th>
+ <td><p>The reference data.frame</p></td>
+ </tr>
+ <tr>
+ <th>split.col</th>
+ <td><p>Name of the column used to split the dataset</p></td>
+ </tr>
+ <tr>
+ <th>stat.cols</th>
+ <td><p>Names of the columns to summarise. If this vector is named
+those names will be used in the output.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>data.frame with the summarised measure, scaled and ranked</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/summariseStats.html b/docs/reference/summariseStats.html
new file mode 100644
index 0000000000000000000000000000000000000000..33cc0a8b61ef9a6ce1fea985aac3a59764487704
--- /dev/null
+++ b/docs/reference/summariseStats.html
@@ -0,0 +1,206 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Summarise statistics — summariseStats • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Summarise statistics — summariseStats" />
+<meta property="og:description" content="Summarise columns of a data.frame using a single measure." />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Summarise statistics</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>summariseStats.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Summarise columns of a data.frame using a single measure.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>summariseStats</span>(<span class='no'>data</span>, <span class='no'>split.col</span>, <span class='no'>stat.cols</span>, <span class='kw'>measure</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"MAD"</span>, <span class='st'>"MAE"</span>,
+ <span class='st'>"RMSE"</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>data</th>
+ <td><p>The data.frame to summarise</p></td>
+ </tr>
+ <tr>
+ <th>split.col</th>
+ <td><p>Name of the column used to split the dataset</p></td>
+ </tr>
+ <tr>
+ <th>stat.cols</th>
+ <td><p>Names of the columns to summarise. If this vector is named
+those names will be used in the output.</p></td>
+ </tr>
+ <tr>
+ <th>measure</th>
+ <td><p>The measure to use for summarisation.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>data.frame with the summarised measure, scaled and ranked</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/tidyStatSumm.html b/docs/reference/tidyStatSumm.html
new file mode 100644
index 0000000000000000000000000000000000000000..375ee92915c448f593942cd9f4c3da72138ddcf7
--- /dev/null
+++ b/docs/reference/tidyStatSumm.html
@@ -0,0 +1,196 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Tidy summarised statistics — tidyStatSumm • Splatter</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+
+<meta property="og:title" content="Tidy summarised statistics — tidyStatSumm" />
+<meta property="og:description" content="Convert a statistic summary to tidy format and add ranks and scaled values" />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
+<script>
+ window.dataLayer = window.dataLayer || [];
+ function gtag(){dataLayer.push(arguments);}
+ gtag('js', new Date());
+
+ gtag('config', 'UA-52309538-4');
+</script>
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">Splatter</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fas fa fas fa-home fa-lg"></span>
+
+ </a>
+</li>
+<li>
+ <a href="../articles/splatter.html">Get started</a>
+</li>
+<li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <a href="https://github.com/Oshlack/splatter">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Tidy summarised statistics</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/compare.R'><code>R/compare.R</code></a></small>
+ <div class="hidden name"><code>tidyStatSumm.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Convert a statistic summary to tidy format and add ranks and scaled values</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>tidyStatSumm</span>(<span class='no'>stat.summ</span>, <span class='kw'>measure</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"MAD"</span>, <span class='st'>"MAE"</span>, <span class='st'>"RMSE"</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>stat.summ</th>
+ <td><p>The summary to convert</p></td>
+ </tr>
+ <tr>
+ <th>measure</th>
+ <td><p>The name of the summarisation measure</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>tidy data.frame with the summarised measure, scaled and ranked</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index ad3548cb5e3d7f4613be0539de95c4acf7846208..88d989c74485af377ba52e0b20667775b6074124 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Winsorize vector — winsorize • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Winsorize vector — winsorize" />
+<meta property="og:title" content="Winsorize vector — winsorize" />
<meta property="og:description" content="Set outliers in a numeric vector to a specified percentile." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Set outliers in a numeric vector to a specified percentile.</p>
-
</div>
<pre class="usage"><span class='fu'>winsorize</span>(<span class='no'>x</span>, <span class='no'>q</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -140,31 +158,30 @@
<td><p>Percentile to set from each end</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Winsorized numeric vector</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -172,6 +189,8 @@
+
</body>
</html>
+
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 47f4a54d1e446d936938e8183452bc370d07e286..8eaa6e888d68e98215cc88634c2b8ce2e0d2cf1d 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>Estimate ZINB-WaVE simulation parameters — zinbEstimate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,16 +36,18 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Estimate ZINB-WaVE simulation parameters — zinbEstimate" />
+<meta property="og:title" content="Estimate ZINB-WaVE simulation parameters — zinbEstimate" />
<meta property="og:description" content="Estimate simulation parameters for the ZINB-WaVE simulation from a real
dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,6 +65,7 @@ dataset." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -67,14 +74,15 @@ dataset." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -82,7 +90,7 @@ dataset." />
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -92,15 +100,26 @@ dataset." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -111,6 +130,7 @@ dataset." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -122,10 +142,8 @@ dataset." />
</div>
<div class="ref-description">
-
<p>Estimate simulation parameters for the ZINB-WaVE simulation from a real
dataset.</p>
-
</div>
<pre class="usage"><span class='fu'>zinbEstimate</span>(<span class='no'>counts</span>, <span class='kw'>design.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
@@ -145,7 +163,7 @@ dataset.</p>
<span class='kw'>design.genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>common.disp</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>iter.init</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>iter.opt</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>stop.opt</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(),
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>(), <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -169,7 +187,7 @@ features is estimated.</p></td>
</tr>
<tr>
<th>iter.init</th>
- <td><p>number of iterations to use for initalization.</p></td>
+ <td><p>number of iterations to use for initialization.</p></td>
</tr>
<tr>
<th>iter.opt</th>
@@ -195,54 +213,101 @@ single core.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>additional arguments passes to <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code>.</p></td>
+ <td><p>additional arguments passes to <code><a href='https://rdrr.io/pkg/zinbwave/man/zinbFit.html'>zinbFit</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>ZINBParams object containing the estimated parameters.</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>The function is a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> that takes
+ <p>The function is a wrapper around <code><a href='https://rdrr.io/pkg/zinbwave/man/zinbFit.html'>zinbFit</a></code> that takes
the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParams</a></code> object. See
<code><a href='ZINBParams.html'>ZINBParams</a></code> for more details on the parameters and
-<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> for details of the estimation procedure.</p>
-
+<code><a href='https://rdrr.io/pkg/zinbwave/man/zinbFit.html'>zinbFit</a></code> for details of the estimation procedure.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>zinbEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span>
-<span class='co'># }</span></pre>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"zinbwave"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>scater</span>)
+ <span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span>(<span class='fl'>1</span>)
+ <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/scater/man/mockSCE.html'>mockSCE</a></span>(<span class='kw'>ncells</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>ngenes</span> <span class='kw'>=</span> <span class='fl'>100</span>)
+
+ <span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>zinbEstimate</span>(<span class='no'>sce</span>)
+ <span class='no'>params</span>
+}</div><div class='output co'>#> <span class='message'>Removing all zero genes...</span></div><div class='output co'>#> <span class='message'>Fitting model...</span></div><div class='output co'>#> <span class='message'>Create model:</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> <span class='message'>Initialize parameters:</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> <span class='message'>Optimize parameters:</span></div><div class='output co'>#> <span class='message'>Iteration 1</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -9797.17396398215</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -9593.51924068794</span></div><div class='output co'>#> user system elapsed
+#> 0.279 0.008 0.292 </div><div class='output co'>#> <span class='message'>After right optimization = -9289.80824341391</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -9289.80824341391</span></div><div class='output co'>#> user system elapsed
+#> 0.045 0.003 0.048 </div><div class='output co'>#> <span class='message'>After left optimization = -9285.37100307917</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -9285.37100307917</span></div><div class='output co'>#> <span class='message'>Iteration 2</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -9285.37100307917</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -9235.11865883047</span></div><div class='output co'>#> user system elapsed
+#> 0.206 0.005 0.216 </div><div class='output co'>#> <span class='message'>After right optimization = -9229.79015780275</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -9229.79015780275</span></div><div class='output co'>#> user system elapsed
+#> 0.068 0.006 0.075 </div><div class='output co'>#> <span class='message'>After left optimization = -9229.25013725032</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -9229.25013725032</span></div><div class='output co'>#> <span class='message'>Iteration 3</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -9229.25013725032</span></div><div class='output co'>#> <span class='message'>After dispersion optimization = -9228.6543711739</span></div><div class='output co'>#> user system elapsed
+#> 0.192 0.005 0.203 </div><div class='output co'>#> <span class='message'>After right optimization = -9228.44378457059</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -9228.44378457059</span></div><div class='output co'>#> user system elapsed
+#> 0.041 0.002 0.043 </div><div class='output co'>#> <span class='message'>After left optimization = -9228.40710924322</span></div><div class='output co'>#> <span class='message'>After orthogonalization = -9228.40710924322</span></div><div class='output co'>#> <span class='message'>Iteration 4</span></div><div class='output co'>#> <span class='message'>penalized log-likelihood = -9228.40710924322</span></div><div class='output co'>#> <span class='message'>ok</span></div><div class='output co'>#> A Params object of class ZINBParams
+#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+#> Secondary parameters are usually set during simulation
+#>
+#> Global:
+#> (Genes) (CELLS) [Seed]
+#> 100 20 955861
+#>
+#> 1 additional parameters
+#>
+#> Model:
+#> ZinbModel with 100 features, 20 samples, 0 latent factors and 241 parameters
+#>
+#> Parameters of the ZinbModel
+#>
+#> Model Design:
+#> (SAMPLES) (Genes)
+#> 1, 1, 1, 1,... 1, 1, 1, 1,...
+#>
+#> Model Offsets:
+#> (MU) (PI)
+#> 20 x 100 matrix 20 x 100 matrix
+#>
+#> Model Indices:
+#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
+#> 1 1 1 1
+#>
+#> Model Intercepts:
+#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
+#> TRUE TRUE TRUE TRUE
+#>
+#> Model Latent factors:
+#> (W)
+#> 20 x 0 matrix
+#>
+#> Model Coefficients:
+#> (SAMPLE MU) (GENE MU) (Latent Mu) (SAMPLE PI) (GENE PI) (Latent Pi)
+#> -0.459768269108686, 1.62119422809804, -0.223102757788152, 0.0429479357333727,... 4.26299872242102, 4.29178871361806, 4.44953744138558, 3.86260697728158,... 0 x 100 matrix 1.90228646100659, -6.94249109253294, -1.07943871883735, -0.430729773518204,... -0.983749678057473, -1.35076635474983, -1.23286376482938, -1.26061065393089,... 0 x 100 matrix
+#>
+#> Model Regularisation:
+#> (Sample Mu) (GENE MU) (Sample Pi) (GENE PI)
+#> 1 5 1 5
+#> (LATENT) (Latent coeffs) (Zeta) (Logit)
+#> 5 1 100 0.001
+#> </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -250,6 +315,8 @@ the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParam
+
</body>
</html>
+
diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
index f75ed36cbf8daef9071b29d9580ac2c0dddddb62..e0b3919a918347769eac4f0431f53e7c14363608 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -8,21 +8,25 @@
<title>ZINB-WaVE simulation — zinbSimulate • Splatter</title>
+
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@@ -32,15 +36,17 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="ZINB-WaVE simulation — zinbSimulate" />
+<meta property="og:title" content="ZINB-WaVE simulation — zinbSimulate" />
<meta property="og:description" content="Simulate counts using the ZINB-WaVE method." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -58,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -66,14 +73,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -81,7 +89,7 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
- <span class="fa fa-home fa-lg"></span>
+ <span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
@@ -91,15 +99,26 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/Oshlack/splatter">
- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
@@ -110,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -121,13 +141,11 @@
</div>
<div class="ref-description">
-
<p>Simulate counts using the ZINB-WaVE method.</p>
-
</div>
<pre class="usage"><span class='fu'>zinbSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newZINBParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -145,19 +163,17 @@
<code>params</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>SingleCellExperiment containing simulated counts</p>
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://rdrr.io/pkg/zinbwave/man/zinbSim.html'>zinbSim</a></code> that
takes a <code><a href='ZINBParams.html'>ZINBParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> and the ZINB-WaVE paper for
+output to a <code><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></code> object.
+See <code><a href='https://rdrr.io/pkg/zinbwave/man/zinbSim.html'>zinbSim</a></code> and the ZINB-WaVE paper for
more details about how the simulation works.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
@@ -168,36 +184,34 @@ and flexible method for signal extraction from single-cell RNA-seq data
bioRxiv (2017).</p>
<p>Paper: <a href='10.1101/125112'>10.1101/125112</a></p>
<p>Code: <a href='https://github.com/drisso/zinbwave'>https://github.com/drisso/zinbwave</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>zinbSimulate</span>()</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'>
+ <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span>(<span class='st'>"zinbwave"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) {
+ <span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>zinbSimulate</span>()
+}</div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
+
<footer>
<div class="copyright">
<p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
@@ -205,6 +219,8 @@ bioRxiv (2017).</p>
+
</body>
</html>
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index aa9d8d203d73e2543e4af1799371052490904b10..d7457b5c10a9627ddae21b2cc7fece4afb01e64c 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -12,6 +12,9 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/BASiCSSimulate.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/KersplatParams.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/Lun2Params.html</loc>
</url>
@@ -51,6 +54,9 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/bridge.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/bringItemsForward.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/compareSCEs.html</loc>
</url>
@@ -60,6 +66,9 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/expandParams.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/getBetaStepProbs.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/getLNormFactors.html</loc>
</url>
@@ -72,6 +81,54 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/getPathOrder.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatEstBCV.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatEstLib.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatEstMean.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatEstimate.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatGenNetwork.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSample.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSelectRegs.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSetup.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimAmbientCounts.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimCellCounts.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimCellMeans.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimCounts.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimGeneMeans.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimLibSizes.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimPaths.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/kersplatSimulate.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/listSims.html</loc>
</url>
@@ -117,12 +174,18 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/rbindMatched.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/sampleDensity.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/scDDEstimate.html</loc>
</url>
<url>
<loc>http://oshlack.github.io/splatter/reference/scDDSimulate.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/selectFit.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/setParam.html</loc>
</url>
@@ -210,6 +273,15 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/summariseDiff.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/summariseKS.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/summariseStats.html</loc>
+ </url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/tidyStatSumm.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/winsorize.html</loc>
</url>
@@ -219,6 +291,9 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/zinbSimulate.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/articles/splat_params.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/articles/splatter.html</loc>
</url>
diff --git a/index.md b/index.md
index b6419effa352d13587d7ce0a7bb6e69d950d6d1e..39bfbe1e0d8123ee6feecb7b246330571c0e5bc6 100644
--- a/index.md
+++ b/index.md
@@ -5,7 +5,7 @@
[](https://bioconductor.org/packages/devel/bioc/html/splatter.html)
[](https://bioconductor.org/packages/devel/bioc/html/splatter.html)
-
+
Splatter is an R package for the simple simulation of single-cell RNA sequencing
data. Splatter provides a common interface to multiple simulations that have:
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index b43862c6092f087996a77f7134806fe2df05ec25..39facd952f2bf5a52bdfc88bf61310d5e146b6fd 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,6 +1,17 @@
\name{NEWS}
\title{News for Package \pkg{splatter}}
+\section{Version 1.8.0, Bioconductor 3.9 Release (2018-04-18)}{
+ \itemize{
+ \item{Add a Splat parameters vignette}
+ \item{Rename the Splat path.length parameter to path.nSteps}
+ \item{Fix a bug with parameter order in setParams}
+ \item{Fix a bug where Splat groups were being simulated in alphanumeric
+ order}
+ \item{Protect against integer overflow in simulation functions}
+ }
+}
+
\section{Version 1.6.0, Bioconductor 3.8 Release (2018-10-29)}{
\itemize{
\item{Fix bug and improve normality testing in splatEstLib}
diff --git a/inst/WORDLIST b/inst/WORDLIST
new file mode 100644
index 0000000000000000000000000000000000000000..8c3439ae0093d36e1e09b40f8269d19a600e84af
--- /dev/null
+++ b/inst/WORDLIST
@@ -0,0 +1,138 @@
+addFeatureStats
+addGeneLengths
+analyzers
+AppVeyor
+BASiCS
+BASiCSEstimate
+BASiCSParams
+BASiCSSimulate
+bcv
+BCV
+Bioc
+Biocondutor
+biocViews
+bioRxiv
+BPPARAM
+Chu
+compareSCEs
+compareSCESets
+cpm
+cutoff
+df
+diffSCEs
+diffSCESets
+DM
+doi
+DP
+Dudoit
+EE
+eg
+etc
+fpkm
+FPKM
+gam
+getLNormFactors
+Github
+Gribkova
+ImmunoOncology
+ingroup
+JC
+KD
+Kersplat
+KersplatParams
+Korthauer
+KR
+len
+Lifecycle
+listSims
+loProb
+lun
+Lun
+LunParams
+lunSimulate
+MADs
+MAEs
+Marioni
+meanlog
+MeanZeros
+mfa
+MFA
+MFAParams
+mfaSimulate
+mockSCE
+modeling
+nGenes
+nGroups
+NOTEs
+params
+Params
+Parra
+Perraudeau
+PhenoParams
+PhenoPath
+PLoS
+poisson
+Poisson
+PROSSTT
+pseudotime
+Quickstart
+RG
+Risso
+RMSEs
+Roxygen
+RStudio
+RStudio's
+sc
+scater
+scDD
+SCDD
+scDDEstimate
+SCDDParams
+scDDSimulate
+SCE
+SCESets
+scRNA
+sd
+sdlog
+selectFit
+seq
+SimpleParams
+SingleCellExperiment
+SingleCellExperiments
+SNE
+Söding
+SparseDC
+sparseDCEstimate
+SparseDCParams
+SparseParams
+splatEstimate
+splatEstLib
+splatParams
+SplatParams
+splatSimulate
+splatSimulatePaths
+Splatter's
+splotchEstimate
+SplotchParams
+splotchSimulate
+summariseDiff
+SummarizedExperiment
+th
+thining
+tpm
+TPM
+UMAP
+UpperCamelCase
+Vallejos
+WaVE
+Wellcome
+Wilks
+winsorize
+Winsorize
+winsorized
+Winsorized
+WithSpikes
+Yau
+ZINB
+ZINBParams
+zinbwave
diff --git a/man/BASiCSEstimate.Rd b/man/BASiCSEstimate.Rd
index b7d28f782a8c97c1c79b5f2b22ad5d608a518f59..c06c7fb099186293aa733625c87e93d1660b8210 100644
--- a/man/BASiCSEstimate.Rd
+++ b/man/BASiCSEstimate.Rd
@@ -68,13 +68,13 @@ information is provided there must be at least two batches. See
\dontrun{
# Load example data
library(scater)
-data("sc_example_counts")
+set.seed(1)
+sce <- mockSCE()
-spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
+spike.info <- data.frame(Name = rownames(sce)[1:10],
Input = rnorm(10, 500, 200),
stringsAsFactors = FALSE)
-params <- BASiCSEstimate(sc_example_counts[1:100, 1:30],
- spike.info)
+params <- BASiCSEstimate(sce[1:100, 1:30], spike.info)
params
}
}
diff --git a/man/BASiCSParams.Rd b/man/BASiCSParams.Rd
index 0bfb09a000d4d203dedf0eb6e7f73e5161080802..852e5d15b03d2a83f0583f17abdce4d1809145f3 100644
--- a/man/BASiCSParams.Rd
+++ b/man/BASiCSParams.Rd
@@ -25,7 +25,7 @@ The BASiCS simulation uses the following parameters:
\item{\emph{Gene parameters}}{
\describe{
\item{\code{gene.params}}{A \code{data.frame} containing gene
- parameters with two coloumns: \code{Mean} (mean expression for
+ parameters with two columns: \code{Mean} (mean expression for
each biological gene) and \code{Delta} (cell-to-cell
heterogeneity for each biological gene).}
}
@@ -39,7 +39,7 @@ The BASiCS simulation uses the following parameters:
\item{\emph{Cell parameters}}{
\describe{
\item{\code{cell.params}}{A \code{data.frame} containing gene
- parameters with two coloumns: \code{Phi} (mRNA content factor for
+ parameters with two columns: \code{Phi} (mRNA content factor for
each cell, scaled to sum to the number of cells in each batch)
and \code{S} (capture efficient for each cell).}
}
diff --git a/man/BASiCSSimulate.Rd b/man/BASiCSSimulate.Rd
index 9a26e0d14e88a7cd42945651af0a26f882999ea4..acdfb16115cf167fa2b7f07daf06206e8ed2ac2d 100644
--- a/man/BASiCSSimulate.Rd
+++ b/man/BASiCSSimulate.Rd
@@ -28,11 +28,13 @@ See \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
works.
}
\examples{
-sim <- BASiCSSimulate()
+if (requireNamespace("BASiCS", quietly = TRUE)) {
+ sim <- BASiCSSimulate()
+}
}
\references{
Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
-Single-Cell Sequencing data. PLoS Comput. Biol. (2015).
+Single-Cell Sequencing data. PLoS Computational Biology (2015).
Paper: \url{10.1371/journal.pcbi.1004333}
diff --git a/man/KersplatParams.Rd b/man/KersplatParams.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..3aaf411ceb3ace4443785ddd2e56d5124041c0c3
--- /dev/null
+++ b/man/KersplatParams.Rd
@@ -0,0 +1,105 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R
+\docType{class}
+\name{KersplatParams}
+\alias{KersplatParams}
+\alias{KersplatParams-class}
+\title{The KersplatParams class}
+\description{
+S4 class that holds parameters for the Kersplat simulation.
+}
+\section{Parameters}{
+
+
+The Kersplat simulation uses the following parameters:
+
+\describe{
+ \item{\code{nGenes}}{The number of genes to simulate.}
+ \item{\code{nCells}}{The number of cells to simulate.}
+ \item{\code{[seed]}}{Seed to use for generating random numbers.}
+ \item{\emph{Mean parameters}}{
+ \describe{
+ \item{\code{mean.shape}}{Shape parameter for the mean gamma
+ distribution.}
+ \item{\code{mean.rate}}{Rate parameter for the mean gamma
+ distribution.}
+ \item{\code{mean.outProb}}{Probability that a gene is an
+ expression outlier.}
+ \item{\code{mean.outFacLoc}}{Location (meanlog) parameter for
+ the expression outlier factor log-normal distribution.}
+ \item{\code{mean.outFacScale}}{Scale (sdlog) parameter for the
+ expression outlier factor log-normal distribution.}
+ \item{\code{mean.dens}}{\code{\link{density}} object describing
+ the log gene mean density.}
+ \item{\code{[mean.method]}}{Method to use for simulating gene
+ means. Either "fit" to sample from a gamma distribution (with
+ expression outliers) or "density" to sample from the provided
+ density object.}
+ \item{\code{[mean.values]}}{Vector of means for each gene.}
+ }
+ }
+ \item{\emph{Biological Coefficient of Variation parameters}}{
+ \describe{
+ \item{\code{bcv.common}}{Underlying common dispersion across all
+ genes.}
+ \item{\code{[bcv.df]}}{Degrees of Freedom for the BCV inverse
+ chi-squared distribution.}
+ }
+ }
+ \item{\emph{Network parameters}}{
+ \describe{
+ \item{\code{[network.graph]}}{Graph containing the gene network.}
+ \item{\code{[network.nRegs]}}{Number of regulators in the
+ network.}
+ }
+ }
+ \item{\emph{Paths parameters}}{
+ \describe{
+ \item{\code{[paths.programs]}}{Number of expression programs.}
+ \item{\code{[paths.design]}}{data.frame describing path
+ structure. See \code{\link{kersplatSimPaths}} for details.}
+ }
+ }
+ \item{\emph{Library size parameters}}{
+ \describe{
+ \item{\code{lib.loc}}{Location (meanlog) parameter for the
+ library size log-normal distribution, or mean parameter if a
+ normal distribution is used.}
+ \item{\code{lib.scale}}{Scale (sdlog) parameter for the library
+ size log-normal distribution, or sd parameter if a normal
+ distribution is used.}
+ \item{\code{lib.dens}}{\code{\link{density}} object describing
+ the library size density.}
+ \item{\code{[lib.method]}}{Method to use for simulating library
+ sizes. Either "fit" to sample from a log-normal distribution or
+ "density" to sample from the provided density object.}
+ }
+ }
+ \item{\emph{Design parameters}}{
+ \describe{
+ \item{\code{[cells.design]}}{data.frame describing cell
+ structure. See \code{\link{kersplatSimCellMeans}} for details.}
+ }
+ }
+ \item{\emph{Doublet parameters}}{
+ \describe{
+ \item{\code{[doublet.prop]}}{Proportion of cells that are
+ doublets.}
+ }
+ }
+ \item{\emph{Ambient parameters}}{
+ \describe{
+ \item{\code{[ambient.scale]}}{Scaling factor for the library
+ size log-normal distribution when generating ambient library
+ sizes.}
+ \item{\code{[ambient.nEmpty]}}{Number of empty cells to
+ simulate.}
+ }
+ }
+}
+
+The parameters not shown in brackets can be estimated from real data using
+\code{\link{kersplatEstimate}}. For details of the Kersplat simulation
+see \code{\link{kersplatSimulate}}.
+}
+
diff --git a/man/Lun2Params.Rd b/man/Lun2Params.Rd
index db97ba60ce719bf195a30172f9ae3b870fa2cb68..260bb5fbd1496c992a7d7575f0e99cd6eb389166 100644
--- a/man/Lun2Params.Rd
+++ b/man/Lun2Params.Rd
@@ -20,10 +20,10 @@ The Lun2 simulation uses the following parameters:
\item{\emph{Gene parameters}}{
\describe{
\item{\code{gene.params}}{A \code{data.frame} containing gene
- parameters with two coloumns: \code{Mean} (mean expression for
+ parameters with two columns: \code{Mean} (mean expression for
each gene) and \code{Disp} (dispersion for each gene).}
\item{\code{zi.params}}{A \code{data.frame} containing
- zero-inflated gene parameters with three coloumns: \code{Mean}
+ zero-inflated gene parameters with three columns: \code{Mean}
(mean expression for each gene), \code{Disp} (dispersion for
each, gene), and \code{Prop} (zero proportion for each gene).}
}
@@ -31,7 +31,7 @@ The Lun2 simulation uses the following parameters:
\item{\code{[nPlates]}}{The number of plates to simulate.}
\item{\emph{Plate parameters}}{
\describe{
- \item{\code{plate.ingroup}}{Character vecotor giving the plates
+ \item{\code{plate.ingroup}}{Character vector giving the plates
considered to be part of the "ingroup".}
\item{\code{plate.mod}}{Plate effect modifier factor. The plate
effect variance is divided by this value.}
diff --git a/man/SplatParams.Rd b/man/SplatParams.Rd
index fbd581d43994495630cf5fe84bd32ce32b79f350..f2954c507114419c5e44aa5fe830b564e8b7b3fd 100644
--- a/man/SplatParams.Rd
+++ b/man/SplatParams.Rd
@@ -6,12 +6,12 @@
\alias{SplatParams-class}
\title{The SplatParams class}
\description{
-S4 class that holds parameters for the Splatter simulation.
+S4 class that holds parameters for the Splat simulation.
}
\section{Parameters}{
-The Splatter simulation requires the following parameters:
+The Splat simulation requires the following parameters:
\describe{
\item{\code{nGenes}}{The number of genes to simulate.}
@@ -70,7 +70,7 @@ The Splatter simulation requires the following parameters:
\describe{
\item{\code{[de.prob]}}{Probability that a gene is differentially
expressed in a group. Can be a vector.}
- \item{\code{[de.loProb]}}{Probability that a differentially
+ \item{\code{[de.downProb]}}{Probability that a differentially
expressed gene is down-regulated. Can be a vector.}
\item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
differential expression factor log-normal distribution. Can be a
@@ -111,9 +111,10 @@ The Splatter simulation requires the following parameters:
this form would have a "from" parameter of c(0, 1, 1) (where 0 is
the origin). If no vector is given all paths will start at the
origin.}
- \item{\code{[path.length]}}{Vector giving the number of steps to
+ \item{\code{[path.nSteps]}}{Vector giving the number of steps to
simulate along each path. If a single value is given it will be
- applied to all paths.}
+ applied to all paths. This parameter was previously called
+ \code{path.length}.}
\item{\code{[path.skew]}}{Vector giving the skew of each path.
Values closer to 1 will give more cells towards the starting
population, values closer to 0 will give more cells towards the
@@ -132,7 +133,7 @@ The Splatter simulation requires the following parameters:
}
The parameters not shown in brackets can be estimated from real data using
-\code{\link{splatEstimate}}. For details of the Splatter simulation
+\code{\link{splatEstimate}}. For details of the Splat simulation
see \code{\link{splatSimulate}}.
}
diff --git a/man/bringItemsForward.Rd b/man/bringItemsForward.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..92d0c8d26c0bf96ef4f7e28a90945b595b39d13a
--- /dev/null
+++ b/man/bringItemsForward.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{bringItemsForward}
+\alias{bringItemsForward}
+\title{Bring items forward}
+\usage{
+bringItemsForward(ll, items)
+}
+\arguments{
+\item{ll}{list to adjust item order.}
+
+\item{items}{vector of items to bring to the front. Any not in the list will
+be ignored.}
+}
+\value{
+list with selected items first
+}
+\description{
+Move selected items to the start of a list.
+}
diff --git a/man/compareSCEs.Rd b/man/compareSCEs.Rd
index 711a2bee5edcc810c0834dad862b2303bd03c58c..db1f4d798ee236d6e24c58b106fb38be316a9483 100644
--- a/man/compareSCEs.Rd
+++ b/man/compareSCEs.Rd
@@ -30,9 +30,9 @@ basic plots comparing them.
The returned list has three items:
\describe{
- \item{\code{FeatureData}}{Combined feature data from the provided
+ \item{\code{RowData}}{Combined row data from the provided
SingleCellExperiments.}
- \item{\code{PhenoData}}{Combined pheno data from the provided
+ \item{\code{ColData}}{Combined column data from the provided
SingleCellExperiments.}
\item{\code{Plots}}{Comparison plots
\describe{
@@ -40,7 +40,7 @@ The returned list has three items:
\item{\code{Variances}}{Boxplot of variance distribution.}
\item{\code{MeanVar}}{Scatter plot with fitted lines showing the
mean-variance relationship.}
- \item{\code{LibraySizes}}{Boxplot of the library size
+ \item{\code{LibrarySizes}}{Boxplot of the library size
distribution.}
\item{\code{ZerosGene}}{Boxplot of the percentage of each gene
that is zero.}
@@ -48,6 +48,8 @@ The returned list has three items:
that is zero.}
\item{\code{MeanZeros}}{Scatter plot with fitted lines showing
the mean-zeros relationship.}
+ \item{\code{VarGeneCor}}{Heatmap of correlation of the 100 most
+ variable genes.}
}
}
}
diff --git a/man/diffSCEs.Rd b/man/diffSCEs.Rd
index a24a5c28f095a7318c6eae93b42f5d00ddd60e26..97cb53bbf1fb22d06b5fb14435f0d835fc68d903 100644
--- a/man/diffSCEs.Rd
+++ b/man/diffSCEs.Rd
@@ -41,9 +41,9 @@ The returned list has five items:
\describe{
\item{\code{Reference}}{The SingleCellExperiment used as the reference.}
- \item{\code{FeatureData}}{Combined feature data from the provided
+ \item{\code{RowData}}{Combined feature data from the provided
SingleCellExperiments.}
- \item{\code{PhenoData}}{Combined pheno data from the provided
+ \item{\code{ColData}}{Combined column data from the provided
SingleCellExperiments.}
\item{\code{Plots}}{Difference plots
\describe{
@@ -51,7 +51,7 @@ The returned list has five items:
\item{\code{Variances}}{Boxplot of variance differences.}
\item{\code{MeanVar}}{Scatter plot showing the difference from
the reference variance across expression ranks.}
- \item{\code{LibraySizes}}{Boxplot of the library size
+ \item{\code{LibraeySizes}}{Boxplot of the library size
differences.}
\item{\code{ZerosGene}}{Boxplot of the differences in the
percentage of each gene that is zero.}
diff --git a/man/getBetaStepProbs.Rd b/man/getBetaStepProbs.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..0ce1ea1930e4a48bd2f36d9ea4b416d867aac037
--- /dev/null
+++ b/man/getBetaStepProbs.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{getBetaStepProbs}
+\alias{getBetaStepProbs}
+\title{Get Beta step probabilities}
+\usage{
+getBetaStepProbs(steps, alpha, beta)
+}
+\arguments{
+\item{steps}{Number of steps}
+
+\item{alpha}{Alpha parameter}
+
+\item{beta}{Beta parameter}
+}
+\value{
+Vector of probabilities
+}
+\description{
+Use a Beta distribution for set probabilities along a path
+}
+\details{
+The density is sampled from a Beta distribution between 0 and 1. Infinite
+densities at edges are adjusted and then the values are scaled to give
+probabilities.
+}
diff --git a/man/getCounts.Rd b/man/getCounts.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..4117bbd488f154decd0caef508d3a64d51e968a0
--- /dev/null
+++ b/man/getCounts.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SCE-functions.R
+\name{getCounts}
+\alias{getCounts}
+\title{Get counts}
+\usage{
+getCounts(sce)
+}
+\arguments{
+\item{sce}{}
+}
+\value{
+Counts matrix
+}
+\description{
+Get counts matrix from a SingleCellExperiment object. If counts is missing
+a warning is issued and the first assay is returned.
+}
diff --git a/man/getPathOrder.Rd b/man/getPathOrder.Rd
index 7d125e77ef9f75165b78d11c626f28a22efe13cd..8b4782f3337303c91f820eafaf0bd2be5762d0a0 100644
--- a/man/getPathOrder.Rd
+++ b/man/getPathOrder.Rd
@@ -7,7 +7,7 @@
getPathOrder(path.from)
}
\arguments{
-\item{path.from}{vector giving the path endpoints that each path orginates
+\item{path.from}{vector giving the path endpoints that each path originates
from.}
}
\value{
diff --git a/man/kersplatEstBCV.Rd b/man/kersplatEstBCV.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..58eab2941f1e9928ec2d24e3614bd74e20eeb38c
--- /dev/null
+++ b/man/kersplatEstBCV.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-estimate.R
+\name{kersplatEstBCV}
+\alias{kersplatEstBCV}
+\title{Estimate Kersplat BCV parameters}
+\usage{
+kersplatEstBCV(counts, params, verbose)
+}
+\arguments{
+\item{counts}{counts matrix.}
+
+\item{params}{KersplatParams object to store estimated values in.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with estimated BCV parameters
+}
+\description{
+Estimate Biological Coefficient of Variation (BCV) parameters for the
+Kersplat simulation
+}
+\details{
+The \code{\link[edgeR]{estimateDisp}} function is used to estimate the common
+dispersion across the dataset. An exponential correction is applied based on
+fitting an exponential relationship between simulated and estimated values.
+If this results in a negative dispersion a simpler linear correction is
+applied instead.
+}
diff --git a/man/kersplatEstLib.Rd b/man/kersplatEstLib.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..34ca4c88e5536e4ecbab624ef822b1a9d03134f7
--- /dev/null
+++ b/man/kersplatEstLib.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-estimate.R
+\name{kersplatEstLib}
+\alias{kersplatEstLib}
+\title{Estimate Kersplat library size parameters}
+\usage{
+kersplatEstLib(counts, params, verbose)
+}
+\arguments{
+\item{counts}{counts matrix.}
+
+\item{params}{KersplatParams object to store estimated values in.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with library size parameters
+}
+\description{
+Estimate the library size parameters for the Kersplat simulation
+}
+\details{
+Parameters for the log-normal distribution are estimated by fitting the
+library sizes using \code{\link[fitdistrplus]{fitdist}}. All the fitting
+methods are tried and the fit with the best Cramer-von Mises statistic is
+selected. The density of the library sizes is also estimated using
+\code{\link[stats]{density}}.
+}
diff --git a/man/kersplatEstMean.Rd b/man/kersplatEstMean.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f81b31cb66db56f895015f6f525d0217e9384fb5
--- /dev/null
+++ b/man/kersplatEstMean.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-estimate.R
+\name{kersplatEstMean}
+\alias{kersplatEstMean}
+\title{Estimate Kersplat means}
+\usage{
+kersplatEstMean(norm.counts, params, verbose)
+}
+\arguments{
+\item{norm.counts}{library size normalised counts matrix.}
+
+\item{params}{KersplatParams object to store estimated values in.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with estimated means
+}
+\description{
+Estimate mean parameters for the Kersplat simulation
+}
+\details{
+Parameters for the gamma distribution are estimated by fitting the mean
+normalised counts using \code{\link[fitdistrplus]{fitdist}}. All the fitting
+methods are tried and the fit with the best Cramer-von Mises statistic is
+selected. The density of the means is also estimated using
+\code{\link[stats]{density}}.
+
+Expression outlier genes are detected using the Median Absolute Deviation
+(MAD) from median method. If the log2 mean expression of a gene is greater
+than two MADs above the median log2 mean expression it is designated as an
+outlier. The proportion of outlier genes is used to estimate the outlier
+probability. Factors for each outlier gene are calculated by dividing mean
+expression by the median mean expression. A log-normal distribution is then
+fitted to these factors in order to estimate the outlier factor location and
+scale parameters using the \code{\link[fitdistrplus]{fitdist}} MLE method.
+}
diff --git a/man/kersplatEstimate.Rd b/man/kersplatEstimate.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..e73ebd97bcea7f4ee5780568f946156e19222743
--- /dev/null
+++ b/man/kersplatEstimate.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-estimate.R
+\name{kersplatEstimate}
+\alias{kersplatEstimate}
+\alias{kersplatEstimate.SingleCellExperiment}
+\alias{kersplatEstimate.matrix}
+\title{Estimate Kersplat simulation parameters}
+\usage{
+kersplatEstimate(counts, params = newKersplatParams(), verbose = TRUE)
+
+\method{kersplatEstimate}{SingleCellExperiment}(counts,
+ params = newKersplatParams(), verbose = TRUE)
+
+\method{kersplatEstimate}{matrix}(counts, params = newKersplatParams(),
+ verbose = TRUE)
+}
+\arguments{
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
+
+\item{params}{KersplatParams object to store estimated values in.}
+
+\item{verbose}{logical. Whether to print progress messages.}
+}
+\value{
+KersplatParams object containing the estimated parameters.
+}
+\description{
+Estimate simulation parameters for the Kersplat simulation from a real
+dataset. See the individual estimation functions for more details on how this
+is done.
+}
+\examples{
+# Load example data
+library(scater)
+set.seed(1)
+sce <- mockSCE()
+
+params <- kersplatEstimate(sce)
+params
+}
+\seealso{
+\code{\link{kersplatEstMean}}, \code{\link{kersplatEstBCV}},
+\code{\link{kersplatEstLib}}
+}
diff --git a/man/kersplatGenNetwork.Rd b/man/kersplatGenNetwork.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f7bb618115fc89a0d3c6cbd5d22aa8e71de1b794
--- /dev/null
+++ b/man/kersplatGenNetwork.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatGenNetwork}
+\alias{kersplatGenNetwork}
+\title{Generate Kersplat gene network}
+\usage{
+kersplatGenNetwork(params, verbose)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with gene network
+}
+\description{
+Generate a gene network for the Kersplat simulation
+}
+\details{
+Currently a very simple approach is used which needs to be improved. A
+network is generated using the \code{\link[igraph]{sample_forestfire}}
+function and edge weights are sampled from a standard normal distribution.
+}
diff --git a/man/kersplatSample.Rd b/man/kersplatSample.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..30eb2551f445fc09ac16afa9db4ce864e8dc717b
--- /dev/null
+++ b/man/kersplatSample.Rd
@@ -0,0 +1,94 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSample}
+\alias{kersplatSample}
+\title{Kersplat sample}
+\usage{
+kersplatSample(params, verbose = TRUE)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+SingleCellExperiment object containing the simulated counts and
+intermediate values.
+}
+\description{
+Sample cells for the Kersplat simulation
+}
+\details{
+The second stage is a two-step Kersplat simulation is to generate cells based
+on a complete \code{\link{KersplatParams}} object.
+intermediate parameters.
+
+The sampling process involves the following steps:
+\enumerate{
+ \item Simulate library sizes for each cell
+ \item Simulate means for each cell
+ \item Simulate endogenous counts for each cell
+ \item Simulate ambient counts for each cell
+ \item Simulate final counts for each cell
+}
+
+The final output is a
+\code{\link[SingleCellExperiment]{SingleCellExperiment}} object that
+contains the simulated counts but also the values for various intermediate
+steps. These are stored in the \code{\link{colData}} (for cell specific
+information), \code{\link{rowData}} (for gene specific information) or
+\code{\link{assays}} (for gene by cell matrices) slots. This additional
+information includes:
+\describe{
+ \item{\code{colData}}{
+ \describe{
+ \item{Cell}{Unique cell identifier.}
+ \item{Type}{Whether the cell is a Cell, Doublet or Empty.}
+ \item{CellLibSize}{The expected number of endogenous counts for
+ that cell.}
+ \item{AmbientLibSize}{The expected number of ambient counts for
+ that cell.}
+ \item{Path}{The path the cell belongs to.}
+ \item{Step}{How far along the path each cell is.}
+ \item{Path1}{For doublets the path of the first partner in the
+ doublet (otherwise \code{NA}).}
+ \item{Step1}{For doublets the step of the first partner in the
+ doublet (otherwise \code{NA}).}
+ \item{Path2}{For doublets the path of the second partner in the
+ doublet (otherwise \code{NA}).}
+ \item{Step2}{For doublets the step of the second partner in the
+ doublet (otherwise \code{NA}).}
+ }
+ }
+ \item{\code{rowData}}{
+ \describe{
+ \item{Gene}{Unique gene identifier.}
+ \item{BaseMean}{The base expression level for that gene.}
+ \item{AmbientMean}{The ambient expression level for that gene.}
+ }
+ }
+ \item{\code{assays}}{
+ \describe{
+ \item{CellMeans}{The mean expression of genes in each cell
+ after any differential expression and adjusted for expected
+ library size.}
+ \item{CellCounts}{Endogenous count matrix.}
+ \item{AmbientCounts}{Ambient count matrix.}
+ \item{counts}{Final count matrix.}
+ }
+ }
+}
+
+Values that have been added by Splatter are named using \code{UpperCamelCase}
+in order to differentiate them from the values added by analysis packages
+which typically use \code{underscore_naming}.
+}
+\examples{
+params <- kersplatSetup()
+sim <- kersplatSample(params)
+}
+\seealso{
+\code{\link{kersplatSimLibSizes}}, \code{\link{kersplatSimCellMeans}},
+\code{\link{kersplatSimCellCounts}}, \code{\link{kersplatSimAmbientCounts}},
+\code{\link{kersplatSimCounts}}
+}
diff --git a/man/kersplatSelectRegs.Rd b/man/kersplatSelectRegs.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..ef727ae8a6f35a1ed75a26a7bf7f2aded3d04046
--- /dev/null
+++ b/man/kersplatSelectRegs.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSelectRegs}
+\alias{kersplatSelectRegs}
+\title{Select Kersplat regulators}
+\usage{
+kersplatSelectRegs(params, verbose)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with gene regulators
+}
+\description{
+Select regulator genes in the gene network for a Kersplat simulation
+}
+\details{
+Regulators are randomly selected, weighted according to the difference
+between their out degree and in degree. This is an arbitrary weighting and
+may be improved or replace in the future.
+}
diff --git a/man/kersplatSetup.Rd b/man/kersplatSetup.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..e25afe290553404bcce4f50f12cdfd7f529941f9
--- /dev/null
+++ b/man/kersplatSetup.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSetup}
+\alias{kersplatSetup}
+\title{Kersplat setup}
+\usage{
+kersplatSetup(params = newKersplatParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+
+\item{...}{any additional parameter settings to override what is provided in
+\code{params}.}
+}
+\value{
+A complete KersplatParams object
+}
+\description{
+Setup the parameters required for the Kersplat simulation
+}
+\details{
+The first stage is a two-step Kersplat simulation is to generate some of the
+intermediate parameters. The resulting parameters allow multiple simulated
+datasets to be generated from the same biological structure (using
+\code{\link{kersplatSample}}). As with all the other parameters these values
+can be manually overwritten if desired.
+
+The setup involves the following steps:
+\enumerate{
+ \item Generate a gene network (if not already present)
+ \item Select regulator genes (if not already present)
+ \item Simulate gene means (if not already present)
+ \item Simulate cell paths
+}
+
+The resulting \code{\link{KersplatParams}} object will have the following
+parameters set (if they weren't already).
+
+\itemize{
+ \item \code{mean.values}
+ \item \code{network.graph}
+ \item \code{network.regsSet}
+ \item \code{paths.means}
+}
+
+See \code{\link{KersplatParams}} for more details about these parameters and
+the functions for the individual steps for more details about the process.
+}
+\examples{
+params <- kersplatSetup()
+}
+\seealso{
+\code{\link{kersplatGenNetwork}}, \code{\link{kersplatSelectRegs}},
+\code{\link{kersplatSimGeneMeans}}, \code{\link{kersplatSimPaths}},
+\code{\link{KersplatParams}}
+}
diff --git a/man/kersplatSimAmbientCounts.Rd b/man/kersplatSimAmbientCounts.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..596501adf54e1f02a0c48c11858c1c7bc805e4cf
--- /dev/null
+++ b/man/kersplatSimAmbientCounts.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimAmbientCounts}
+\alias{kersplatSimAmbientCounts}
+\title{Simulate Kersplat ambient counts}
+\usage{
+kersplatSimAmbientCounts(sim, params, verbose)
+}
+\arguments{
+\item{sim}{SingleCellExperiment containing simulation.}
+
+\item{params}{KersplatParams object with simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+SingleCellExperiment with ambient counts
+}
+\description{
+Simulate Kersplat ambient counts
+}
+\details{
+The overall expression profile to calculated by averaging the cell counts
+of the (non-empty) cells. This is then multiplied by the ambient library
+sizes to get a mean for each cell. Counts are then sampled from a Poisson
+distribution using these means.
+}
diff --git a/man/kersplatSimCellCounts.Rd b/man/kersplatSimCellCounts.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..900468d717232ca892dfd697ab0360e2e0bd64d7
--- /dev/null
+++ b/man/kersplatSimCellCounts.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimCellCounts}
+\alias{kersplatSimCellCounts}
+\title{Simulate Kersplat cell counts}
+\usage{
+kersplatSimCellCounts(sim, params, verbose)
+}
+\arguments{
+\item{sim}{SingleCellExperiment containing simulation.}
+
+\item{params}{KersplatParams object with simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+SingleCellExperiment with cell counts
+}
+\description{
+Simulate cell counts for the Kersplat simulation
+}
+\details{
+Counts are sampled from a Poisson distribution with lambda equal to the
+cell means matrix.
+}
diff --git a/man/kersplatSimCellMeans.Rd b/man/kersplatSimCellMeans.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..dfceec9d5057d94f3d2f825a533db818ce28b377
--- /dev/null
+++ b/man/kersplatSimCellMeans.Rd
@@ -0,0 +1,63 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimCellMeans}
+\alias{kersplatSimCellMeans}
+\title{Simulate Kersplat cell means}
+\usage{
+kersplatSimCellMeans(sim, params, verbose)
+}
+\arguments{
+\item{sim}{SingleCellExperiment containing simulation.}
+
+\item{params}{KersplatParams object with simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+SingleCellExperiment with cell means
+}
+\description{
+Simulate endogenous counts for each cell in a Kersplat simulation
+}
+\details{
+Cells are first assigned to a path and a step along that path. This is
+controlled by the \code{cells.design} parameter which is a \code{data.frame}
+with the columns "Path", "Probability", "Alpha" and "Beta". The Path field
+is an ID for each path and the Probability field is the probability that a
+cell will come from that path (must sum to 1). The Alpha and Beta parameters
+control the density of cells along the path. After they are assigned to paths
+the step for each cell is sampled from a Beta distribution with parameters
+shape1 equals Alpha and shape2 equals beta. This approach is very flexible
+and allows almost any distribution of cells along a path. The distribution
+can be viewed using \code{hist(rbeta(10000, Alpha, Beta), breaks = 100)}.
+Some useful combinations of parameters are:
+
+\describe{
+ \item{\code{Alpha = 1}, \code{Beta = 1}}{Uniform distribution along the
+ path}
+ \item{\code{Alpha = 0}, \code{Beta = 1}}{All cells at the start of the
+ path.}
+ \item{\code{Alpha = 1}, \code{Beta = 0}}{All cells at the end of the
+ path.}
+ \item{\code{Alpha = 0}, \code{Beta = 0}}{Cells only at each end of the
+ path.}
+ \item{\code{Alpha = 1}, \code{Beta = 2}}{Linear skew towards the start
+ of the path}
+ \item{\code{Alpha = 0.5}, \code{Beta = 1}}{Curved skew towards the start
+ of the path}
+ \item{\code{Alpha = 2}, \code{Beta = 1}}{Linear skew towards the end
+ of the path}
+ \item{\code{Alpha = 1}, \code{Beta = 0.5}}{Curved skew towards the end
+ of the path}
+ \item{\code{Alpha = 0.5}, \code{Beta = 0.5}}{Curved skew towards both
+ ends of the path}
+ \item{\code{Alpha = 0.5}, \code{Beta = 0.5}}{Curved skew away from both
+ ends of the path}
+}
+
+Once cells are assigned to paths and steps the correct means are extracted
+from the \code{paths.means} parameter and adjusted based on each cell's
+library size. An adjustment for BCV is then applied. Doublets are also
+simulated at this stage by selecting two path/step combinations and averaging
+the means.
+}
diff --git a/man/kersplatSimCounts.Rd b/man/kersplatSimCounts.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..024e7ef38870e8cbf051fd3a7758eaf73369396d
--- /dev/null
+++ b/man/kersplatSimCounts.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimCounts}
+\alias{kersplatSimCounts}
+\title{Simulate Kersplat final counts}
+\usage{
+kersplatSimCounts(sim, params, verbose)
+}
+\arguments{
+\item{sim}{SingleCellExperiment containing simulation.}
+
+\item{params}{KersplatParams object with simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+SingleCellExperiment with counts matrix
+}
+\description{
+Simulate the final counts matrix for a Kersplat simulation
+}
+\details{
+The cell counts matrix and ambient counts matrix are added together. The
+result is then downsampled to the cell library size (for cells and doublets)
+or the ambient library size (for empty cells) using the
+\code{\link[DropletUtils]{downsampleMatrix}} function.
+}
+\seealso{
+\code{\link[DropletUtils]{downsampleMatrix}}
+}
diff --git a/man/kersplatSimGeneMeans.Rd b/man/kersplatSimGeneMeans.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..adf039c6fdd80df54ac05148f13381beea1ada4b
--- /dev/null
+++ b/man/kersplatSimGeneMeans.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimGeneMeans}
+\alias{kersplatSimGeneMeans}
+\title{Simulate Kersplat gene means}
+\usage{
+kersplatSimGeneMeans(params, verbose)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with gene means
+}
+\description{
+Simulate Kersplat gene means
+}
+\details{
+Gene means are simulated in one of two ways depending on the value of the
+\code{mean.method} parameter.
+
+If \code{mean.method} is "fit" (default) then means are sampled from a Gamma
+distribution with shape equals \code{mean.shape} and rate equals
+\code{mean.rate}. Expression outliers are then added by replacing some
+values with the median multiplied by a factor from a log-normal distribution.
+This is the same process used for the Splat simulation.
+
+If \code{mean.method} is "density" then means are sampled from the
+density object in the \code{mean.density} parameter using a rejection
+sampling method. This approach is more flexible but may violate some
+statistical assumptions.
+}
diff --git a/man/kersplatSimLibSizes.Rd b/man/kersplatSimLibSizes.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..81eedf732939e30ac949388fc75c71566e84ffd3
--- /dev/null
+++ b/man/kersplatSimLibSizes.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimLibSizes}
+\alias{kersplatSimLibSizes}
+\title{Simulate Kersplat library sizes}
+\usage{
+kersplatSimLibSizes(sim, params, verbose)
+}
+\arguments{
+\item{sim}{SingleCellExperiment containing simulation.}
+
+\item{params}{KersplatParams object with simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+SingleCellExperiment with library sizes
+}
+\description{
+Generate library sizes for cells in the Kersplat simulation
+}
+\details{
+Library sizes are simulated in one of two ways depending on the value of the
+\code{lib.method} parameter.
+
+If \code{lib.method} is "fit" (default) then means are sampled from a
+log-normal distribution with meanlog equals \code{lib.loc} and sdlog equals
+\code{lib.scale}.
+
+If \code{mean.method} is "density" then library sizes are sampled from the
+density object in the \code{lib.density} parameter using a rejection
+sampling method. This approach is more flexible but may violate some
+statistical assumptions.
+
+Ambient library sizes are also generated from a log-normal distribution based
+on the parameters for the cell library size and adjusted using the
+\code{ambient.scale} parameter.
+}
diff --git a/man/kersplatSimPaths.Rd b/man/kersplatSimPaths.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..af07653c321446c4337402b8611ed775466a8112
--- /dev/null
+++ b/man/kersplatSimPaths.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimPaths}
+\alias{kersplatSimPaths}
+\title{Simulate Kersplat paths}
+\usage{
+kersplatSimPaths(params, verbose)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+KersplatParams object with path means
+}
+\description{
+Simulate gene means for each step along each path of a Kersplat simulation
+}
+\details{
+The method of simulating paths is inspired by the method used in the PROSSTT
+simulation. Changes in expression are controlled by \code{paths.nPrograms}
+regulatory programs. Each of the regulatory genes in the gene network has
+some association with each program. This is analogous to there being changes
+in the environment (the programs) which are sensed by receptors (regulatory
+genes) and cause changes in expression downstream. For each path a random
+walk is generated for each program and the changes passed on to the
+regulatory genes. At each step the changes propagate through the network
+according to the weights on edges between genes. This algorithm is fairly
+simple but should result in correlation relationships between genes. However
+it is likely to be improved and adjusted in the future.
+
+The path structure itself is specified by the \code{paths.design} parameter.
+This is a \code{data.frame} with three columns: "Path", "From", and "Steps".
+The Path field is an ID for each path while the Steps field controls the
+length of each path. Increasing the number of steps will increase the
+difference in expression between the ends of the paths. The From field sets
+the originating point of each path. For example a From of \code{0, 0, 0}
+would indicate three paths from the origin while a From of \code{0, 1, 1}
+would give a branching structure with Path 1 beginning at the origin and
+Path 2 and Path 3 beginning at the end of Path 1.
+}
+\references{
+Papadopoulos N, Parra RG, Söding J. PROSSTT: probabilistic simulation of
+single-cell RNA-seq data for complex differentiation processes.
+Bioinformatics (2019). \url{https://doi.org/10.1093/bioinformatics/btz078}.
+}
diff --git a/man/kersplatSimulate.Rd b/man/kersplatSimulate.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..8afe6311e9d024ea9594366534ed6a93e250fd1b
--- /dev/null
+++ b/man/kersplatSimulate.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{kersplatSimulate}
+\alias{kersplatSimulate}
+\title{Kersplat simulation}
+\usage{
+kersplatSimulate(params = newKersplatParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{KersplatParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+
+\item{...}{any additional parameter settings to override what is provided in
+\code{params}.}
+}
+\value{
+SingleCellExperiment containing simulated counts and intermediate
+values
+}
+\description{
+Simulate scRNA-seq count data using the Kersplat model
+}
+\details{
+This functions is for simulating data in a single step. It consists of a
+call to \code{\link{kersplatSetup}} followed by a call to
+\code{\link{kersplatSample}}. Please see the documentation for those
+functions for more details of the individual steps.
+}
+\examples{
+sim <- kersplatSimulate()
+
+}
+\seealso{
+\code{\link{kersplatSetup}}, \code{\link{kersplatSample}}
+}
diff --git a/man/logistic.Rd b/man/logistic.Rd
index a98711efe8c53579679313ccbefae629e03ed0ab..d424745bdc5f6f9d088e32c6a4a8452b8631c9f0 100644
--- a/man/logistic.Rd
+++ b/man/logistic.Rd
@@ -14,7 +14,7 @@ logistic(x, x0, k)
\item{k}{shape parameter. Gives the slope of the function.}
}
\value{
-Value of logistic funciton with given parameters
+Value of logistic function with given parameters
}
\description{
Implementation of the logistic function
diff --git a/man/lun2Estimate.Rd b/man/lun2Estimate.Rd
index 4031807d32f32bea968858acfe354f3e6d69e148..956aa5a11d57a12bac9e8ecaa8be21d73f5af3cd 100644
--- a/man/lun2Estimate.Rd
+++ b/man/lun2Estimate.Rd
@@ -46,11 +46,11 @@ See \code{\link{Lun2Params}} for more details on the parameters.
\dontrun{
# Load example data
library(scater)
-data("sc_example_counts")
-data("sc_example_cell_info")
+set.seed(1)
+sce <- mockSCE()
-plates <- factor(sc_example_cell_info$Mutation_Status)
-params <- lun2Estimate(sc_example_counts, plates, min.size = 20)
+plates <- as.numeric(factor(colData(sce)$Mutation_Status))
+params <- lun2Estimate(sce, plates, min.size = 20)
params
}
}
diff --git a/man/lun2Simulate.Rd b/man/lun2Simulate.Rd
index df77ac55ec57956a28bf8b8cb8571087cca5511c..38c9ab3326c08ceace1ed2ce4f5613637539d5ad 100644
--- a/man/lun2Simulate.Rd
+++ b/man/lun2Simulate.Rd
@@ -34,9 +34,9 @@ added between two groups of plates (an "ingroup" and all other plates).
Library size factors are also applied and optionally a zero-inflated
negative-binomial can be used.
-If the number of genes to simulate differs from the number of provied gene
+If the number of genes to simulate differs from the number of provided gene
parameters or the number of cells to simulate differs from the number of
-library sizes the relevant paramters will be sampled with a warning. This
+library sizes the relevant parameters will be sampled with a warning. This
allows any number of genes or cells to be simulated regardless of the
number in the dataset used in the estimation step but has the downside that
some genes or cells may be simulated multiple times.
diff --git a/man/lunEstimate.Rd b/man/lunEstimate.Rd
index 207fd60a778f4697adab651973f5f7c798045aeb..c313ad8d9abacc62e065e19c4e49cef5b8976d31 100644
--- a/man/lunEstimate.Rd
+++ b/man/lunEstimate.Rd
@@ -33,8 +33,9 @@ for more details on the parameters.
\examples{
# Load example data
library(scater)
-data("sc_example_counts")
+set.seed(1)
+sce <- mockSCE()
-params <- lunEstimate(sc_example_counts)
+params <- lunEstimate(sce)
params
}
diff --git a/man/makeOverallPanel.Rd b/man/makeOverallPanel.Rd
index e6d54243855bdd2dad54b57f6cbbe8e6c9e18fbc..4a0af661354ed4fd81b1d2b57bd3e4d9080d126f 100644
--- a/man/makeOverallPanel.Rd
+++ b/man/makeOverallPanel.Rd
@@ -29,7 +29,7 @@ single panel.
\dontrun{
sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-comparison <- compSCEs(list(Splat = sim1, Simple = sim2))
+comparison <- compareSCEs(list(Splat = sim1, Simple = sim2))
difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
panel <- makeOverallPanel(comparison, difference)
}
diff --git a/man/mfaEstimate.Rd b/man/mfaEstimate.Rd
index c8ad13e6cf8ff7775d21c36ae89b991470df3b40..58a14f7d6e9e5fe5e696f3c671fe9513e92a649a 100644
--- a/man/mfaEstimate.Rd
+++ b/man/mfaEstimate.Rd
@@ -33,9 +33,12 @@ details on the parameters.
}
\examples{
# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("mfa", quietly = TRUE)) {
+ library(mfa)
+ synth <- create_synthetic(C = 20, G = 5, zero_negative = TRUE,
+ model_dropout = TRUE)
-params <- mfaEstimate(sc_example_counts)
-params
+ params <- mfaEstimate(synth$X)
+ params
+}
}
diff --git a/man/mfaSimulate.Rd b/man/mfaSimulate.Rd
index ec2a98e243fd7942f29bc715cac6890b68b4397e..016bb04b23c334caab222ca71631f7ece920135e 100644
--- a/man/mfaSimulate.Rd
+++ b/man/mfaSimulate.Rd
@@ -29,7 +29,9 @@ output from log-expression to counts and returns a
how the simulation works.
}
\examples{
-sim <- mfaSimulate()
+if (requireNamespace("mfa", quietly = TRUE)) {
+ sim <- mfaSimulate()
+}
}
\references{
Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell
diff --git a/man/newParams.Rd b/man/newParams.Rd
index 5af67eca1394c8a87c63411f333873952b52fc08..71d00e6bfe36b0735dfe4867aecd073cfe2f9c1e 100644
--- a/man/newParams.Rd
+++ b/man/newParams.Rd
@@ -1,11 +1,13 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/BASiCSParams-methods.R,
-% R/Lun2Params-methods.R, R/LunParams-methods.R, R/MFAParams-methods.R,
-% R/PhenoParams-methods.R, R/SCDDParams-methods.R, R/SimpleParams-methods.R,
-% R/SparseDCParams-methods.R, R/SplatParams-methods.R, R/ZINBParams-methods.R
+% R/KersplatParams-methods.R, R/Lun2Params-methods.R, R/LunParams-methods.R,
+% R/MFAParams-methods.R, R/PhenoParams-methods.R, R/SCDDParams-methods.R,
+% R/SimpleParams-methods.R, R/SparseDCParams-methods.R,
+% R/SplatParams-methods.R, R/ZINBParams-methods.R
\name{newParams}
\alias{newParams}
\alias{newBASiCSParams}
+\alias{newKersplatParams}
\alias{newLun2Params}
\alias{newLunParams}
\alias{newMFAParams}
@@ -19,6 +21,8 @@
\usage{
newBASiCSParams(...)
+newKersplatParams(...)
+
newLun2Params(...)
newLunParams(...)
diff --git a/man/phenoEstimate.Rd b/man/phenoEstimate.Rd
index 1c102ba3d2f02c73a5d5101298d5bfa7cac957ed..ede408036be4bdd00e1175b9a990dcfbda1db101 100644
--- a/man/phenoEstimate.Rd
+++ b/man/phenoEstimate.Rd
@@ -32,10 +32,13 @@ input data. The total number of genes is evenly divided into the four types.
See \code{\link{PhenoParams}} for more details on the parameters.
}
\examples{
-# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("phenopath", quietly = TRUE)) {
+ # Load example data
+ library(scater)
+ set.seed(1)
+ sce <- mockSCE()
-params <- phenoEstimate(sc_example_counts)
-params
+ params <- phenoEstimate(sce)
+ params
+}
}
diff --git a/man/phenoSimulate.Rd b/man/phenoSimulate.Rd
index 34f5efb79b85a6acbcbefed7142e797d6f10034e..24c43a8a41fcc9d104a5fd2f08913b4d432109d9 100644
--- a/man/phenoSimulate.Rd
+++ b/man/phenoSimulate.Rd
@@ -31,8 +31,9 @@ See \code{\link[phenopath]{simulate_phenopath}} and the PhenoPath paper for
more details about how the simulation works.
}
\examples{
-sim <- phenoSimulate()
-
+if (requireNamespace("phenopath", quietly = TRUE)) {
+ sim <- phenoSimulate()
+}
}
\references{
Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
diff --git a/man/sampleDensity.Rd b/man/sampleDensity.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..2efc5d7ebe6dea4615fd11185ace13a6e99225e5
--- /dev/null
+++ b/man/sampleDensity.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-simulate.R
+\name{sampleDensity}
+\alias{sampleDensity}
+\title{Sample density}
+\usage{
+sampleDensity(n, dens, lower = 0)
+}
+\arguments{
+\item{n}{Number of values to sample}
+
+\item{dens}{Density object to sample from}
+
+\item{lower}{Lower x-axis bound on sampled values}
+}
+\value{
+Vector of sampled values
+}
+\description{
+Sample from a density object using rejection sampling
+}
+\details{
+Random points (x and y) are generated inside the range of the density object.
+If they value is less than the density for that x value (and x is greater
+than \code{lower}) then that x value is retained. Ten thousand points are
+generated at a time until enough valid values have been sampled.
+}
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 9f15d6d8bd91b933c6e7531f70e222938629c98d..75bc1affd60790a841304e6eec7dd497a5654ce9 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -53,13 +53,14 @@ simulate. The output is then converted to a SCDDParams object. See
\code{\link[scDD]{preprocess}} and \code{\link[scDD]{scDD}} for details.
}
\examples{
-\dontrun{
-# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("scDD", quietly = TRUE)) {
+ library(scater)
+ set.seed(1)
+ sce <- mockSCE(ncells = 20, ngenes = 100)
-conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
-params <- scDDEstimate(sc_example_counts, conditions = conditions)
-params
+ colData(sce)$condition <- sample(1:2, ncol(sce), replace = TRUE)
+ params <- scDDEstimate(sce, condition = "condition")
+ params
}
+
}
diff --git a/man/selectFit.Rd b/man/selectFit.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..20540c479c2a669acbb500ba41a11902091890f8
--- /dev/null
+++ b/man/selectFit.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/kersplat-estimate.R
+\name{selectFit}
+\alias{selectFit}
+\title{Select fit}
+\usage{
+selectFit(data, distr, weights = NULL, verbose = TRUE)
+}
+\arguments{
+\item{data}{The data to fit}
+
+\item{distr}{Name of the distribution to fit}
+
+\item{weights}{Optional vector of weights}
+
+\item{verbose}{logical. Whether to print progress messages}
+}
+\value{
+The selected fit object
+}
+\description{
+Try a variety of fitting methods and select the best one
+}
+\details{
+The distribution is fitted to the data using each of the
+\code{\link[fitdistrplus]{fitdist}} fitting methods. The fit with the
+smallest Cramer-von Mises statistic is selected.
+}
diff --git a/man/setParam.Rd b/man/setParam.Rd
index 378560f36fab9d73f53da98db53106e2d4f0eb6f..7f8e4ea71a13c09bc77f406fbb8646712530e378 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -1,12 +1,13 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/BASiCSParams-methods.R,
-% R/Lun2Params-methods.R, R/LunParams-methods.R, R/Params-methods.R,
-% R/PhenoParams-methods.R, R/SCDDParams-methods.R, R/SplatParams-methods.R,
-% R/ZINBParams-methods.R
+% R/KersplatParams-methods.R, R/Lun2Params-methods.R, R/LunParams-methods.R,
+% R/Params-methods.R, R/PhenoParams-methods.R, R/SCDDParams-methods.R,
+% R/SplatParams-methods.R, R/ZINBParams-methods.R
\docType{methods}
\name{setParam}
\alias{setParam}
\alias{setParam,BASiCSParams-method}
+\alias{setParam,KersplatParams-method}
\alias{setParam,Lun2Params-method}
\alias{setParam,LunParams-method}
\alias{setParam,Params-method}
@@ -20,6 +21,8 @@ setParam(object, name, value)
\S4method{setParam}{BASiCSParams}(object, name, value)
+\S4method{setParam}{KersplatParams}(object, name, value)
+
\S4method{setParam}{Lun2Params}(object, name, value)
\S4method{setParam}{LunParams}(object, name, value)
@@ -39,7 +42,7 @@ setParam(object, name, value)
\item{name}{name of the parameter to set.}
-\item{value}{value to set the paramter to.}
+\item{value}{value to set the parameter to.}
}
\value{
Object with new parameter value.
diff --git a/man/setParamUnchecked.Rd b/man/setParamUnchecked.Rd
index e8d1b40b4ab543c8b2ca227cf9a935ab5f035210..9ebd4825460616d43760857dcbc7673b7588eee7 100644
--- a/man/setParamUnchecked.Rd
+++ b/man/setParamUnchecked.Rd
@@ -15,7 +15,7 @@ setParamUnchecked(object, name, value)
\item{name}{name of the parameter to set.}
-\item{value}{value to set the paramter to.}
+\item{value}{value to set the parameter to.}
}
\value{
Object with new parameter value.
diff --git a/man/setParams.Rd b/man/setParams.Rd
index d8accc7d1e2933530dc1b12e7432c0a29d165ffe..0e62af22920d3b2e02fdd886d767827fdb8e5621 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -1,13 +1,24 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/params-functions.R
+% Please edit documentation in R/AllGenerics.R, R/KersplatParams-methods.R,
+% R/Params-methods.R, R/SplatParams-methods.R
+\docType{methods}
\name{setParams}
\alias{setParams}
+\alias{setParams,KersplatParams-method}
+\alias{setParams,Params-method}
+\alias{setParams,SplatParams-method}
\title{Set parameters}
\usage{
-setParams(params, update = NULL, ...)
+setParams(object, update = NULL, ...)
+
+\S4method{setParams}{KersplatParams}(object, update = NULL, ...)
+
+\S4method{setParams}{Params}(object, update = NULL, ...)
+
+\S4method{setParams}{SplatParams}(object, update = NULL, ...)
}
\arguments{
-\item{params}{Params object to set parameters in.}
+\item{object}{Params object to set parameters in.}
\item{update}{list of parameters to set where \code{names(update)} are the
names of the parameters to set and the items in the list are values.}
@@ -37,4 +48,5 @@ params
# Set via update list
params <- setParams(params, list(mean.rate = 0.2, mean.shape = 0.8))
params
+
}
diff --git a/man/showDFs.Rd b/man/showDFs.Rd
index 783c88d53f58ee753af2914b7b859f1d9f21f3f8..8ad52b26b7df89959916864649ab195a388d6324 100644
--- a/man/showDFs.Rd
+++ b/man/showDFs.Rd
@@ -11,6 +11,9 @@ showDFs(dfs, not.default)
\item{not.default}{logical vector giving which have changed from the default.}
}
+\value{
+Print data.frame parameters
+}
\description{
Function used for pretty printing data.frame parameters.
}
diff --git a/man/showValues.Rd b/man/showValues.Rd
index ddd813ae68a61d411e44d5b6340b21833e3bc4d0..5019be3e25c8880b90fc1ed74ea3a431af62dd3a 100644
--- a/man/showValues.Rd
+++ b/man/showValues.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/params-functions.R
\name{showValues}
\alias{showValues}
-\title{Show vales}
+\title{Show values}
\usage{
showValues(values, not.default)
}
@@ -11,6 +11,9 @@ showValues(values, not.default)
\item{not.default}{logical vector giving which have changed from the default.}
}
+\value{
+Print values
+}
\description{
-Function used for pretty printing scale or vector parameters.
+Function used for pretty printing scalar or vector parameters.
}
diff --git a/man/simpleEstimate.Rd b/man/simpleEstimate.Rd
index 441accff81ae11b622594476e13ff0ce206a9531..d764e1eff30fef86e169d0d4da5eda83f738ddd1 100644
--- a/man/simpleEstimate.Rd
+++ b/man/simpleEstimate.Rd
@@ -35,8 +35,9 @@ details on the parameters.
\examples{
# Load example data
library(scater)
-data("sc_example_counts")
+set.seed(1)
+sce <- mockSCE()
-params <- simpleEstimate(sc_example_counts)
+params <- simpleEstimate(sce)
params
}
diff --git a/man/sparseDCEstimate.Rd b/man/sparseDCEstimate.Rd
index c9abf4fb5c2318220fef6b2050d54e8486073227..ba3d010f979c5b458454851c56e37ff30f1150c8 100644
--- a/man/sparseDCEstimate.Rd
+++ b/man/sparseDCEstimate.Rd
@@ -23,7 +23,7 @@ containing count data to estimate parameters from.}
\item{nclusters}{number of cluster present in the dataset.}
-\item{norm}{logical, whether to libray size normalise counts before
+\item{norm}{logical, whether to library size normalise counts before
estimation. Set this to FALSE if counts is already normalised.}
\item{params}{PhenoParams object to store estimated values in.}
@@ -46,14 +46,15 @@ input data. The counts are preprocessed using
See \code{\link{SparseDCParams}} for more details on the parameters.
}
\examples{
-# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("SparseDC", quietly = TRUE)) {
+ # Load example data
+ library(scater)
+ set.seed(1)
+ sce <- mockSCE(ncells = 20, ngenes = 100)
-set.seed(1)
-conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
+ conditions <- sample(1:2, ncol(sce), replace = TRUE)
-params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
- nclusters = 3)
-params
+ params <- sparseDCEstimate(sce, conditions, nclusters = 3)
+ params
+}
}
diff --git a/man/sparseDCSimulate.Rd b/man/sparseDCSimulate.Rd
index 4c1f3419e0c5f8724ae20a893d26b0dd0eda3a80..c88ac8d89f80c86d8a3a9a0f9065508d6f444ae9 100644
--- a/man/sparseDCSimulate.Rd
+++ b/man/sparseDCSimulate.Rd
@@ -31,8 +31,9 @@ See \code{\link[SparseDC]{sim_data}} and the SparseDC paper for
more details about how the simulation works.
}
\examples{
-sim <- sparseDCSimulate()
-
+if (requireNamespace("SparseDC", quietly = TRUE)) {
+ sim <- sparseDCSimulate()
+}
}
\references{
Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
diff --git a/man/splatEstLib.Rd b/man/splatEstLib.Rd
index 30df262739e3b918071748c8198b1f62f7f20e82..29f69c1645731f217575b135f53c47fc15adb808 100644
--- a/man/splatEstLib.Rd
+++ b/man/splatEstLib.Rd
@@ -12,7 +12,7 @@ splatEstLib(counts, params)
\item{params}{splatParams object to store estimated values in.}
}
\value{
-splatParams object with estimated values.
+SplatParams object with estimated values.
}
\description{
The Shapiro-Wilks test is used to determine if the library sizes are
diff --git a/man/splatEstMean.Rd b/man/splatEstMean.Rd
index c019f6782a4bb61e4ca5605b09d65ad9725a07e9..a9192dff43ccf4e8037ef97d064af2c8e2ef58e1 100644
--- a/man/splatEstMean.Rd
+++ b/man/splatEstMean.Rd
@@ -19,7 +19,7 @@ Estimate rate and shape parameters for the gamma distribution used to
simulate gene expression means.
}
\details{
-Parameter for the gamma distribution are estimated by fitting the mean
+Parameters for the gamma distribution are estimated by fitting the mean
normalised counts using \code{\link[fitdistrplus]{fitdist}}. The 'maximum
goodness-of-fit estimation' method is used to minimise the Cramer-von Mises
distance. This can fail in some situations, in which case the 'method of
diff --git a/man/splatEstimate.Rd b/man/splatEstimate.Rd
index 736f41b02d235c96b7097350ffc71e55cd0fc879..d0287115201d5caaeba73926827205de04717076 100644
--- a/man/splatEstimate.Rd
+++ b/man/splatEstimate.Rd
@@ -30,9 +30,10 @@ is done.
\examples{
# Load example data
library(scater)
-data("sc_example_counts")
+set.seed(1)
+sce <- mockSCE()
-params <- splatEstimate(sc_example_counts)
+params <- splatEstimate(sce)
params
}
\seealso{
diff --git a/man/splatSimDE.Rd b/man/splatSimDE.Rd
index 257fb1c7d43b6fbf1a6c9fc11f9d8c0864eae720..55f3bcde77f396bffa1f4753d0a6aebe79084902 100644
--- a/man/splatSimDE.Rd
+++ b/man/splatSimDE.Rd
@@ -21,6 +21,6 @@ SingleCellExperiment with simulated differential expression.
\description{
Simulate differential expression. Differential expression factors for each
group are produced using \code{\link{getLNormFactors}} and these are added
-along with updated means for each group. For paths care is taked to make sure
+along with updated means for each group. For paths care is taken to make sure
they are simulated in the correct order.
}
diff --git a/man/splatSimDropout.Rd b/man/splatSimDropout.Rd
index 7f68ba3c5ede69f35e49615d824f8f22df785766..8222b77c648f827bd2d61e436f2b33dc0873409d 100644
--- a/man/splatSimDropout.Rd
+++ b/man/splatSimDropout.Rd
@@ -15,7 +15,7 @@ splatSimDropout(sim, params)
SingleCellExperiment with simulated dropout and observed counts.
}
\description{
-A logistic function is used to form a relationshop between the expression
+A logistic function is used to form a relationship between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped.
diff --git a/man/splatSimulate.Rd b/man/splatSimulate.Rd
index 53851871e45168d6890ee3c0ac22f6c56b6c4f18..578477f52ecea2b7c747e9bf772bc5c0aa697f5d 100644
--- a/man/splatSimulate.Rd
+++ b/man/splatSimulate.Rd
@@ -67,7 +67,7 @@ information), \code{\link{rowData}} (for gene specific information) or
\code{\link{assays}} (for gene by cell matrices) slots. This additional
information includes:
\describe{
- \item{\code{phenoData}}{
+ \item{\code{colData}}{
\describe{
\item{Cell}{Unique cell identifier.}
\item{Group}{The group or path the cell belongs to.}
@@ -75,7 +75,7 @@ information includes:
\item{Step (paths only)}{how far along the path each cell is.}
}
}
- \item{\code{featureData}}{
+ \item{\code{rowData}}{
\describe{
\item{Gene}{Unique gene identifier.}
\item{BaseGeneMean}{The base expression level for that gene.}
@@ -91,7 +91,7 @@ information includes:
non-linear changes in expression along a path.}
}
}
- \item{\code{assayData}}{
+ \item{\code{assays}}{
\describe{
\item{BatchCellMeans}{The mean expression of genes in each cell
after adding batch effects.}
diff --git a/man/summariseDiff.Rd b/man/summariseDiff.Rd
index 10b3b0622f8d88dca7db9516cbe5f22bbb61e66c..fc13108955e63f56eaf8a848a1ba9067ab3138cb 100644
--- a/man/summariseDiff.Rd
+++ b/man/summariseDiff.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/compare.R
\name{summariseDiff}
\alias{summariseDiff}
-\title{Summarise diffSCESs}
+\title{Summarise diffSCEs}
\usage{
summariseDiff(diff)
}
@@ -14,8 +14,9 @@ data.frame with MADs, MAEs, RMSEs, scaled statistics and ranks
}
\description{
Summarise the results of \code{\link{diffSCEs}}. Calculates the Median
-Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
-Error (RMSE) for the various properties and ranks them.
+Absolute Deviation (MAD), Mean Absolute Error (MAE), Root Mean Squared
+Error (RMSE) and Kolmogorov-Smirnov (KS) statistics for the various
+properties and ranks them.
}
\examples{
sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
diff --git a/man/summariseKS.Rd b/man/summariseKS.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..7e8f43a1ac47e5247bb2dedc11f6a9911ecee419
--- /dev/null
+++ b/man/summariseKS.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compare.R
+\name{summariseKS}
+\alias{summariseKS}
+\title{Summarise KS}
+\usage{
+summariseKS(data, ref, split.col, stat.cols)
+}
+\arguments{
+\item{data}{The data.frame to summarise}
+
+\item{ref}{The reference data.frame}
+
+\item{split.col}{Name of the column used to split the dataset}
+
+\item{stat.cols}{Names of the columns to summarise. If this vector is named
+those names will be used in the output.}
+}
+\value{
+data.frame with the summarised measure, scaled and ranked
+}
+\description{
+Summarise columns of a data.frame compared to a reference using the KS test.
+}
diff --git a/man/summariseStats.Rd b/man/summariseStats.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..72459e4a20a6eb15855f1eb923b12d3ae3429ee2
--- /dev/null
+++ b/man/summariseStats.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compare.R
+\name{summariseStats}
+\alias{summariseStats}
+\title{Summarise statistics}
+\usage{
+summariseStats(data, split.col, stat.cols, measure = c("MAD", "MAE",
+ "RMSE"))
+}
+\arguments{
+\item{data}{The data.frame to summarise}
+
+\item{split.col}{Name of the column used to split the dataset}
+
+\item{stat.cols}{Names of the columns to summarise. If this vector is named
+those names will be used in the output.}
+
+\item{measure}{The measure to use for summarisation.}
+}
+\value{
+data.frame with the summarised measure, scaled and ranked
+}
+\description{
+Summarise columns of a data.frame using a single measure.
+}
diff --git a/man/tidyStatSumm.Rd b/man/tidyStatSumm.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..fb4948984e23c9b36e23a2e90dd4e03ac8d53ae3
--- /dev/null
+++ b/man/tidyStatSumm.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compare.R
+\name{tidyStatSumm}
+\alias{tidyStatSumm}
+\title{Tidy summarised statistics}
+\usage{
+tidyStatSumm(stat.summ, measure = c("MAD", "MAE", "RMSE"))
+}
+\arguments{
+\item{stat.summ}{The summary to convert}
+
+\item{measure}{The name of the summarisation measure}
+}
+\value{
+tidy data.frame with the summarised measure, scaled and ranked
+}
+\description{
+Convert a statistic summary to tidy format and add ranks and scaled values
+}
diff --git a/man/zinbEstimate.Rd b/man/zinbEstimate.Rd
index 5c854a4c252594b067af178e675d697056f3ce06..11bece29173050be618fdf8d50c84033ca8580aa 100644
--- a/man/zinbEstimate.Rd
+++ b/man/zinbEstimate.Rd
@@ -33,7 +33,7 @@ containing count data to estimate parameters from.}
\item{common.disp}{logical. Whether or not a single dispersion for all
features is estimated.}
-\item{iter.init}{number of iterations to use for initalization.}
+\item{iter.init}{number of iterations to use for initialization.}
\item{iter.opt}{number of iterations to use for optimization.}
@@ -63,12 +63,13 @@ the fitted model and inserts it into a \code{\link{ZINBParams}} object. See
\code{\link[zinbwave]{zinbFit}} for details of the estimation procedure.
}
\examples{
-\dontrun{
-# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("zinbwave", quietly = TRUE)) {
+ library(scater)
+ set.seed(1)
+ sce <- mockSCE(ncells = 20, ngenes = 100)
-params <- zinbEstimate(sc_example_counts)
-params
+ params <- zinbEstimate(sce)
+ params
}
+
}
diff --git a/man/zinbSimulate.Rd b/man/zinbSimulate.Rd
index 17c6611ee19c0ce88a5412947f5945b2737f3738..ab3d22722800ca590375d2c7f4f50e570af9142c 100644
--- a/man/zinbSimulate.Rd
+++ b/man/zinbSimulate.Rd
@@ -28,7 +28,9 @@ See \code{\link[zinbwave]{zinbSim}} and the ZINB-WaVE paper for
more details about how the simulation works.
}
\examples{
-sim <- zinbSimulate()
+if (requireNamespace("zinbwave", quietly = TRUE)) {
+ sim <- zinbSimulate()
+}
}
\references{
diff --git a/tests/spelling.R b/tests/spelling.R
new file mode 100644
index 0000000000000000000000000000000000000000..6713838fc0fa213b458ec6f984a9987f3fb69576
--- /dev/null
+++ b/tests/spelling.R
@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
diff --git a/tests/testthat/test-BASiCS-simulate.R b/tests/testthat/test-BASiCS-simulate.R
index 98d6cade8d45e99a33f0b9c99891bae84cffd483..081ada534571ca9819c5e5b365c583c148d92cc3 100644
--- a/tests/testthat/test-BASiCS-simulate.R
+++ b/tests/testthat/test-BASiCS-simulate.R
@@ -2,5 +2,5 @@ context("BASiCS simulation")
test_that("BASiCS simulation output is valid", {
skip_if_not_installed("BASiCS")
- expect_true(validObject(sparseDCSimulate()))
+ expect_true(validObject(BASiCSSimulate()))
})
diff --git a/tests/testthat/test-BASiCSEstimate.R b/tests/testthat/test-BASiCSEstimate.R
index 3e1df27accc507d6fbd9a58cfe8b85b26a7d33a6..0f89b2ca33913470a8cb57984c5562fe323008ee 100644
--- a/tests/testthat/test-BASiCSEstimate.R
+++ b/tests/testthat/test-BASiCSEstimate.R
@@ -1,28 +1,27 @@
context("BASiCSEstimate")
library(scater)
-data("sc_example_counts")
+set.seed(1)
+counts <- counts(mockSCE(ncells = 30, ngenes = 100))
test_that("BASiCSEstimate works", {
skip_if_not_installed("BASiCS")
set.seed(1)
- spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
+ spike.info <- data.frame(Name = rownames(counts)[1:10],
Input = rnorm(10, 500, 200),
stringsAsFactors = FALSE)
- counts <- sc_example_counts[, 1:30]
counts <- counts[rowSums(counts) != 0, ]
- params <- BASiCSEstimate(counts[1:100, ],
- spike.info, verbose = FALSE, progress = FALSE)
+ params <- BASiCSEstimate(counts, spike.info, verbose = FALSE,
+ progress = FALSE)
expect_true(validObject(params))
})
test_that("BASiCSEstimate works without spikes", {
skip_if_not_installed("BASiCS")
set.seed(1)
- counts <- sc_example_counts[, 1:30]
counts <- counts[rowSums(counts) != 0, ]
batch <- sample(1:2, ncol(counts), replace = TRUE)
- params <- BASiCSEstimate(counts[1:100, ], batch = batch,
+ params <- BASiCSEstimate(counts, batch = batch,
verbose = FALSE, progress = FALSE)
expect_true(validObject(params))
})
diff --git a/tests/testthat/test-MFAEstimate.R b/tests/testthat/test-MFAEstimate.R
index ab703c70f0e294c9ee079447acfd6bd7eed927ef..817ba8245bdc19c5c3e76ada449c6597a44d33dd 100644
--- a/tests/testthat/test-MFAEstimate.R
+++ b/tests/testthat/test-MFAEstimate.R
@@ -1,10 +1,13 @@
context("MFAEstimate")
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("mfa", quietly = TRUE)) {
+ library(mfa)
+ synth <- create_synthetic(C = 20, G = 5, zero_negative = TRUE,
+ model_dropout = TRUE)
+}
test_that("MFAEstimate works", {
skip_if_not_installed("mfa")
- params <- mfaEstimate(sc_example_counts)
+ params <- mfaEstimate(synth$X)
expect_true(validObject(params))
})
diff --git a/tests/testthat/test-SplatParams.R b/tests/testthat/test-SplatParams.R
index d7d6752b7fba3774671d9b0d0118d55817007866..bc9479ef3462bd809a6db3c5c84123e00156d580 100644
--- a/tests/testthat/test-SplatParams.R
+++ b/tests/testthat/test-SplatParams.R
@@ -44,3 +44,11 @@ test_that("dropout.type checks work", {
expect_error(setParam(params, "dropout.type", "a"),
"dropout.type must be one of: ")
})
+
+
+test_that("setParams order doesn't matter", {
+ expect_silent(setParams(params, group.prob = c(0.5, 0.5),
+ de.facLoc = c(0.1, 5)))
+ expect_silent(setParams(params, de.facLoc = c(0.1, 5),
+ group.prob = c(0.5, 0.5)))
+})
diff --git a/tests/testthat/test-compare.R b/tests/testthat/test-compare.R
index 04d652082f78507a9edfa5fa0da889c5f4d4e59b..960cbf44b4c8abf9ab607297b505e8d25f302484 100644
--- a/tests/testthat/test-compare.R
+++ b/tests/testthat/test-compare.R
@@ -8,13 +8,13 @@ difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
test_that("compareSCEs works", {
expect_length(comparison, 3)
- expect_true(all(c("FeatureData", "PhenoData", "Plots") %in%
+ expect_true(all(c("RowData", "ColData", "Plots") %in%
names(comparison)))
- checkmate::expect_class(comparison$PhenoData, "data.frame")
- checkmate::expect_class(comparison$FeatureData, "data.frame")
- expect_length(comparison$Plots, 7)
+ checkmate::expect_class(comparison$ColData, "data.frame")
+ checkmate::expect_class(comparison$RowData, "data.frame")
+ expect_length(comparison$Plots, 8)
expect_true(all(c("Means", "Variances", "MeanVar", "LibrarySizes",
- "ZerosGene", "ZerosCell", "MeanZeros") %in%
+ "ZerosGene", "ZerosCell", "MeanZeros", "VarGeneCor") %in%
names(comparison$Plots)))
for (plot in names(comparison$Plots)) {
checkmate::expect_class(comparison$Plots[[plot]], "ggplot")
@@ -23,11 +23,11 @@ test_that("compareSCEs works", {
test_that("diffSCEs works", {
expect_length(difference, 5)
- expect_true(all(c("Reference", "FeatureData", "PhenoData", "Plots",
+ expect_true(all(c("Reference", "RowData", "ColData", "Plots",
"QQPlots") %in% names(difference)))
checkmate::expect_class(difference$Reference, "SingleCellExperiment")
- checkmate::expect_class(difference$PhenoData, "data.frame")
- checkmate::expect_class(difference$FeatureData, "data.frame")
+ checkmate::expect_class(difference$ColData, "data.frame")
+ checkmate::expect_class(difference$RowData, "data.frame")
expect_length(difference$Plots, 7)
expect_true(all(c("Means", "Variances", "MeanVar", "LibrarySizes",
"ZerosGene", "ZerosCell", "MeanZeros") %in%
diff --git a/tests/testthat/test-kersplat-simulate.R b/tests/testthat/test-kersplat-simulate.R
new file mode 100644
index 0000000000000000000000000000000000000000..3b003a1b8a6f2173c999459f2f7b37085f5355e5
--- /dev/null
+++ b/tests/testthat/test-kersplat-simulate.R
@@ -0,0 +1,7 @@
+context("Kersplat simulations")
+
+test.params <- newKersplatParams()
+
+test_that("kersplatSimulate output is valid", {
+ expect_true(validObject(kersplatSimulate(test.params)))
+})
diff --git a/tests/testthat/test-lun-simulate.R b/tests/testthat/test-lun-simulate.R
index 5f68442f19b882f75d5b8d7d05af1de97246469d..586181d3df91b121d6d8d29c6a2aa88004cf4527 100644
--- a/tests/testthat/test-lun-simulate.R
+++ b/tests/testthat/test-lun-simulate.R
@@ -3,4 +3,4 @@ context("Lun simulation")
test_that("Lun simulation output is valid", {
expect_true(validObject(lunSimulate()))
expect_true(validObject(lunSimulate(groupCells = c(10, 10))))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-lunEstimate.R b/tests/testthat/test-lunEstimate.R
index 010ae358c0b9a825902f30e7d791e91abf409a7e..10aeb53c50523f80a35e6f415001ba6841ae564b 100644
--- a/tests/testthat/test-lunEstimate.R
+++ b/tests/testthat/test-lunEstimate.R
@@ -1,9 +1,10 @@
context("lunEstimate")
library(scater)
-data("sc_example_counts")
+set.seed(1)
+counts <- counts(mockSCE())
test_that("lunEstimate works", {
- params <- lunEstimate(sc_example_counts)
+ params <- lunEstimate(counts)
expect_true(validObject(params))
})
diff --git a/tests/testthat/test-phenoEstimate.R b/tests/testthat/test-phenoEstimate.R
index d0ffc66d0aa485d6d2ebb38c99cca59f54dded1f..3beb1249586d5d2086a4d795de6641edbec3f25c 100644
--- a/tests/testthat/test-phenoEstimate.R
+++ b/tests/testthat/test-phenoEstimate.R
@@ -1,10 +1,11 @@
context("phenoEstimate")
library(scater)
-data("sc_example_counts")
+set.seed(1)
+counts <- counts(mockSCE())
test_that("phenoEstimate works", {
skip_if_not_installed("phenopath")
- params <- phenoEstimate(sc_example_counts)
+ params <- phenoEstimate(counts)
expect_true(validObject(params))
})
diff --git a/tests/testthat/test-simpleEstimate.R b/tests/testthat/test-simpleEstimate.R
index 3b581e1e25d09f87b79959934edcf82b6f93883f..1a4df185906b16f3cbf61d682ea7e4c4a71bac34 100644
--- a/tests/testthat/test-simpleEstimate.R
+++ b/tests/testthat/test-simpleEstimate.R
@@ -1,9 +1,25 @@
context("simpleEstimate")
library(scater)
-data("sc_example_counts")
+set.seed(1)
+counts <- counts(mockSCE())
test_that("simpleEstimate works", {
- params <- simpleEstimate(sc_example_counts)
+ params <- simpleEstimate(counts)
expect_true(validObject(params))
})
+
+test_that("simpleEstimate works with SingleCellExperiment", {
+ sce <- SingleCellExperiment::SingleCellExperiment(
+ assays = list(counts = counts)
+ )
+ params <- simpleEstimate(sce)
+ expect_true(validObject(params))
+})
+
+test_that("simpleEstimate works with SingleCellExperiment without counts", {
+ sce <- SingleCellExperiment::SingleCellExperiment(
+ assays = list(TEST = counts)
+ )
+ expect_warning(simpleEstimate(sce), "counts assay is missing")
+})
diff --git a/tests/testthat/test-sparseDCEstimate.R b/tests/testthat/test-sparseDCEstimate.R
index 2e18499c025c42db212159e4e92787ea730aa189..203ea116ed814fcfa8e26a10500785c687d69f74 100644
--- a/tests/testthat/test-sparseDCEstimate.R
+++ b/tests/testthat/test-sparseDCEstimate.R
@@ -1,13 +1,13 @@
context("sparseDCEstimate")
library(scater)
-data("sc_example_counts")
+set.seed(1)
+counts <- counts(mockSCE())
test_that("sparseDCEstimate works", {
skip_if_not_installed("SparseDC")
set.seed(1)
- conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
- params <- sparseDCEstimate(sc_example_counts, conditions,
- nclusters = 3)
+ conditions <- sample(1:2, ncol(counts), replace = TRUE)
+ params <- sparseDCEstimate(counts, conditions, nclusters = 3)
expect_true(validObject(params))
})
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..097b241637da023174b0f2e3715bd0291d9ded37
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/splat-model.png b/vignettes/splat-model.png
new file mode 100644
index 0000000000000000000000000000000000000000..1e5ca99ce1ce487c534d6e849c6643ee73b94a05
Binary files /dev/null and b/vignettes/splat-model.png differ
diff --git a/vignettes/splat_params.Rmd b/vignettes/splat_params.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..f8639d29cc71d5da3c11bffaa46f7b414853491a
--- /dev/null
+++ b/vignettes/splat_params.Rmd
@@ -0,0 +1,534 @@
+---
+title: "Splat simulation parameters"
+date: "Last updated: 18 April 2019"
+output:
+ BiocStyle::html_document:
+ toc: true
+ toc_float: true
+vignette: >
+ %\VignetteIndexEntry{Splat simulation parameters}
+ %\VignetteEngine{knitr::rmarkdown}
+ %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>"
+)
+```
+
+This vignette describes the Splat simulation model and the parameters it uses
+in more detail.
+
+```{r setup}
+library("splatter")
+library("scater")
+library("ggplot2")
+```
+
+# The base Splat model
+
+This figure, taken from the Splatter publication, describes the core of the
+Splat simulation model.
+
+
+
+The Splat simulation uses a hierarchical probabilistic where different aspects
+of a dataset are generated from appropriate statistical distributions. The
+first stage generates a mean expression level for each gene. These are
+originally chosen from a Gamma distribution. For some genes that are selected
+to be outliers with high expression a factor is generated from a log-normal
+distribution. These factors are then multiplied by the median gene mean to
+create new means for those genes.
+
+The next stage incorporates variation in the counts per cell. An expected
+library size (total counts) is chosen for each cell from a log-normal
+distribution. The library sizes are then used to scale the gene means for each
+cell, resulting in a range a counts per cell in the simulated dataset. The gene
+means are then further adjusted to enforce a relationship between the mean
+expression level and the variability.
+
+The final cell by gene matrix of gene means is then used to generate a count
+matrix using a Poisson distribution. The result is a synthetic dataset
+consisting of counts from a Gamma-Poisson (or negative-binomial) distribution.
+An additional optional step can be used to replicate a "dropout" effect. A
+probability of dropout is generated using a logistic function based on the
+underlying mean expression level. A Bernoulli distribution is then used to
+create a dropout matrix which sets some of the generated counts to zero.
+
+The model described here will generate a single population of cells but the
+Splat simulation has been designed to be as flexible as possible and can
+create scenarios including multiple groups of cells (cell types), continuous
+paths between cell types and multiple experimental batches. The parameters used
+to create these types of simulations and how they interact with the model are
+described below.
+
+# Splat simulation parameters
+
+Within Splatter the parameters for the Splat simulation model are held in the
+`SplatParams` object. Let's create one of these objects and see what it looks
+like.
+
+```{r splat-params}
+params <- newSplatParams()
+params
+```
+
+Like all the parameter objects in Splatter printing this object displays all the
+parameters required for this simulation. As we haven't set any of the parameters
+the default values are shown but if we were to change any of them they would be
+highlighted. We can also see which parameters can be estimated by the Splat
+estimation procedure and which can't. The default values have been chosen to be
+fairly realistic but it is recommended that estimation is used to get a
+simulation that is more like the data you are interested in. Parameters can be
+modified by setting them in the `SplatParams` object or by providing them
+directly to the simulation function.
+
+The rest of this section provides details of all this parameters and explains
+how they can be used with examples.
+
+## Global parameters
+
+These parameters are used in every simulation model and control global features
+of the dataset produced.
+
+### `nGenes` - Number of genes
+
+The number of genes to simulate.
+
+```{r nGenes}
+# Set the number of genes to 1000
+params <- setParam(params, "nGenes", 1000)
+
+sim <- splatSimulate(params, verbose = FALSE)
+dim(sim)
+```
+
+### `nCells` - Number of cells
+
+The number of genes to simulate. In the Splat simulation this cannot be set
+directly but must be controlled using the `batchCells` parameter.
+
+### `seed` - Random seed
+
+Seed to use for generating random numbers including selecting values from
+distributions. By changing this value multiple simulated datasets with the same
+parameters can be produced. Simulations produced using the same set of
+parameters and random seed should be identical but there may be differences
+between operating systems, software versions etc.
+
+## Batch parameters
+
+These parameters control experimental batches in the simulated dataset. The
+overall effect of how batch effects are included in the model is similar to
+technical replicates (i.e. the same biological sample sequenced multiple times).
+This means that the underlying structure is consistent between batches but a
+global technical signature is added may separate them.
+
+### `nBatches` - Number of batches
+
+The number of batches in the simulation. This cannot be set directly but is
+controlled by setting `batchCells`.
+
+### `batchCells` - Cells per batch
+
+A vector specifying the number of cells in each batch. The number of batches
+(`nBatches`) is equal to the length of the vector and the number of cells
+(`nCells`) is equal to the sum.
+
+```{r batches}
+# Simulation with two batches of 100 cells
+sim <- splatSimulate(params, batchCells = c(100, 100), verbose = FALSE)
+
+# PCA plot using scater
+sim <- normalize(sim)
+plotPCA(sim, colour_by = "Batch")
+```
+
+### `batch.facLoc` - Batch factor location and `batch.facScale` - Batch factor scale
+
+Batches are specified by generating a small scaling factor for each gene in
+each batch from a log-normal distribution. These factors are then applied to the
+underlying gene means in each batch. Modifying these parameters affects how
+different the batches are from each other by generating bigger or smaller
+factors.
+
+```{r batch-factors}
+# Simulation with small batch effects
+sim1 <- splatSimulate(params, batchCells = c(100, 100),
+ batch.facLoc = 0.001, batch.facScale = 0.001,
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Batch") + ggtitle("Small batch effects")
+
+# Simulation with big batch effects
+sim2 <- splatSimulate(params, batchCells = c(100, 100),
+ batch.facLoc = 0.5, batch.facScale = 0.5,
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Batch") + ggtitle("Big batch effects")
+```
+
+
+## Mean parameters
+
+These parameters control the distribution that is used to generate the
+underlying original gene means.
+
+### `mean.shape` - Mean shape and `mean.rate` - Mean rate
+
+These parameters control the Gamma distribution that gene means are drawn from.
+The relationship between shape and rate can be complex and it is often better
+to use values estimated from a real dataset than to try and manually set them.
+Although these parameters control the base gene means the means in the final
+simulation will depend upon other parts of the model, particularly the simulated
+total counts per cell (library sizes).
+
+## Library size parameters
+
+These parameters control the expected number of counts for each cell. Note that
+because of sampling the actual counts per cell in the final simulation may be
+different. Turning on the dropout effect will also effect this. We use the term
+"library size" here for consistency but expected total counts would be more
+appropriate.
+
+### `lib.loc` - Library size location and `lib.scale` - Library size scale
+
+These parameters control the shape of the distribution that is used to generate
+library sizes for each cell. Increasing `lib.loc` will lead to more counts per
+cell and increasing `lib.scale` will result in more variability in the counts
+per cell.
+
+### `lib.norm` - Library size distribution
+
+The default (and recommended) distribution used for library sizes in the Splat
+simulation is a log-normal. However, in rare cases a normal distribution might
+be more appropriate. Setting `lib.norm` to `TRUE` will use a normal distribution
+instead of a log-normal.
+
+## Expression outlier parameters
+
+When developing the Splat simulation we found that while the Gamma distribution
+was generally a good match for gene means for some datasets it did not properly
+capture highly expressed genes. For this reason we added expression outliers to
+the Splat model.
+
+### `out.prob` - Expression outlier probability
+
+This parameter controls the probability that genes will be selected to be
+expression outliers. Higher values will results in more outlier genes.
+
+```{r outlier-prob}
+# Few outliers
+sim1 <- splatSimulate(out.prob = 0.001, verbose = FALSE)
+ggplot(as.data.frame(rowData(sim1)),
+ aes(x = log10(GeneMean), fill = OutlierFactor != 1)) +
+ geom_histogram(bins = 100) +
+ ggtitle("Few outliers")
+
+# Lots of outliers
+sim2 <- splatSimulate(out.prob = 0.2, verbose = FALSE)
+ggplot(as.data.frame(rowData(sim2)),
+ aes(x = log10(GeneMean), fill = OutlierFactor != 1)) +
+ geom_histogram(bins = 100) +
+ ggtitle("Lots of outliers")
+```
+
+### `out.facLoc` - Expression outlier factor location and `out.facScale` - Expression outlier factor scale
+
+The expression outlier factors are drawn from a log-normal distribution
+controlled by these parameters. The generated factors are applied to the median
+mean expression rather than the existing mean for the selected genes. This is
+to be consistent with the estimation procedure for these factors and to make
+sure that the final means are outliers. For example to avoid the situation where
+a factor is applied to a lowly expressed gene, making it just moderately
+expressed rather than an expression outlier.
+
+### Group parameters
+
+Up until this stage of the simulation only a single population of cells is
+considered but we often want to simulate datasets with multiple kinds of cells.
+We do this by assigning cells to groups.
+
+### `nGroups` - Number of groups
+
+The number of groups to simulate. This parameter cannot be set directly and is
+controlled using `group.prob`.
+
+### `group.prob` - Group probabilities
+
+A vector giving the probability that cells will be assigned to groups. The
+length of the vector gives the number of groups (`nGroups`) and the
+probabilities must sum to 1. Adjusting the number and relative values of the
+probabilities changes the number and relative sizes of the groups. To simulate
+groups we also need to use the `splatSimulateGroups` function or set
+`method = "groups"`.
+
+```{r groups}
+params.groups <- newSplatParams(batchCells = 500, nGenes = 1000)
+
+# One small group, one big group
+sim1 <- splatSimulateGroups(params.groups, group.prob = c(0.9, 0.1),
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("One small group, one big group")
+
+# Five groups
+sim2 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.2, 0.2, 0.2, 0.2, 0.2),
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Five groups")
+```
+
+**Note:** Once there are more than three or four groups it becomes difficult to
+properly view them in PCA space. We use PCA here for simplicity but generally a
+non-linear dimensionality reduction such as t-SNE or UMAP is a more useful way
+to visualise the groups.
+
+### Differential expression parameters
+
+Different groups are created by modifying the base expression levels of selected
+genes. The process for doing this is to simulate differential expression (DE)
+between each group and a fictional base cell. Altering the differential
+expression parameters controls how similar groups are to each other.
+
+### `de.prob` - DE probability
+
+This parameter controls the probability that a gene will be selected to be
+differentially expressed.
+
+```{r de-prob}
+# Few DE genes
+sim1 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.prob = 0.01, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("Few DE genes")
+
+# Lots of DE genes
+sim2 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.prob = 0.3, verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Lots of DE genes")
+```
+
+### `de.downProb` - Down-regulation probability
+
+A selected DE gene can be either down-regulated (has a factor less than one) or
+up-regulated (has a factor greater than one). This parameter controls the
+probability that a selected gene will be down-regulated.
+
+### `de.facLoc` - DE factor location and `de.facScale` - DE factor scale
+
+Differential expression factors are produced from a log-normal distribution in
+a similar way to batch effect factors and expression outlier factors. Changing
+these parameters can result in more or less extreme differences between groups.
+
+```{r de-factors}
+# Small DE factors
+sim1 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.facLoc = 0.01, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("Small DE factors")
+
+# Big DE factors
+sim2 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.facLoc = 0.3, verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Big DE factors")
+```
+
+Just looking at the PCA plots this effect seems similar to adjusting `de.prob`
+but the effect is achieved in a different way. A higher `de.prob` means that
+more genes are differentially expressed but changing the DE factors changes the
+level of DE for the same number of genes.
+
+### Complex differential expression
+
+Each of the differential expression parameters can be specified for each group
+by providing a vector of values. These vectors must be the same length as
+`group.prob`. Specifying parameters as vectors allows more complex simulations
+where groups are more or less different to each other rather than being equally
+distinct. Here are some examples of different DE scenarios.
+
+```{r complex-de}
+# Different DE probs
+sim1 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.2, 0.2, 0.2, 0.2, 0.2),
+ de.prob = c(0.01, 0.01, 0.1, 0.1, 0.3),
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") +
+ labs(title = "Different DE probabilities",
+ caption = paste("Groups 1 and 2 have very few DE genes,",
+ "Groups 3 and 4 have the default number,",
+ "Group 5 has many DE genes"))
+
+
+# Different DE factors
+sim2 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.2, 0.2, 0.2, 0.2, 0.2),
+ de.facLoc = c(0.01, 0.01, 0.1, 0.1, 0.2),
+ de.facScale = c(0.2, 0.5, 0.2, 0.5, 0.4),
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") +
+ labs(title = "Different DE factors",
+ caption = paste("Group 1 has factors with small location (value),",
+ "and scale (variability),",
+ "Group 2 has small location and greater scale.\n",
+ "Groups 3 and 4 have greater location with small,",
+ "and large scales",
+ "Group 5 has bigger factors with moderate",
+ "variability"))
+
+# Combination of everything
+sim3 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.05, 0.2, 0.2, 0.2, 0.35),
+ de.prob = c(0.3, 0.1, 0.2, 0.01, 0.1),
+ de.downProb = c(0.1, 0.4, 0.9, 0.6, 0.5),
+ de.facLoc = c(0.6, 0.1, 0.1, 0.01, 0.2),
+ de.facScale = c(0.1, 0.4, 0.2, 0.5, 0.4),
+ verbose = FALSE)
+sim3 <- normalize(sim3)
+plotPCA(sim3, colour_by = "Group") +
+ labs(title = "Different DE factors",
+ caption = paste(
+ "Group 1 is small with many very up-regulated DE genes,",
+ "Group 2 has the default DE parameters,\n",
+ "Group 3 has many down-regulated DE genes,",
+ "Group 4 has very few DE genes,",
+ "Group 5 is large with moderate DE factors")
+ )
+```
+
+## Biological Coefficient of Variation (BCV) parameters
+
+The BCV parameters control the variability of the genes in the simulated
+dataset.
+
+### `bcv.common` - Common BCV
+
+The `bcv.common` parameter controls the underlying common variability across
+all genes in the dataset.
+
+### `bcv.df` - BCV Degrees of Freedom
+
+This parameter sets the degrees of freedom used in the BCV inverse chi-squared
+distribution. Changing this changes the effect of mean expression on the
+variability of a gene.
+
+## Dropout parameters
+
+These parameters control whether additional dropout is added to increase the
+number of zeros in the simulated dataset and if it is how that is applied.
+
+### `dropout.type` - Dropout type
+
+This parameter determines the kind of dropout effect to simulate. Setting it to
+`"none"` means no dropout, "`experiment`" is global dropout using the same set
+of parameters for every cell, `"batch"` uses the same parameters for every cell
+in the same batch, `"group"` uses the same parameters for every cell in the
+same group and `"cell"` uses a different set of parameters for every cell.
+
+### `dropout.mid` - Dropout mid point and `dropout.shape` - Dropout shape
+
+The probability that a particular count in a particular cell is set to zero is
+related to the mean expression of that gene in that cell. This relationship is
+represented using a logistic function with these parameters. The `dropout.mid`
+parameter control the point at which the probability is equal to 0.5 and the
+`dropout.shape` controls how it changes with increasing expression. These
+parameters must be vectors of the appropriate length depending on the selected
+dropout type.
+
+## Path parameters
+
+For many uses simulating groups is sufficient but in some cases it is more
+appropriate to simulate continuous changes between cell types. The number of
+paths and the probability of assigning cells to them is still controlled by the
+`group.prob` parameter and the amount of change along a path is controlled by
+the DE parameters but other aspects of the `splatSimulatePaths` model are
+controlled by these parameters.
+
+### `path.from` - Path origin
+
+This parameter controls the order of differentiation paths. It is a vector the
+same length as `group.prob` giving the starting position of each path. For
+example a `path.from` of `c(0, 1, 1, 3)` would indicate the Path 1 starts at
+the origin (0), Path 2 starts at the end of Path 1, Path 3 also starts at the
+end of Path 1 (a branch point) and Path 4 starts at the end of Path 3.
+
+```{r paths}
+# Linear paths
+sim1 <- splatSimulatePaths(params.groups,
+ group.prob = c(0.25, 0.25, 0.25, 0.25),
+ de.prob = 0.5, de.facLoc = 0.2,
+ path.from = c(0, 1, 2, 3),
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("Linear paths")
+
+# Branching path
+sim2 <- splatSimulatePaths(params.groups,
+ group.prob = c(0.25, 0.25, 0.25, 0.25),
+ de.prob = 0.5, de.facLoc = 0.2,
+ path.from = c(0, 1, 1, 3),
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Branching path")
+```
+
+### `path.nSteps` - Number of steps
+
+A path is created by using the same differential expression procedure as used
+for groups to generate an end point. Interpolation is then used to create a
+series of steps between the start and end points. This parameter controls the
+number of steps along a path and therefore how discrete or smooth it is.
+
+```{r paths-steps}
+# Few steps
+sim1 <- splatSimulatePaths(params.groups, path.nSteps = 3,
+ de.prob = 0.5, de.facLoc = 0.2, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Step") + ggtitle("Few steps")
+
+# Lots of steps
+sim2 <- splatSimulatePaths(params.groups, path.nSteps = 1000,
+ de.prob = 0.5, de.facLoc = 0.2, verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Step") + ggtitle("Lots of steps")
+```
+
+### `path.skew` - Path skew
+
+By default cells are evenly distributed along a path but it sometimes be useful
+to introduce a skew in the distribution, For example you may want to simulate
+a scenario with few stem-like cells and many differentiated cells. Setting
+`path.skew` to 0 will mean that all cells come from the end point while
+higher values up to 1 will skew them towards the start point.
+
+```{r paths-skew}
+# Skew towards the end
+sim1 <- splatSimulatePaths(params.groups, path.skew = 0.1,
+ de.prob = 0.5, de.facLoc = 0.2, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Step") + ggtitle("Skewed towards the end")
+```
+
+### `path.nonlinearProb` - Non-linear probability
+
+Most genes are interpolated in a linear way along a path but in reality this
+may not always be the case. For example it is easy to imagine a gene that
+is lowly-expressed at the start of a process, highly-expressed in the middle
+and lowly-expressed again at the end. The `path.nonlinearProb` parameter
+controls the probability that a gene will change in a non-linear way along a
+path.
+
+### `path.sigmaFac` - Path skew
+
+Non-linear changes along a path are achieved by building a Brownian bridge
+between the two end points. A Brownian bridge is Brownian motion controlled in
+such a way that the end points are fixed. The `path.sigmaFac` parameter controls
+how extreme each step in the Brownian motion is and therefore how much the
+interpolation differs from a linear path.
diff --git a/vignettes/splatter-logo-small.png b/vignettes/splatter-logo-small.png
index cd78c46e70f630623a5916269309b09f5f438e0b..0c606de481f139402d10d5b10dbb07394aa51260 100644
Binary files a/vignettes/splatter-logo-small.png and b/vignettes/splatter-logo-small.png differ
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index af3eeff28682164c346d4be2b23230396de48a23..8bb64af30582846ec389c7dd34195d3a7a69b371 100644
--- a/vignettes/splatter.Rmd
+++ b/vignettes/splatter.Rmd
@@ -45,17 +45,19 @@ BiocManager::install("Oshlack/splatter", dependencies = TRUE,
Assuming you already have a matrix of count data similar to that you wish to
simulate there are two simple steps to creating a simulated data set with
-Splatter. Here is an example using the example dataset in the `scater` package:
+Splatter. Here is an example a mock dataset generated with the `scater` package:
```{r quickstart}
# Load package
library(splatter)
-# Load example data
+# Create mock data
library(scater)
-data("sc_example_counts")
-# Estimate parameters from example data
-params <- splatEstimate(sc_example_counts)
+set.seed(1)
+sce <- mockSCE()
+
+# Estimate parameters from mock data
+params <- splatEstimate(sce)
# Simulate data using estimated parameters
sim <- splatSimulate(params)
```
@@ -84,71 +86,6 @@ types of cells or differentiation paths between different cells types where
expression changes in a continuous way. These are described further in the
[simulating counts] section.
-## Parameters
-
-The parameters required for the Splat simulation are briefly described here:
-
-* **Global parameters**
- * `nGenes` - The number of genes to simulate.
- * `nCells` - The number of cells to simulate.
- * `seed` - Seed to use for generating random numbers.
-* **Batch parameters**
- * `nBatches` - The number of batches to simulate.
- * `batchCells` - The number of cells in each batch.
- * `batch.facLoc` - Location (meanlog) parameter for the batch effects factor
- log-normal distribution.
- * `batch.facScale` - Scale (sdlog) parameter for the batch effects factor
- log-normal distribution.
-* **Mean parameters**
- * `mean.shape` - Shape parameter for the mean gamma distribution.
- * `mean.rate` - Rate parameter for the mean gamma distribution.
-* **Library size parameters**
- * `lib.loc` - Location (meanlog) parameter for the library size log-normal
- distribution, or mean for the normal distribution.
- * `lib.scale` - Scale (sdlog) parameter for the library size log-normal
- distribution, or sd for the normal distribution.
- * `lib.norm` - Whether to use a normal distribution instead of the usual
- log-normal distribution.
-* **Expression outlier parameters**
- * `out.prob` - Probability that a gene is an expression outlier.
- * `out.facLoc` - Location (meanlog) parameter for the expression outlier
- factor log-normal distribution.
- * `out.facScale` - Scale (sdlog) parameter for the expression outlier factor
- log-normal distribution.
-* **Group parameters**
- * `nGroups` - The number of groups or paths to simulate.
- * `group.prob` - The probabilities that cells come from particular groups.
-* **Differential expression parameters**
- * `de.prob` - Probability that a gene is differentially expressed in each
- group or path.
- * `de.loProb` - Probability that a differentially expressed gene is
- down-regulated.
- * `de.facLoc` - Location (meanlog) parameter for the differential expression
- factor log-normal distribution.
- * `de.facScale` - Scale (sdlog) parameter for the differential expression
- factor log-normal distribution.
-* **Biological Coefficient of Variation parameters**
- * `bcv.common` - Underlying common dispersion across all genes.
- * `bcv.df` - Degrees of Freedom for the BCV inverse chi-squared
- distribution.
-* **Dropout parameters**
- * `dropout.type` - Type of dropout to simulate.
- * `dropout.mid` - Midpoint parameter for the dropout logistic function.
- * `dropout.shape` - Shape parameter for the dropout logistic function.
-* **Differentiation path parameters**
- * `path.from` - Vector giving the originating point of each path.
- * `path.length` - Vector giving the number of steps to simulate along each
- path.
- * `path.skew` - Vector giving the skew of each path.
- * `path.nonlinearProb` - Probability that a gene changes expression in a
- non-linear way along the differentiation path.
- * `path.sigmaFac` - Sigma factor for non-linear gene paths.
-
-While this may look like a lot of parameters Splatter attempts to make it easy
-for the user, both by providing sensible defaults and making it easy to estimate
-many of the parameters from real data. For more details on the parameters see
-`?SplatParams`.
-
# The `SplatParams` object
All the parameters for the Splat simulation are stored in a `SplatParams`
@@ -164,7 +101,8 @@ As well as telling us what type of object we have ("A `Params` object of class
some extra information. We can see which parameters can be estimated by the
`splatEstimate` function (those in parentheses), which can't be estimated
(those in brackets) and which have been changed from their default values (those
-in ALL CAPS).
+in ALL CAPS). For more details about the parameters of the Splat simulation
+refer to the [Splat parameters vignette](splat_params.html).
## Getting and setting
@@ -212,15 +150,20 @@ Splat allows you to estimate many of it's parameters from a data set containing
counts using the `splatEstimate` function.
```{r splatEstimate}
-# Check that sc_example counts is an integer matrix
-class(sc_example_counts)
-typeof(sc_example_counts)
+# Get the mock counts matrix
+counts <- counts(sce)
+
+# Check that counts is an integer matrix
+class(counts)
+typeof(counts)
+
# Check the dimensions, each row is a gene, each column is a cell
-dim(sc_example_counts)
+dim(counts)
+
# Show the first few entries
-sc_example_counts[1:5, 1:5]
+counts[1:5, 1:5]
-params <- splatEstimate(sc_example_counts)
+params <- splatEstimate(counts)
```
Here we estimated parameters from a counts matrix but `splatEstimate` can also
@@ -259,7 +202,7 @@ Looking at the output of `splatSimulate` we can see that `sim` is
`r ncol(sim)` samples (cells). The main part of this object is a features
by samples matrix containing the simulated counts (accessed using `counts`),
although it can also hold other expression measures such as FPKM or TPM.
-Additionaly a `SingleCellExperiment` contains phenotype information about
+Additionally a `SingleCellExperiment` contains phenotype information about
each cell (accessed using `colData`) and feature information about each gene
(accessed using `rowData`). Splatter uses these slots, as well as `assays`, to
store information about the intermediate values of the simulation.
@@ -298,12 +241,12 @@ For more details about the `SingleCellExperiment` object refer to the [vignette]
The `splatSimulate` function outputs the following additional information about
the simulation:
-* **Cell information (`pData`)**
+* **Cell information (`colData`)**
* `Cell` - Unique cell identifier.
* `Group` - The group or path the cell belongs to.
* `ExpLibSize` - The expected library size for that cell.
* `Step` (paths only) - How far along the path each cell is.
-* **Gene information (`fData`)**
+* **Gene information (`rowData`)**
* `Gene` - Unique gene identifier.
* `BaseGeneMean` - The base expression level for that gene.
* `OutlierFactor` - Expression outlier factor for that gene (1 is not an
@@ -313,7 +256,7 @@ the simulation:
in a particular group (1 is not differentially expressed).
* `GeneMean[Group]` - Expression level of a gene in a particular group after
applying differential expression factors.
-* **Gene by cell information (`assayData`)**
+* **Gene by cell information (`assays`)**
* `BaseCellMeans` - The expression of genes in each cell adjusted for
expected library size.
* `BCV` - The Biological Coefficient of Variation for each gene in
@@ -347,9 +290,9 @@ sim.groups <- normalize(sim.groups)
plotPCA(sim.groups, colour_by = "Group")
```
-As we have set both the group probabilites to 0.5 we should get approximately
+As we have set both the group probabilities to 0.5 we should get approximately
equal numbers of cells in each group (around 50 in this case). If we wanted
-uneven groups we could set `group.prob` to any set of probabilites that sum to
+uneven groups we could set `group.prob` to any set of probabilities that sum to
1.
## Simulating paths
@@ -408,7 +351,7 @@ made the batch effects dominate.
Each of the Splatter simulation methods has it's own convenience function.
To simulate a single population use `splatSimulateSingle()` (equivalent to
-`splatSimulate(method = "single")`), to simulate grops use
+`splatSimulate(method = "single")`), to simulate groups use
`splatSimulateGroups()` (equivalent to `splatSimulate(method = "groups")`) or to
simulate paths use `splatSimulatePaths()` (equivalent to
`splatSimulate(method = "paths")`).
@@ -424,12 +367,6 @@ the available simulations run the `listSims()` function:
listSims()
```
-(or more conveniently for the vignette as a table)
-
-```{r listSims-table}
-knitr::kable(listSims(print = FALSE))
-```
-
Each simulation has it's own prefix which gives the name of the functions
associated with that simulation. For example the prefix for the simple
simulation is `simple` so it would store it's parameters in a `SimpleParams`
@@ -489,7 +426,7 @@ names(comparison$Plots)
```
The returned list has three items. The first two are the combined datasets by
-gene (`FeatureData`) and by cell (`PhenoData`) and the third contains some
+gene (`RowData`) and by cell (`ColData`) and the third contains some
comparison plots (produced using `ggplot2`), for example a plot of the
distribution of means:
@@ -503,8 +440,7 @@ number of expressed genes against the library size:
```{r comparison-libsize-features}
library("ggplot2")
-ggplot(comparison$PhenoData,
- aes(x = total_counts, y = total_features_by_counts, colour = Dataset)) +
+ggplot(comparison$ColData, aes(x = sum, y = detected, colour = Dataset)) +
geom_point()
```