diff --git a/DESCRIPTION b/DESCRIPTION
index 2f30b33373b0035637419a46a44ec1c93dc1f5c8..795ecc79f43cea99021682218138d0d6067695d0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,9 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.7
-Date: 2019-09-19
-Author: Luke Zappia
+Version: 1.9.7.9019
+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,
@@ -42,7 +40,8 @@ Imports:
SummarizedExperiment,
utils,
crayon,
- S4Vectors
+ S4Vectors,
+ rlang
Suggests:
BiocStyle,
covr,
@@ -62,7 +61,9 @@ Suggests:
zinbwave,
SparseDC,
BiocManager,
- spelling
+ spelling,
+ igraph,
+ DropletUtils
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
diff --git a/NAMESPACE b/NAMESPACE
index c9b65bdf8f29dc8cb1fdd86c22292094c7709fd9..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)
@@ -108,6 +116,7 @@ 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)
@@ -124,12 +133,17 @@ 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)
diff --git a/NEWS.md b/NEWS.md
index 283654bbce89a1e6085247f499e85fd1bad18873..90be82e60dfcd02b302650d967504d46e4089e78 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,39 @@
+# DEVELOPMENT VERSION
+
+## Version 1.9.8
+
+### 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
@@ -6,10 +42,33 @@
* 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
@@ -18,10 +77,49 @@
* 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
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 1da947a4586fee93e38cf7b87ae43d95ec4c86ed..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.}
@@ -189,7 +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
@@ -255,6 +255,168 @@ setClass("SplatParams",
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.
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 4f01bfecfd454763b738bc1127239dbaca742459..6bb8a0005dae65e2981a66712cdfabe90ba9e5a6 100644
--- a/R/Params-methods.R
+++ b/R/Params-methods.R
@@ -48,8 +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/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/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 dba07d35a4f4c65458856f0c508dff84f06aaaf1..3243d8894a9063a8e89de186a4f18bafa9e03254 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -52,9 +52,9 @@
#' names(comparison)
#' names(comparison$Plots)
#' @importFrom ggplot2 ggplot aes_string geom_point geom_smooth geom_boxplot
-#' geom_tile scale_y_continuous scale_y_log10 scale_x_log10 scale_colour_manual
-#' scale_fill_manual scale_fill_distiller coord_fixed facet_wrap xlab ylab
-#' ggtitle theme_minimal
+#' geom_violin geom_tile scale_y_continuous scale_y_log10 scale_x_log10
+#' scale_colour_manual scale_fill_manual scale_fill_distiller coord_fixed
+#' facet_wrap xlab ylab ggtitle theme_minimal
#' @importFrom S4Vectors metadata<- metadata
#' @importFrom SingleCellExperiment cpm<- cpm
#' @importFrom stats cor
@@ -89,12 +89,12 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
colData(sce)$PctZero <- 100 * (1 - n.features / nrow(sce))
rowData(sce)$PctZero <- 100 - rowData(sce)$detected
- var.genes <- rev(order(rowData(sce)$VarLogCPM))[1:100]
+ var.genes <- rev(order(rowData(sce)$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$VarGeneA <- rep(paste0("VarGene", 1:100), 100)
- var.cors$VarGeneB <- rep(paste0("VarGene", 1:100), each = 100)
+ 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")]
@@ -125,8 +125,12 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
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()
@@ -134,8 +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()
@@ -154,9 +162,13 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
libs <- ggplot(cells,
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()
@@ -164,9 +176,13 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
z.gene <- ggplot(features,
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()
@@ -174,9 +190,13 @@ 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()
@@ -413,7 +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") +
@@ -423,7 +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)"))) +
@@ -447,7 +467,7 @@ 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 library size")) +
ggtitle("Difference in library sizes") +
@@ -457,7 +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") +
@@ -467,7 +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") +
@@ -489,7 +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)"))) +
@@ -500,7 +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)"))) +
@@ -511,7 +531,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
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") +
@@ -523,7 +543,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
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") +
@@ -534,7 +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") +
@@ -846,7 +866,7 @@ 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), Root Mean Squared
@@ -962,7 +982,7 @@ summariseStats <- function(data, split.col, stat.cols,
#' Summarise KS
#'
-#' Summarise columns of a data.frame compared to a referenc using the KS test.
+#' 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
diff --git a/R/kersplat-estimate.R b/R/kersplat-estimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..2bc5b81715a6edaacecc61c4b8c8509896e7117e
--- /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 <- BiocGenerics::counts(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/params-functions.R b/R/params-functions.R
index cfdb02c4a37f676c12131bfa7f2601c37c3709b6..eed27d1e542fd901a2a80f0b06bd81049fc4c418 100644
--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -15,7 +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)
+ params.list <- lapply(names, getParam, object = params)
+ names(params.list) <- names
+
+ return(params.list)
}
#' Set parameters UNCHECKED
@@ -70,13 +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])
@@ -88,13 +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) {
@@ -102,13 +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]))
@@ -118,15 +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,
@@ -145,6 +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) {
@@ -173,6 +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/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/sparseDC-simulate.R b/R/sparseDC-simulate.R
index 5aa9a4ed6939262d8935d8d2597808a85123ee76..abd69b3e389450a911d00272dbc88fe63724591b 100644
--- a/R/sparseDC-simulate.R
+++ b/R/sparseDC-simulate.R
@@ -81,7 +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 0d7201359f38694097948a3acb2660776a437fdf..459606d7c10c56bbbe2fb6d6d8531e48d8395656 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -70,7 +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
@@ -111,7 +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 8063afe5424927e29f45a6c7c4b4fe365e6ba367..927e0c69896e71f2fa8729bf814cfac360a60b19 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -589,9 +589,9 @@ splatSimPathCellMeans <- function(sim, params) {
return(probs)
})
- steps <- sapply(factor(groups), function(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) {
@@ -774,10 +774,10 @@ splatSimDropout <- function(sim, params) {
if (dropout.type != "none") {
# Generate probabilities based on expression
- drop.prob <- sapply(seq_len(nCells), function(idx) {
+ 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),
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 7dee99d299c98497b5e0eaa9c352a24003b9ef47..679977e4aa4f5543fb4de74a90981ed5647fd697 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -8,21 +8,25 @@
<title>License • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,10 +36,12 @@
<link href="extra.css" rel="stylesheet">
+
<meta property="og:title" content="License" />
+
<!-- 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>
@@ -56,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -72,7 +79,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -80,7 +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>
@@ -106,11 +113,10 @@
<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>
@@ -121,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -810,19 +817,23 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/index.html b/docs/articles/index.html
index dc87dfc3d2ccb8c0dfbe1ac187b040e2cab16484..5b054c57bf648ed2e43fb68c70d2bbe13d2ec6f4 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -8,21 +8,25 @@
<title>Articles • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,10 +36,12 @@
<link href="../extra.css" rel="stylesheet">
+
<meta property="og:title" content="Articles" />
+
<!-- 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>
@@ -56,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -72,7 +79,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -80,7 +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>
@@ -106,11 +113,10 @@
<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>
@@ -121,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -141,19 +148,23 @@
</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> 1.3.0.</p>
+ <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.html b/docs/articles/splat_params.html
index 66f02796940c5d8570c08697c5c8f122cd96ee20..de92495615ef07727693823dd6a7dcae375d422a 100644
--- a/docs/articles/splat_params.html
+++ b/docs/articles/splat_params.html
@@ -7,8 +7,9 @@
<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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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><!-- 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">
+<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="">
@@ -37,7 +38,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -45,7 +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>
@@ -74,7 +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>
@@ -87,6 +88,7 @@
<!--/.navbar -->
+
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
@@ -102,71 +104,76 @@
<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://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"splatter"</span>)</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">#> Warning: package 'splatter' was built under R version 3.6.1</span></a>
-<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co">#> Loading required package: SingleCellExperiment</span></a>
-<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">#> Warning: package 'SingleCellExperiment' was built under R version 3.6.1</span></a>
-<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">#> Loading required package: SummarizedExperiment</span></a>
-<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">#> Warning: package 'SummarizedExperiment' was built under R version 3.6.1</span></a>
-<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co">#> Loading required package: GenomicRanges</span></a>
+<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">#> Loading required package: parallel</span></a>
-<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="co">#> Attaching package: 'BiocGenerics'</span></a>
-<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co">#> The following objects are masked from 'package:parallel':</span></a>
-<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="co">#> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,</span></a>
-<a class="sourceLine" id="cb1-16" data-line-number="16"><span class="co">#> clusterExport, clusterMap, parApply, parCapply, parLapply,</span></a>
-<a class="sourceLine" id="cb1-17" data-line-number="17"><span class="co">#> parLapplyLB, parRapply, parSapply, parSapplyLB</span></a>
-<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co">#> The following objects are masked from 'package:stats':</span></a>
-<a class="sourceLine" id="cb1-19" data-line-number="19"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-20" data-line-number="20"><span class="co">#> IQR, mad, sd, var, xtabs</span></a>
-<a class="sourceLine" id="cb1-21" data-line-number="21"><span class="co">#> The following objects are masked from 'package:base':</span></a>
-<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-23" data-line-number="23"><span class="co">#> anyDuplicated, append, as.data.frame, basename, cbind,</span></a>
-<a class="sourceLine" id="cb1-24" data-line-number="24"><span class="co">#> colnames, dirname, do.call, duplicated, eval, evalq, Filter,</span></a>
-<a class="sourceLine" id="cb1-25" data-line-number="25"><span class="co">#> Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,</span></a>
-<a class="sourceLine" id="cb1-26" data-line-number="26"><span class="co">#> mapply, match, mget, order, paste, pmax, pmax.int, pmin,</span></a>
-<a class="sourceLine" id="cb1-27" data-line-number="27"><span class="co">#> pmin.int, Position, rank, rbind, Reduce, rownames, sapply,</span></a>
-<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="co">#> setdiff, sort, table, tapply, union, unique, unsplit, which,</span></a>
-<a class="sourceLine" id="cb1-29" data-line-number="29"><span class="co">#> which.max, which.min</span></a>
-<a class="sourceLine" id="cb1-30" data-line-number="30"><span class="co">#> Loading required package: S4Vectors</span></a>
-<a class="sourceLine" id="cb1-31" data-line-number="31"><span class="co">#> Warning: package 'S4Vectors' was built under R version 3.6.1</span></a>
-<a class="sourceLine" id="cb1-32" data-line-number="32"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-33" data-line-number="33"><span class="co">#> Attaching package: 'S4Vectors'</span></a>
-<a class="sourceLine" id="cb1-34" data-line-number="34"><span class="co">#> The following object is masked from 'package:base':</span></a>
-<a class="sourceLine" id="cb1-35" data-line-number="35"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-36" data-line-number="36"><span class="co">#> expand.grid</span></a>
-<a class="sourceLine" id="cb1-37" data-line-number="37"><span class="co">#> Loading required package: IRanges</span></a>
-<a class="sourceLine" id="cb1-38" data-line-number="38"><span class="co">#> Loading required package: GenomeInfoDb</span></a>
-<a class="sourceLine" id="cb1-39" data-line-number="39"><span class="co">#> Loading required package: Biobase</span></a>
-<a class="sourceLine" id="cb1-40" data-line-number="40"><span class="co">#> Welcome to Bioconductor</span></a>
-<a class="sourceLine" id="cb1-41" data-line-number="41"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-42" data-line-number="42"><span class="co">#> Vignettes contain introductory material; view with</span></a>
-<a class="sourceLine" id="cb1-43" data-line-number="43"><span class="co">#> 'browseVignettes()'. To cite Bioconductor, see</span></a>
-<a class="sourceLine" id="cb1-44" data-line-number="44"><span class="co">#> 'citation("Biobase")', and for packages 'citation("pkgname")'.</span></a>
-<a class="sourceLine" id="cb1-45" data-line-number="45"><span class="co">#> Loading required package: DelayedArray</span></a>
-<a class="sourceLine" id="cb1-46" data-line-number="46"><span class="co">#> Loading required package: matrixStats</span></a>
-<a class="sourceLine" id="cb1-47" data-line-number="47"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-48" data-line-number="48"><span class="co">#> Attaching package: 'matrixStats'</span></a>
-<a class="sourceLine" id="cb1-49" data-line-number="49"><span class="co">#> The following objects are masked from 'package:Biobase':</span></a>
-<a class="sourceLine" id="cb1-50" data-line-number="50"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-51" data-line-number="51"><span class="co">#> anyMissing, rowMedians</span></a>
-<a class="sourceLine" id="cb1-52" data-line-number="52"><span class="co">#> Loading required package: BiocParallel</span></a>
-<a class="sourceLine" id="cb1-53" data-line-number="53"><span class="co">#> Warning: package 'BiocParallel' was built under R version 3.6.1</span></a>
-<a class="sourceLine" id="cb1-54" data-line-number="54"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-55" data-line-number="55"><span class="co">#> Attaching package: 'DelayedArray'</span></a>
-<a class="sourceLine" id="cb1-56" data-line-number="56"><span class="co">#> The following objects are masked from 'package:matrixStats':</span></a>
-<a class="sourceLine" id="cb1-57" data-line-number="57"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-58" data-line-number="58"><span class="co">#> colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</span></a>
-<a class="sourceLine" id="cb1-59" data-line-number="59"><span class="co">#> The following objects are masked from 'package:base':</span></a>
-<a class="sourceLine" id="cb1-60" data-line-number="60"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb1-61" data-line-number="61"><span class="co">#> aperm, apply, rowsum</span></a>
-<a class="sourceLine" id="cb1-62" data-line-number="62"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"scater"</span>)</a>
-<a class="sourceLine" id="cb1-63" data-line-number="63"><span class="co">#> Warning: package 'scater' was built under R version 3.6.1</span></a>
-<a class="sourceLine" id="cb1-64" data-line-number="64"><span class="co">#> Loading required package: ggplot2</span></a>
-<a class="sourceLine" id="cb1-65" data-line-number="65"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"ggplot2"</span>)</a></code></pre></div>
+<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>
@@ -187,50 +194,51 @@
<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">#> </span></a>
-<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co">#> Global: </span></a>
-<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co">#> (Genes) (Cells) [Seed] </span></a>
-<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="co">#> 10000 100 575939 </span></a>
-<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#> 28 additional parameters </span></a>
-<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co">#> Batches: </span></a>
-<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co">#> [Batches] [Batch Cells] [Location] [Scale] </span></a>
-<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co">#> 1 100 0.1 0.1 </span></a>
-<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co">#> Mean: </span></a>
-<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co">#> (Rate) (Shape) </span></a>
-<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co">#> 0.3 0.6 </span></a>
-<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co">#> Library size: </span></a>
-<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co">#> (Location) (Scale) (Norm) </span></a>
-<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co">#> 11 0.2 FALSE </span></a>
-<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co">#> Exprs outliers: </span></a>
-<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co">#> (Probability) (Location) (Scale) </span></a>
-<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co">#> 0.05 4 0.5 </span></a>
-<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co">#> Groups: </span></a>
-<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co">#> [Groups] [Group Probs] </span></a>
-<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co">#> 1 1 </span></a>
-<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co">#> Diff expr: </span></a>
-<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co">#> [Probability] [Down Prob] [Location] [Scale] </span></a>
-<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co">#> 0.1 0.5 0.1 0.4 </span></a>
-<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co">#> BCV: </span></a>
-<a class="sourceLine" id="cb2-37" data-line-number="37"><span class="co">#> (Common Disp) (DoF) </span></a>
-<a class="sourceLine" id="cb2-38" data-line-number="38"><span class="co">#> 0.1 60 </span></a>
-<a class="sourceLine" id="cb2-39" data-line-number="39"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-40" data-line-number="40"><span class="co">#> Dropout: </span></a>
-<a class="sourceLine" id="cb2-41" data-line-number="41"><span class="co">#> [Type] (Midpoint) (Shape) </span></a>
-<a class="sourceLine" id="cb2-42" data-line-number="42"><span class="co">#> none 0 -1 </span></a>
-<a class="sourceLine" id="cb2-43" data-line-number="43"><span class="co">#> </span></a>
-<a class="sourceLine" id="cb2-44" data-line-number="44"><span class="co">#> Paths: </span></a>
-<a class="sourceLine" id="cb2-45" data-line-number="45"><span class="co">#> [From] [Steps] [Skew] [Non-linear] </span></a>
-<a class="sourceLine" id="cb2-46" data-line-number="46"><span class="co">#> 0 100 0.5 0.1 </span></a>
-<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="co">#> [Sigma Factor] </span></a>
-<a class="sourceLine" id="cb2-48" data-line-number="48"><span class="co">#> 0.8</span></a></code></pre></div>
+<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">
@@ -245,7 +253,7 @@
<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://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(sim)</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">
@@ -273,14 +281,14 @@
<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://www.rdocumentation.org/packages/base/topics/c">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="cb4-2" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim, <span class="dt">colour_by =</span> <span class="st">"Batch"</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>
@@ -289,27 +297,27 @@
<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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="dv">100</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb5-9" 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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="dv">100</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb6-11" 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>
@@ -349,16 +357,16 @@
<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://www.rdocumentation.org/packages/base/topics/as.data.frame">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://www.rdocumentation.org/packages/base/topics/Log">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="cb7-3" 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://www.rdocumentation.org/packages/base/topics/as.data.frame">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://www.rdocumentation.org/packages/base/topics/Log">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="cb8-4" 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>
@@ -385,26 +393,26 @@
<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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.9</span>, <span class="fl">0.1</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb9-10" 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://www.rdocumentation.org/packages/base/topics/c">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="cb10-4" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb10-11" 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>
@@ -419,25 +427,25 @@
<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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb11-8" 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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb12-10" 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>
@@ -451,25 +459,25 @@
<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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb13-8" 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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb14-10" 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>
@@ -480,16 +488,16 @@
<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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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="cb15-3" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim1, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb15-10" 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://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Groups 1 and 2 have very few DE genes,"</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>
@@ -498,42 +506,43 @@
<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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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="cb16-5" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim2, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb16-14" 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://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Group 1 has factors with small location (value),"</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 variability"</span>))</a>
-<a class="sourceLine" id="cb16-22" data-line-number="22"><span class="co">#> Warning: call 'runPCA' explicitly to compute results</span></a></code></pre></div>
+<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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">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="cb17-4" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim3)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim3, <span class="dt">colour_by =</span> <span class="st">"Group"</span>) <span class="op">+</span></a>
+<a class="sourceLine" id="cb17-15" 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://www.rdocumentation.org/packages/base/topics/paste">paste</a></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>
@@ -581,33 +590,33 @@
<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://www.rdocumentation.org/packages/base/topics/c">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>
+<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://www.rdocumentation.org/packages/base/topics/c">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="cb18-3" 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://www.rdocumentation.org/packages/base/topics/c">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="cb18-5" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb18-11" 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://www.rdocumentation.org/packages/base/topics/c">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="cb19-4" 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://www.rdocumentation.org/packages/base/topics/c">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="cb19-6" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb19-13" 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>
@@ -618,23 +627,23 @@
<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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb20-8" 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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim2)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb21-10" 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>
@@ -645,11 +654,11 @@
<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://www.rdocumentation.org/packages/scater/topics/normalize">normalize</a></span>(sim1)</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://www.rdocumentation.org/packages/scater/topics/plot_reddim">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="cb22-8" 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>
@@ -668,6 +677,7 @@
</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>
@@ -692,17 +702,20 @@
</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> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
+
</footer>
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+
</body>
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diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index a7ea371e2076657d28d7781a50576cb5f3be778b..85228f2dc3f4b610ad3d269cd7a95940161eaec2 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -7,8 +7,9 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Introduction to Splatter • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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><!-- 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">
+<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="">
@@ -37,7 +38,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -45,7 +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>
@@ -74,7 +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>
@@ -87,13 +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">2019-08-20</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>
@@ -110,27 +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"><a href="https://www.rdocumentation.org/packages/base/topics/ns-load">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://www.rdocumentation.org/packages/utils/topics/install.packages">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://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="https://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 a mock dataset generted with 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"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(splatter)</a></code></pre></div>
-<pre><code>## Warning: package 'splatter' was built under R version 3.6.1</code></pre>
+<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>
@@ -159,14 +162,18 @@
##
## 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>
@@ -183,18 +190,18 @@
<pre><code>## The following objects are masked from 'package:base':
##
## aperm, apply, rowsum</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="co"># Create mock data</span></a>
-<a class="sourceLine" id="cb34-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(scater)</a></code></pre></div>
+<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>
-<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Random">set.seed</a></span>(<span class="dv">1</span>)</a>
-<a class="sourceLine" id="cb37-2" data-line-number="2">sce <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/mockSCE">mockSCE</a></span>()</a>
-<a class="sourceLine" id="cb37-3" data-line-number="3"></a>
-<a class="sourceLine" id="cb37-4" data-line-number="4"><span class="co"># Estimate parameters from mock data</span></a>
-<a class="sourceLine" id="cb37-5" 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>
+<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="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1"><span class="co"># Simulate data using estimated parameters</span></a>
-<a class="sourceLine" id="cb39-2" 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>
+<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>
@@ -215,14 +222,15 @@
<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="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" 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="cb48-2" 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 575939
+## 10000 100 955861
##
## 28 additional parameters
##
@@ -268,17 +276,17 @@
<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="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" 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="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" 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="cb52-2" 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="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
-<a class="sourceLine" id="cb54-2" 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://www.rdocumentation.org/packages/base/topics/list">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="cb54-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
-<a class="sourceLine" id="cb54-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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
##
@@ -287,15 +295,16 @@
##
## $mean.shape
## [1] 0.6</code></pre>
-<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
-<a class="sourceLine" id="cb56-2" 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="cb56-3" 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 575939
+## 8000 100 955861
##
## 28 additional parameters
##
@@ -338,8 +347,8 @@
## 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="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" 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="cb58-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></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
##
@@ -351,26 +360,26 @@
<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="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" data-line-number="1"><span class="co"># Get the mock counts matrix</span></a>
-<a class="sourceLine" id="cb60-2" data-line-number="2">counts <-<span class="st"> </span><span class="kw">counts</span>(sce)</a>
-<a class="sourceLine" id="cb60-3" data-line-number="3"></a>
-<a class="sourceLine" id="cb60-4" data-line-number="4"><span class="co"># Check that counts is an integer matrix</span></a>
-<a class="sourceLine" id="cb60-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(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="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/typeof">typeof</a></span>(counts)</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="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" 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="cb64-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(counts)</a></code></pre></div>
+<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="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
-<a class="sourceLine" id="cb66-2" 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>
+<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 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="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" 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>
+<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">
@@ -386,7 +395,7 @@
<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="cb70"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb70-1" 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>
@@ -395,7 +404,7 @@
<pre><code>## Simulating counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</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">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 200
## metadata(1): Params
@@ -408,56 +417,56 @@
## 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="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Access the counts</span></a>
-<a class="sourceLine" id="cb81-2" 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>
+<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 683 9103 3101 3110 1637
-## Gene2 634 342 205 179 467
-## Gene3 0 0 0 1 0
-## Gene4 1030 589 527 570 253
-## Gene5 0 4 3 0 2</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"># Information about genes</span></a>
-<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></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>
-## Gene1 Gene1 969.971697306478 1 969.971697306478
-## Gene2 Gene2 212.946759920409 1 212.946759920409
-## Gene3 Gene3 0.212456014089163 1 0.212456014089163
-## Gene4 Gene4 571.327025653128 1 571.327025653128
-## Gene5 Gene5 1.47190829598543 1 1.47190829598543
-## Gene6 Gene6 1.66119397884979 1 1.66119397884979</code></pre>
-<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"># Information about cells</span></a>
-<a class="sourceLine" id="cb85-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
+## 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 335351.08401721
-## Cell2 Cell2 Batch1 353232.031194834
-## Cell3 Cell3 Batch1 348516.116098443
-## Cell4 Cell4 Batch1 345250.205506489
-## Cell5 Cell5 Batch1 358512.781474554
-## Cell6 Cell6 Batch1 366554.730332392</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"># Gene by cell matrices</span></a>
-<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/names">names</a></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="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
-<a class="sourceLine" id="cb89-2" 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 6.802414e+02 8980.2305553 3082.9437264 3143.9692418 1.713283e+03
-## Gene2 6.280572e+02 334.2077963 195.7808953 174.4536072 4.801664e+02
-## Gene3 2.591298e-02 0.6016577 0.2507107 0.5312011 2.894290e-04
-## Gene4 1.031655e+03 578.0587110 488.4155647 544.3943677 2.543278e+02
-## Gene5 1.039024e-01 3.1161482 5.0742619 1.4205449 3.222323e+00</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="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
-<a class="sourceLine" id="cb91-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">normalize</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>
<pre><code>## Warning: 'centreSizeFactors' is deprecated.
## See help("Deprecated")</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"># Plot PCA</span></a>
-<a class="sourceLine" id="cb94-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
+<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>
@@ -516,13 +525,13 @@
<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="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" 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://www.rdocumentation.org/packages/base/topics/c">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="cb96-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb96-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">normalize</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>
<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="kw"><a href="https://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>
+<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 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>
@@ -531,12 +540,12 @@
<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="cb101"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb101-1" 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="cb101-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">normalize</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>
<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://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>
+<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>
@@ -545,22 +554,22 @@
<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="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" 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://www.rdocumentation.org/packages/base/topics/c">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="cb106-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">normalize</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>
<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://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>
+<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="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" 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://www.rdocumentation.org/packages/base/topics/c">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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
-<a class="sourceLine" id="cb111-2" 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="cb111-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">normalize</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>
<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://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>
+<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>
@@ -575,8 +584,8 @@
<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="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" 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
@@ -594,6 +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.
@@ -635,59 +648,59 @@
<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="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" 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="cb118-2" 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="cb118-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></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>
-## Gene1 Gene1 0.000680725267708466 1581
-## Gene2 Gene2 0.370387032192347 845
-## Gene3 Gene3 0.111311537904601 2613
-## Gene4 Gene4 1.00925368493739 2737
-## Gene5 Gene5 0.513708856051692 1140
-## Gene6 Gene6 0.391738896715107 5341</code></pre>
+## 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="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="https://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="cb120-2" 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 0.0000 0.0000 0.00000 0 0.0000
-## Gene2 0.0000 189.1590 369.04667 0 0.0000
-## Gene3 0.0000 0.0000 0.00000 0 0.0000
-## Gene4 108.8018 175.1984 56.96829 0 0.0000
-## Gene5 0.0000 140.2099 136.77388 0 136.7855</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="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" 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="cb122-2" 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="cb122-3" 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://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a>
-<a class="sourceLine" id="cb122-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb122-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/names">names</a></span>(comparison)</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="cb124"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb124-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/names">names</a></span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
+<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">$</span>Plots)</a></code></pre></div>
<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
## [5] "ZerosGene" "ZerosCell" "MeanZeros" "VarGeneCor"</code></pre>
<p>The returned list has three items. The first two are the combined datasets by gene (<code>RowData</code>) and by cell (<code>ColData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode" id="cb126"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb126-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb131"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb131-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode" id="cb127"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb127-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"ggplot2"</span>)</a>
-<a class="sourceLine" id="cb127-2" data-line-number="2"><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(comparison<span class="op">$</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="cb127-3" 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>
+<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">$</span>ColData, <span class="kw"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> sum, <span class="dt">y =</span> detected, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb132-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/geom_point.html">geom_point</a></span>()</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
<div id="comparing-differences" class="section level2">
<h2 class="hasAnchor">
<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode" id="cb128"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb128-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a>
-<a class="sourceLine" id="cb128-2" data-line-number="2">difference<span class="op">$</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">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode" id="cb129"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb129-1" data-line-number="1">difference<span class="op">$</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">
@@ -695,22 +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="cb130"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb130-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
-<a class="sourceLine" id="cb130-2" 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="cb130-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="https://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="cb130-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb130-5" 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="cb130-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="https://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="cb130-7" data-line-number="7"></a>
-<a class="sourceLine" id="cb130-8" 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="cb130-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="https://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="cb131"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb131-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/citation">citation</a></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;
@@ -730,7 +743,7 @@
<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="cb133"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb133-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/sessionInfo">sessionInfo</a></span>()</a></code></pre></div>
+<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
@@ -747,58 +760,58 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.13.15 ggplot2_3.2.1
-## [3] splatter_1.9.3 SingleCellExperiment_1.7.4
-## [5] SummarizedExperiment_1.15.6 DelayedArray_0.11.4
-## [7] BiocParallel_1.19.2 matrixStats_0.54.0
-## [9] Biobase_2.45.0 GenomicRanges_1.37.14
-## [11] GenomeInfoDb_1.21.1 IRanges_2.19.10
-## [13] S4Vectors_0.23.18 BiocGenerics_0.31.5
+## [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] viridis_0.5.1 edgeR_3.27.12
-## [3] BiocSingular_1.1.5 splines_3.6.0
-## [5] viridisLite_0.3.0 lsei_1.2-0
-## [7] DelayedMatrixStats_1.7.1 assertthat_0.2.1
-## [9] sp_1.3-1 BiocManager_1.30.4
+## [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_1.1.4 lattice_0.20-38
-## [17] limma_3.41.15 glue_1.3.1
-## [19] digest_0.6.20 RColorBrewer_1.1-2
+## [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_0.3.6 Matrix_1.2-17
-## [27] pkgconfig_2.0.2 bookdown_0.12
+## [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 xml2_1.2.2
-## [43] beeswarm_0.2.3 tools_3.6.0
-## [45] fitdistrplus_1.0-14 stringr_1.4.0
-## [47] munsell_0.5.0 locfit_1.5-9.1
-## [49] irlba_2.3.3 akima_0.6-2
-## [51] compiler_3.6.0 pkgdown_1.3.0
-## [53] rsvd_1.0.2 rlang_0.4.0.9000
-## [55] grid_3.6.0 RCurl_1.95-4.12
-## [57] BiocNeighbors_1.3.3 rstudioapi_0.10
-## [59] labeling_0.3 bitops_1.0-6
-## [61] rmarkdown_1.14 npsurv_0.4-0
-## [63] gtable_0.3.0 roxygen2_6.1.1
-## [65] R6_2.4.0 gridExtra_2.3
-## [67] knitr_1.24 dplyr_0.8.3
-## [69] commonmark_1.7 rprojroot_1.3-2
-## [71] desc_1.2.0 stringi_1.4.3
-## [73] ggbeeswarm_0.6.0 Rcpp_1.0.2
-## [75] tidyselect_0.2.5 xfun_0.8</code></pre>
+## [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>
@@ -837,17 +850,20 @@
</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> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
+
</footer>
</div>
+
</body>
</html>
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diff --git a/docs/articles/splatter_files/figure-html/paths-1.png b/docs/articles/splatter_files/figure-html/paths-1.png
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diff --git a/docs/articles/splatter_files/figure-html/pca-1.png b/docs/articles/splatter_files/figure-html/pca-1.png
index 74a2c3f51ea5df24ec9e65fb964285d560e2829a..c30dd42f8399e4e55f4dbebe17678e14eacbcbf1 100644
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diff --git a/docs/authors.html b/docs/authors.html
index b153ba9a2e3cf0536224fe3725d610ad7b5ff468..c82dbfac63c52b121e10c20091625b7a19a095b8 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -8,21 +8,25 @@
<title>Citation and Authors • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,10 +36,12 @@
<link href="extra.css" rel="stylesheet">
+
<meta property="og:title" content="Citation and Authors" />
+
<!-- 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>
@@ -56,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -72,7 +79,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -80,7 +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>
@@ -106,11 +113,10 @@
<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>
@@ -121,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -143,21 +150,22 @@ doi: <a href="https://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' alt='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' alt='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' alt='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>
@@ -167,19 +175,23 @@ doi: <a href="https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/index.html b/docs/index.html
index 2ac8ff42716b6cbc8f97d465689280b60b41eed2..f4802b9a8926d565ca3f2b47bf80581e197f7d79 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -7,8 +7,9 @@
<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://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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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><!-- 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">
+<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
@@ -41,7 +42,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -49,7 +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>
@@ -78,7 +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>
@@ -91,11 +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>
@@ -117,20 +119,20 @@
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="https://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><a href="https://www.rdocumentation.org/packages/base/topics/library">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")</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="https://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>
@@ -165,9 +167,9 @@ BiocManager::install("splatter")</a></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" alt="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" alt="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" alt="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>
@@ -185,17 +187,20 @@ BiocManager::install("splatter")</a></code></pre>
</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> 1.3.0.</p>
+ <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/news/index.html b/docs/news/index.html
index f0030471c0dac289e1698d155d2aaa40f7a1d409..00bcbe240a59842ecfcad2e330778bb4ef1d39df 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -8,21 +8,25 @@
<title>Changelog • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,10 +36,12 @@
<link href="../extra.css" rel="stylesheet">
+
<meta property="og:title" content="Changelog" />
+
<!-- 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>
@@ -56,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -72,7 +79,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -80,7 +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>
@@ -106,11 +113,10 @@
<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>
@@ -121,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -130,47 +137,6 @@
<small>Source: <a href='https://github.com/Oshlack/splatter/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
- <div id="version-1-9-4-2019-08-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-4-2019-08-20" class="anchor"></a>Version 1.9.4 (2019-08-20)</h2>
-<ul>
-<li>Fix deprecated column name in diffSCEs QQ plots</li>
-<li>Fix bugs where parameters were not being passed correctly in BASiCSEstimate and sparseDCEstimate</li>
-<li>Replace the sc_example_counts dataset from scater with the mockSCE function</li>
-<li>Tidy and improve estimation function examples</li>
-</ul>
-</div>
- <div id="version-1-9-3-2019-08-08" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-3-2019-08-08" class="anchor"></a>Version 1.9.3 (2019-08-08)</h2>
-<ul>
-<li>Remove deprecated scater functions</li>
-</ul>
-</div>
- <div id="version-1-9-2-2019-06-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-2-2019-06-13" class="anchor"></a>Version 1.9.2 (2019-06-13)</h2>
-<ul>
-<li>Add variable gene correlation plot to compareSCEs</li>
-</ul>
-</div>
- <div id="version-1-9-1-2019-06-05" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-1-2019-06-05" class="anchor"></a>Version 1.9.1 (2019-06-05)</h2>
-<ul>
-<li>Refactor the summariseDiff function</li>
-<li>Add the KS statistic to summariseDiff</li>
-<li>Set gam method for fitted lines in comparison plots</li>
-<li>Add checks for suggested packages in examples</li>
-</ul>
-</div>
- <div id="version-1-9-0-2019-05-03" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-0-2019-05-03" class="anchor"></a>Version 1.9.0 (2019-05-03)</h2>
-<ul>
-<li>Bioconductor 3.10 devel</li>
-</ul>
-</div>
<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>
@@ -785,11 +751,6 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#version-1-9-4-2019-08-20">1.9.4</a></li>
- <li><a href="#version-1-9-3-2019-08-08">1.9.3</a></li>
- <li><a href="#version-1-9-2-2019-06-13">1.9.2</a></li>
- <li><a href="#version-1-9-1-2019-06-05">1.9.1</a></li>
- <li><a href="#version-1-9-0-2019-05-03">1.9.0</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>
@@ -802,19 +763,23 @@
</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> 1.3.0.</p>
+ <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/pkgdown.css b/docs/pkgdown.css
index c03fb08d7092ce6ad54910f27996b28e0ef6df3c..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 {
@@ -102,21 +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;
@@ -133,6 +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;
}
@@ -222,6 +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 {
@@ -234,3 +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 eb7e83d2fecc7e7311197cc294f4a7131cc263e0..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',
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 7e24d0a17c042690e9a03fa2fdfd8a5e07897fd4..fac2f364b8e75a30a0afa9db214fda7a4581062f 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
pandoc: 2.3.1
-pkgdown: 1.3.0
+pkgdown: 1.4.1
pkgdown_sha: ~
articles:
splat_params: splat_params.html
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index 452fba0e9e8aeb343bf8e662731f04712999c70e..8ec7b27267316abb222682ee88011444372db1ab 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate BASiCS simulation parameters — BASiCSEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,9 +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>,
@@ -155,7 +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>
@@ -168,7 +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><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames(counts)</a></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>
@@ -192,7 +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='https://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>
@@ -209,65 +213,64 @@ messages.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Optional parameters passed to <code><a href='https://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='https://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='https://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'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
-<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>mockSCE</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>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://www.rdocumentation.org/packages/stats/topics/Normal'>rnorm</a></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'>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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/BASiCSParams.html b/docs/reference/BASiCSParams.html
index b0ff46af20e2d47beaeca1e3c42a2da8f7f8a397..ec28ffb4e19feb659f9261f8af4a0072c9849490 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -8,21 +8,25 @@
<title>The BASiCSParams class — BASiCSParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,73 +141,73 @@
</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 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 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index 6b06de4a214fbdca4551f0a5ef8ecf898172c607..4eb147902de7d32dcf60911a3ab80149942aca3d 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -8,21 +8,25 @@
<title>BASiCS simulation — BASiCSSimulate • 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>
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+<!-- headroom.js -->
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@@ -32,13 +36,14 @@
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+<meta property="og:title" content="BASiCS simulation — BASiCSSimulate" />
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+
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@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
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+
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@@ -75,7 +81,7 @@
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<span class="navbar-brand">
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
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@@ -83,7 +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>
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@@ -109,11 +115,10 @@
<a href="../news/index.html">Changelog</a>
</li>
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-
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- <span class="fa fa-github fa-lg"></span>
+ <span class="fab fa fab fa-github fa-lg"></span>
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@@ -124,6 +129,7 @@
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+
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<div class="row">
@@ -135,13 +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>
@@ -159,66 +163,59 @@
<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='https://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='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='https://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 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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"BASiCS"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>"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'>No methods found in package ‘scran’ for request: ‘computeSumFactors’ when loading ‘BASiCS’</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='warning'>Warning: 'SingleCellExperiment::`isSpike<-`' is deprecated.</span>
-#> <span class='warning'>Use 'isSpike<-' instead.</span>
-#> <span class='warning'>See help("Deprecated")</span></div><div class='output co'>#> <span class='warning'>Warning: 'spikeNames' is deprecated.</span>
-#> <span class='warning'>See help("Deprecated")</span></div><div class='output co'>#> <span class='warning'>Warning: 'isSpike' is deprecated.</span>
-#> <span class='warning'>See help("Deprecated")</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='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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
+
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+
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+
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">
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+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
+<title>The KersplatParams class — KersplatParams • Splatter</title>
+
+
+<!-- jquery -->
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+<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 459e9e187fa917a7c16c0198d925cce9c94cb651..8f1973eeb17beb3dcaca45c0fa901366540f7636 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -8,21 +8,25 @@
<title>The Lun2Params class — Lun2Params • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +141,17 @@
</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>
@@ -156,59 +163,59 @@
<dt><code>zi.params</code></dt><dd><p>A <code>data.frame</code> containing
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 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/LunParams.html b/docs/reference/LunParams.html
index e7d64ceba1eb500e7eca52f74b3677f59a77aeb2..66fd9f86366f09fe62d0f88b33260e3b3bf1ba87 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -8,21 +8,25 @@
<title>The LunParams class — LunParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -156,12 +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>
@@ -169,38 +174,41 @@
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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/MFAParams.html b/docs/reference/MFAParams.html
index 34fe9c2f31137ba7094648baf2c43abb7111464f..226b26290637e137cb5919388ae5580535f511b4 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -8,21 +8,25 @@
<title>The MFAParams class — MFAParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -156,37 +163,41 @@
<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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/Params.html b/docs/reference/Params.html
index 7f217310b5e3b2895dd843a64874e3a42c99f74d..3ecf3aba1a3907c269f8ebc20cd730cc159d1924 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -8,21 +8,25 @@
<title>The Params virtual class — Params • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,48 +141,53 @@
</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/PhenoParams.html b/docs/reference/PhenoParams.html
index 7954da788d508cdf1612fd1ac2bb6f176ae043bd..d6fb682ffbc19b0c160342b35eb6ef76145fb2e9 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -8,21 +8,25 @@
<title>The PhenoParams class — PhenoParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -157,36 +164,40 @@
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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/SCDDParams.html b/docs/reference/SCDDParams.html
index bd0a8fe4185b5491e3af1d0dc49d0e229b521eb5..4433e4790281a7cf48c30608d7ac57f1f657feb3 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -8,21 +8,25 @@
<title>The SCDDParams class — SCDDParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,21 +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='https://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>
@@ -163,37 +170,41 @@
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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/SimpleParams.html b/docs/reference/SimpleParams.html
index 44c0c90fadb2b8d9399b0f4a34bbc6cd32e3b052..bb2431808a808393990d9ad18ad0ca97db26c74d 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -8,21 +8,25 @@
<title>The SimpleParams class — SimpleParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -155,36 +162,40 @@
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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/SparseDCParams.html b/docs/reference/SparseDCParams.html
index 3646990bebeebb4a987d34b661a9c9e7f6e6744b..9973c3999b91b651c8f4c7eb94de9c20bc216e30 100644
--- a/docs/reference/SparseDCParams.html
+++ b/docs/reference/SparseDCParams.html
@@ -8,21 +8,25 @@
<title>The SparseDCParams class — SparseDCParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -164,36 +171,40 @@
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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/SplatParams.html b/docs/reference/SplatParams.html
index 0222642f13dd2a251dda13eeef4ce208705c8813..51feee86ad5041466cc9fd06688ff36c02a33a47 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -8,21 +8,25 @@
<title>The SplatParams class — SplatParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -156,14 +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
@@ -172,22 +177,19 @@
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>
@@ -198,14 +200,12 @@
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
@@ -216,8 +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
@@ -242,38 +241,41 @@
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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/ZINBParams.html b/docs/reference/ZINBParams.html
index b3fc714c5e4a65535179a5a9cc40d1e992e3b556..a8ab04f4ee9274421020465e917bf640f8e63193 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -8,21 +8,25 @@
<title>The ZINBParams class — ZINBParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,55 +141,60 @@
</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='https://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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/addFeatureStats.html b/docs/reference/addFeatureStats.html
index 3cdc328747dd0592f00045682a613687cc957660..95c9dfa0edd828130686d6ed2442e2f6722167ca 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -8,21 +8,25 @@
<title>Add feature statistics — addFeatureStats • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,14 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>
@@ -170,11 +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
@@ -183,35 +186,36 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/addGeneLengths.html b/docs/reference/addGeneLengths.html
index b56e4d6723226f07a9fc1cb9fea7531da5c9d4fd..149092850384742bebcd9bd16fe2dc34b5436d0b 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -8,21 +8,25 @@
<title>Add gene lengths — addGeneLengths • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,14 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>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>,
+ <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>
@@ -167,74 +171,73 @@
<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='https://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'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>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 0.0138665247174492 6630
-#> Gene2 Gene2 1.25529432999633 4894
-#> Gene3 Gene3 0.0375780248572044 1723
-#> Gene4 Gene4 1.69560565875577 1886
-#> Gene5 Gene5 1.12938171645951 438
-#> Gene6 Gene6 0.14592367445476 1508</div><div class='input'># Sample method (human coding genes)
-</div><span class='co'># NOT RUN {</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/Extremes'>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'>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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/bridge.html b/docs/reference/bridge.html
index 09d46929fad36e0f7899868424314e6e1d0fd0f2..87493098c21f4a8b410957735d8eeeede3aee5ac 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -8,21 +8,25 @@
<title>Brownian bridge — bridge • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ a random walk with fixed end points." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ a random walk with fixed end points." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ a random walk with fixed end points." />
<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>
@@ -125,6 +130,7 @@ a random walk with fixed end points." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -168,37 +172,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/bringItemsForward.html b/docs/reference/bringItemsForward.html
index a1d1b4e9d5e64427fbee46692b6ceff6271e2d5a..9c264777850c4b8beeac1c35ae02c590810ca087 100644
--- a/docs/reference/bringItemsForward.html
+++ b/docs/reference/bringItemsForward.html
@@ -8,21 +8,25 @@
<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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Bring items forward — bringItemsForward" />
+<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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +141,11 @@
</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>
@@ -155,37 +159,39 @@
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>
+ </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> 1.3.0.</p>
+ <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 3558bac8f747874074e45cf9f18ed8c77cdc873f..69284b6990c96eefa88f6f341b0bf5c196dd3381 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -8,21 +8,25 @@
<title>Compare SingleCellExperiment objects — compareSCEs • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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" />
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-<!-- 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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ basic plots comparing them." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ basic plots comparing them." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ basic plots comparing them." />
<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>
@@ -125,6 +130,7 @@ basic plots comparing them." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,15 +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>
@@ -170,11 +174,10 @@ 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>
@@ -198,49 +201,50 @@ compare.</p></td>
<dt><code>MeanZeros</code></dt><dd><p>Scatter plot with fitted lines showing
the mean-zeros relationship.</p></dd>
<dt><code>VarGeneCor</code></dt><dd><p>Heatmap of correlation of the 100 most
- variable genes.</p></dd>
- </dl></p></dd>
+ variable genes.</p></dd></dl></p></dd>
+
</dl>
- <p>The plots returned by this function are created using
+
+<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='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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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://www.rdocumentation.org/packages/base/topics/names'>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://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>comparison</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'>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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/diffSCEs.html b/docs/reference/diffSCEs.html
index 224bcd7a66d21fcb0978e37bdad025cdcc4008a6..e7bf37cf527a0c77a2fac8b6e09169c7c830a678 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -8,21 +8,25 @@
<title>Diff SingleCellExperiment objects — diffSCEs • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ basic plots comparing them to a reference." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ basic plots comparing them to a reference." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ basic plots comparing them to a reference." />
<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>
@@ -125,6 +130,7 @@ basic plots comparing them to a reference." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,15 +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>
@@ -175,11 +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
@@ -208,8 +211,7 @@ Q-Q plots are also returned.</p>
<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>
@@ -218,49 +220,50 @@ 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
+
+<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='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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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://www.rdocumentation.org/packages/base/topics/names'>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://www.rdocumentation.org/packages/base/topics/names'>names</a></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
+
</footer>
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+
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</html>
+
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index d4495b8614bb1c86c1b3a9f442536e45cb91c863..d785e1238255e651da0494ce3cbb380ffbee708d 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -8,21 +8,25 @@
<title>Expand parameters — expandParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ the number of groups." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ the number of groups." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ the number of groups." />
<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>
@@ -125,6 +130,7 @@ the number of groups." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,10 +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>)
@@ -152,7 +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>
@@ -165,37 +169,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/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">
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+
+<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]-->
+
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+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script>
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+ 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>
+
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+</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>
+
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+</li>
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+
+ </div><!--/.nav-collapse -->
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+</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 63d1f8507118eb409352e0c23ed0100b079c7575..7169316eb8fc7ee5105a3234afc0cd2021cd13d6 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -8,21 +8,25 @@
<title>Get log-normal factors — getLNormFactors • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -167,37 +171,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/getParam.html b/docs/reference/getParam.html
index 734d0c02827ba922322bd4031c3ed64e837f96df..5edeb06de31cc5e7ca2a4e62ff76ce16f957ace3 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -8,21 +8,25 @@
<title>Get a parameter — getParam • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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>
@@ -157,11 +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>()
@@ -172,28 +175,30 @@
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/getParams.html b/docs/reference/getParams.html
index fee5de7823a0365bea0e7602073f73c5f01b5630..8f35f1ef8f644bf20f9cfc6682a8c62d7b357512 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -8,21 +8,25 @@
<title>Get parameters — getParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -154,15 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>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
+<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
@@ -176,28 +179,30 @@
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/getPathOrder.html b/docs/reference/getPathOrder.html
index eeb0f53ad0c977bb0ce539d716cde43fff1b5c28..cf81c50dbb5e67a3aa642b7f9953d885c45b6259 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -8,21 +8,25 @@
<title>Get path order — getPathOrder • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ already been simulated." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ already been simulated." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ already been simulated." />
<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>
@@ -125,6 +130,7 @@ already been simulated." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +142,12 @@ 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>
@@ -153,37 +157,39 @@ already been simulated.</p>
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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/index.html b/docs/reference/index.html
index 447789697078670a1a64ab8125d17cfaf920a5d1..f40865b21772d16a71597b7b7b51378704376d18 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -8,21 +8,25 @@
<title>Function reference • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,10 +36,12 @@
<link href="../extra.css" rel="stylesheet">
+
<meta property="og:title" content="Function reference" />
+
<!-- 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>
@@ -56,6 +62,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -72,7 +79,7 @@
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -80,7 +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>
@@ -106,11 +113,10 @@
<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>
@@ -121,6 +127,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -147,7 +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>
@@ -182,6 +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>
@@ -256,6 +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>
@@ -354,6 +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>
@@ -503,7 +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>
@@ -603,7 +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>
@@ -628,19 +653,23 @@
</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> 1.3.0.</p>
+ <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/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>
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+ 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>
+
+
+
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+ <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>
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+
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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 @@
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+ <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>
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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 @@
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+
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+
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+
+<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>
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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 @@
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+ <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>
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+
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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
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+ <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>
+
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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 @@
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+ <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>
+
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+
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+
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+
+
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 @@
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+ <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>
+
+
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+ </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 @@
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+
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+
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+<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>
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+</div>
+
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+ </div>
+
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+ </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 @@
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+<!DOCTYPE html>
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+
+
+
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+
+<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>
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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">
+
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+
+
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+ <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>
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+
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+
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+
+
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 @@
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+ <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>
+
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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 @@
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+</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>
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+
+
+
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+
+<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>
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+</div>
+
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+ </div>
+
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+ </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 @@
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+ <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>
+
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+
+
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 @@
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+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
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+
+
+
+ </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>
+
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+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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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 @@
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+<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>
+
+
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+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
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diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index 33d3e225777547f73e4a7d982e278c50cc4dc59a..a3402c2c634156803bbe7658e8360085dc3c8038 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -8,21 +8,25 @@
<title>List simulations — listSims • 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" />
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+<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" />
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+<!-- 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">
@@ -32,14 +36,15 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -60,6 +65,7 @@ brief description." />
gtag('config', 'UA-52309538-4');
</script>
+
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<body>
@@ -76,7 +82,7 @@ brief description." />
</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">1.9.4</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 +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>
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@@ -110,11 +116,10 @@ brief description." />
<a href="../news/index.html">Changelog</a>
</li>
</ul>
-
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<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>
@@ -125,6 +130,7 @@ brief description." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -152,95 +156,100 @@ 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
#>
-#> <span style='font-weight: bold;'>Splat</span><span> </span><span style='color: #BBBB00;'>(splat)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-017-1305-0</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>Oshlack/splatter</span><span>
+#> Splat (splat)
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> 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.
#>
-#> </span><span style='font-weight: bold;'>Splat Single</span><span> </span><span style='color: #BBBB00;'>(splatSingle)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-017-1305-0</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>Oshlack/splatter</span><span>
+#> Splat Single (splatSingle)
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation with a single population.
#>
-#> </span><span style='font-weight: bold;'>Splat Groups</span><span> </span><span style='color: #BBBB00;'>(splatGroups)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-017-1305-0</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>Oshlack/splatter</span><span>
+#> Splat Groups (splatGroups)
+#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
#> The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution.
#>
-#> </span><span style='font-weight: bold;'>Splat Paths</span><span> </span><span style='color: #BBBB00;'>(splatPaths)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-017-1305-0</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>Oshlack/splatter</span><span>
+#> Splat Paths (splatPaths)
+#> 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.
#>
-#> </span><span style='font-weight: bold;'>Simple</span><span> </span><span style='color: #BBBB00;'>(simple)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-017-1305-0</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>Oshlack/splatter</span><span>
+#> 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.
#>
-#> </span><span style='font-weight: bold;'>Lun</span><span> </span><span style='color: #BBBB00;'>(lun)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-016-0947-7</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>MarioniLab/Deconvolution2016</span><span>
+#> Lun (lun)
+#> DOI: 10.1186/s13059-016-0947-7 GitHub: MarioniLab/Deconvolution2016
#> Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.
#>
-#> </span><span style='font-weight: bold;'>Lun 2</span><span> </span><span style='color: #BBBB00;'>(lun2)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1093/biostatistics/kxw055</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>MarioniLab/PlateEffects2016</span><span>
+#> Lun 2 (lun2)
+#> DOI: 10.1093/biostatistics/kxw055 GitHub: MarioniLab/PlateEffects2016
#> 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.
#>
-#> </span><span style='font-weight: bold;'>scDD</span><span> </span><span style='color: #BBBB00;'>(scDD)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1186/s13059-016-1077-y</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>kdkorthauer/scDD</span><span>
+#> scDD (scDD)
+#> DOI: 10.1186/s13059-016-1077-y GitHub: kdkorthauer/scDD
#> The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.
#>
-#> </span><span style='font-weight: bold;'>BASiCS</span><span> </span><span style='color: #BBBB00;'>(BASiCS)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1371/journal.pcbi.1004333</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>catavallejos/BASiCS</span><span>
+#> BASiCS (BASiCS)
+#> DOI: 10.1371/journal.pcbi.1004333 GitHub: catavallejos/BASiCS
#> The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects.
#>
-#> </span><span style='font-weight: bold;'>mfa</span><span> </span><span style='color: #BBBB00;'>(mfa)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.12688/wellcomeopenres.11087.1</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>kieranrcampbell/mfa</span><span>
+#> mfa (mfa)
+#> DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa
#> The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.
#>
-#> </span><span style='font-weight: bold;'>PhenoPath</span><span> </span><span style='color: #BBBB00;'>(pheno)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1101/159913</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>kieranrcampbell/phenopath</span><span>
+#> PhenoPath (pheno)
+#> DOI: 10.1101/159913 GitHub: kieranrcampbell/phenopath
#> The PhenoPath simulation produces a pseudotime trajectory with different types of genes.
#>
-#> </span><span style='font-weight: bold;'>ZINB-WaVE</span><span> </span><span style='color: #BBBB00;'>(zinb)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1101/125112</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>drisso/zinbwave</span><span>
+#> ZINB-WaVE (zinb)
+#> DOI: 10.1101/125112 GitHub: drisso/zinbwave
#> The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.
#>
-#> </span><span style='font-weight: bold;'>SparseDC</span><span> </span><span style='color: #BBBB00;'>(sparseDC)</span><span>
-#> </span><span style='font-weight: bold;'>DOI:</span><span> </span><span style='color: #00BBBB;'>10.1093/nar/gkx1113</span><span> </span><span style='font-weight: bold;'>GitHub:</span><span> </span><span style='color: #00BBBB;'>cran/SparseDC</span><span>
+#> 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.
-#> </div></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="#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> 1.3.0.</p>
+ <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/logistic.html b/docs/reference/logistic.html
index bc3868ffe35f44b93cf8a22c7415199cc97063e0..b4dd4d529e1277350763377ea0c4637161ca004a 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -8,21 +8,25 @@
<title>Logistic function — logistic • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -158,37 +162,39 @@
<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 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/lun2Estimate.html b/docs/reference/lun2Estimate.html
index c03ca8ec31e9c190ab6e12d636bcd792be2987ea..0ce51e6f0bf044edc00e269bcbd9f40c08804022 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -8,21 +8,25 @@
<title>Estimate Lun2 simulation parameters — lun2Estimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,9 +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>,
@@ -151,7 +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>
@@ -184,56 +188,55 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
-<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>mockSCE</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/numeric'>as.numeric</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/factor'>factor</a></span>(<span class='fu'>colData</span>(<span class='no'>sce</span>)$<span class='no'>Mutation_Status</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/lun2Simulate.html b/docs/reference/lun2Simulate.html
index 779f67620bbb71a2c6b87e452f0e89b25eaafe56..d88e808d38f02d6818d3cae14beb55d4c3d6c394 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -8,21 +8,25 @@
<title>Lun2 simulation — lun2Simulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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"." />
@@ -41,6 +45,7 @@ analyses of single-cell RNA-seq data"." />
+
<!-- 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>
@@ -61,6 +66,7 @@ analyses of single-cell RNA-seq data"." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ analyses of single-cell RNA-seq data"." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ analyses of single-cell RNA-seq data"." />
<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>
@@ -126,6 +131,7 @@ analyses of single-cell RNA-seq data"." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,16 +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>
@@ -168,11 +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
@@ -188,14 +191,12 @@ 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 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>
@@ -204,32 +205,32 @@ expression analyses of single-cell RNA-seq data. Biostatistics (2017).</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/lunEstimate.html b/docs/reference/lunEstimate.html
index b4f9713b0028a7c6fac699776ddb24f381d72ccc..af1332c58340c460150a99da553cf4cb5b9545b2 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate Lun simulation parameters — lunEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,9 +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>())
@@ -148,7 +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>
@@ -162,78 +166,79 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/library'>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://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
-<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>mockSCE</a></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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>LunParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 2000</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 200</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 200 955861
#>
#> 9 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
-#> </span><span style='color: #0000BB;'> [Rate]</span><span> </span><span style='color: #0000BB;'>[Shape]</span><span>
+#> Mean:
+#> [Rate] [Shape]
#> 2 2
#>
-#> </span><span style='font-weight: bold;'>Counts:</span><span>
-#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
+#> Counts:
+#> [Dispersion]
#> 0.1
#>
-#> </span><span style='font-weight: bold;'>Groups:</span><span>
-#> </span><span style='color: #0000BB;font-weight: bold;'> [GROUPS]</span><span> </span><span style='color: #0000BB;font-weight: bold;'>[GROUP CELLS]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 1</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 200</span><span>
+#> Groups:
+#> [GROUPS] [GROUP CELLS]
+#> 1 200
#>
-#> </span><span style='font-weight: bold;'>Diff expr:</span><span>
-#> </span><span style='color: #0000BB;'> [Genes]</span><span> </span><span style='color: #0000BB;'>[Up Prop]</span><span> </span><span style='color: #0000BB;'> [Up FC]</span><span> </span><span style='color: #0000BB;'>[Down FC]</span><span>
+#> Diff expr:
+#> [Genes] [Up Prop] [Up FC] [Down FC]
#> 1000 0.5 5 0
-#> </div></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/lunSimulate.html b/docs/reference/lunSimulate.html
index a11f5013f98649206a9ce6ce2384cb86f4cc17c4..6d853e5e3569fb0b4d2ccd4a94c7e782999353da 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -8,21 +8,25 @@
<title>Lun simulation — lunSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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"." />
@@ -41,6 +45,7 @@ sequencing data with many zero counts"." />
+
<!-- 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>
@@ -61,6 +66,7 @@ sequencing data with many zero counts"." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ sequencing data with many zero counts"." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ sequencing data with many zero counts"." />
<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>
@@ -126,6 +131,7 @@ sequencing data with many zero counts"." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,15 +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>
@@ -163,12 +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
@@ -178,14 +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'>
@@ -195,32 +196,32 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/makeCompPanel.html b/docs/reference/makeCompPanel.html
index fdd8c1237d3bfc2032b07580222eb9cfa1b99062..161820ff9c0c967b5e0b8856d4645577849576a6 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -8,21 +8,25 @@
<title>Make comparison panel — makeCompPanel • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,15 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>
@@ -160,47 +164,47 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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'>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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index 77431dda2cd2cfbee0730e47123744f4ae673078..52fcbf45142b6b7523b424ed249b168f9455b9b6 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -8,21 +8,25 @@
<title>Make difference panel — makeDiffPanel • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,16 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>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='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>
@@ -161,47 +165,47 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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'>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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index b62f07685637f7a103787a58954d8c12c0ab30af..48b6801a5a787ef9e02b8afa40a94f48fe34b205 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -8,21 +8,25 @@
<title>Make overall panel — makeOverallPanel • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ single panel." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ single panel." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ single panel." />
<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>
@@ -125,6 +130,7 @@ single panel." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,17 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>
@@ -167,48 +171,48 @@ 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'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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://www.rdocumentation.org/packages/base/topics/list'>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'>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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 0c01fcddd9fb41ac187e4122a41dd060170026de..cb1e210d8f4ff5d29c5d36d4ccce36c9cb8bd256 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate mfa simulation parameters — mfaEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,9 +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>())
@@ -148,7 +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>
@@ -162,78 +166,78 @@ 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='https://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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>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://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>mfa</span>)
- <span class='no'>synth</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>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'>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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>MFAParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 20</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 5</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 20 5 955861
#>
#> 4 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Transient:</span><span>
-#> </span><span style='color: #0000BB;'>[Proportion]</span><span>
+#> Transient:
+#> [Proportion]
#> 0
#>
-#> </span><span style='font-weight: bold;'>Negative:</span><span>
-#> </span><span style='color: #0000BB;'>[Zero]</span><span>
+#> Negative:
+#> [Zero]
#> TRUE
#>
-#> </span><span style='font-weight: bold;'>Dropout:</span><span>
-#> </span><span style='color: #0000BB;'> [Present]</span><span> </span><span style='font-weight: bold;'> (LAMBDA)</span><span>
-#> FALSE </span><span style='color: #00BB00;font-weight: bold;'>0.27079716144347</span><span>
-#> </div></span></pre>
+#> Dropout:
+#> [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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/mfaSimulate.html b/docs/reference/mfaSimulate.html
index e69fc247a563c284055395a1326f59eb03dad11d..e30ea343590d72e82a6d0c263f95be3fe3edcb60 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -8,21 +8,25 @@
<title>MFA simulation — mfaSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -159,20 +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='https://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='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. See
-<code><a href='https://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
@@ -180,10 +182,9 @@ 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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"mfa"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>"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>
@@ -191,32 +192,32 @@ Open Research (2017).</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/newParams.html b/docs/reference/newParams.html
index 22a4ac0d1a8cee7cb0f382c746aa1d6ba2f5d5c9..46b75adb265674a5e7286472e8cfe484a3b2b19c 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -8,21 +8,25 @@
<title>New Params — newParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ Params subtypes." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ Params subtypes." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ Params subtypes." />
<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>
@@ -125,25 +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>)
@@ -161,7 +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>
@@ -170,11 +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>()
@@ -184,28 +189,30 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/phenoEstimate.html b/docs/reference/phenoEstimate.html
index fcebc27d2b75140b43a51aaa07e8e8e4a1d5522c..c9b2b839d20eaf118bbb8c95623df43c498a3e13 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate PhenoPath simulation parameters — phenoEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ dataset." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ dataset." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ dataset." />
<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>
@@ -125,6 +130,7 @@ dataset." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,10 +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>())
@@ -150,7 +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>
@@ -164,69 +168,69 @@ 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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"phenopath"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>"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://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
- <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>mockSCE</a></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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>PhenoParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 2000</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 200</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 200 955861
#>
#> 4 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Genes:</span><span>
-#> </span><span style='color: #0000BB;font-weight: bold;'> [DE]</span><span> </span><span style='color: #0000BB;font-weight: bold;'> [PST]</span><span> </span><span style='color: #0000BB;font-weight: bold;'> [PST + BETA]</span><span> </span><span style='color: #0000BB;font-weight: bold;'>[DE + PST + BETA]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 500</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 500</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 500</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 500</span><span>
-#> </div></span></pre>
+#> Genes:
+#> [DE] [PST] [PST + BETA] [DE + PST + BETA]
+#> 500 500 500 500
+#> </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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/phenoSimulate.html b/docs/reference/phenoSimulate.html
index 3b92f027afd9dcd2e105fa45feadbad9eff37f52..88e0ca80648b6693cf5881bf39305a7c41f30f9f 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -8,21 +8,25 @@
<title>PhenoPath simulation — phenoSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -159,22 +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='https://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='https://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='https://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
@@ -182,10 +184,9 @@ 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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"phenopath"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>"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>
@@ -193,32 +194,32 @@ and environmental backgrounds across single-cells and populations. bioRxiv
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/rbindMatched.html b/docs/reference/rbindMatched.html
index 77d8fef99fa6a5a6e351fa609ebee7fe5c92b895..417a97337e1ca52b4673d216b2b07ff0af5619b1 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -8,21 +8,25 @@
<title>Bind rows (matched) — rbindMatched • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ to both." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ to both." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ to both." />
<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>
@@ -125,6 +130,7 @@ to both." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -156,38 +160,40 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/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 -->
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+<meta property="og:title" content="Sample density — sampleDensity" />
+<meta property="og:description" content="Sample from a density object using rejection sampling" />
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+<!-- mathjax -->
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+ Articles
+
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+ </a>
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+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
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+</li>
+<li>
+ <a href="../news/index.html">Changelog</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
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+ <span class="fab fa fab fa-github fa-lg"></span>
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+
+
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+ </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>
+
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+
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index c4755d443d1177fde8f6674b6c661173cb120ea7..f7939e3dc74e0ce1ab1d242f8a449da795737f7d 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate scDD simulation parameters — scDDEstimate • 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>
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+<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" />
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+<!-- 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 -->
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@@ -32,13 +36,14 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
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+
</header>
<div class="row">
@@ -135,9 +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>,
@@ -155,7 +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>
@@ -193,36 +197,35 @@ 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='https://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> to the counts then uses
-<code><a href='https://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='https://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> and <code><a href='https://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"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>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://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
- <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>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>)
+ <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>)$<span class='no'>condition</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sample'>sample</a></span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/nrow'>ncol</a></span>(<span class='no'>sce</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>colData</span>(<span class='no'>sce</span>)$<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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SCDDParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 100</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 10</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 100 10 955861
#>
#> 11 additional parameters
#>
@@ -230,52 +233,53 @@ simulate. The output is then converted to a SCDDParams object. See
#> (SCdat)
#> SingleCellExperiment with 95 features and 20 cells
#>
-#> </span><span style='font-weight: bold;'>Genes:</span><span>
-#> </span><span style='font-weight: bold;'>(NDE)</span><span> </span><span style='font-weight: bold;'>(NDP)</span><span> </span><span style='font-weight: bold;'>(NDM)</span><span> </span><span style='font-weight: bold;'>(NDP)</span><span> </span><span style='font-weight: bold;'>(NEE)</span><span> </span><span style='font-weight: bold;'>(NEP)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 0</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 95</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 5</span><span>
+#> Genes:
+#> (NDE) (NDP) (NDM) (NDP) (NEE) (NEP)
+#> 0 0 0 0 95 5
#>
-#> </span><span style='font-weight: bold;'>Fold change:</span><span>
-#> </span><span style='color: #0000BB;'>[SD Range]</span><span> </span><span style='color: #0000BB;'> [Mode FC]</span><span>
+#> Fold change:
+#> [SD Range] [Mode FC]
#> 1, 3 2, 3, 4
#>
-#> </span><span style='font-weight: bold;'>Variance:</span><span>
-#> </span><span style='color: #0000BB;'>[Inflation]</span><span>
+#> Variance:
+#> [Inflation]
#> 1, 1
#>
-#> </span><span style='font-weight: bold;'>Condition:</span><span>
-#> </span><span style='color: #0000BB;'>[Condition]</span><span>
+#> Condition:
+#> [Condition]
#> condition
#> </div><div class='input'>
-</div></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
+
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+
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</html>
+
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index 73fb89ab3d92effa25c336b9c7ce3864c96c9dc4..cbbb965c30be97ec0712180939c4b0d456cae15a 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -8,21 +8,25 @@
<title>scDD simulation — scDDSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,14 +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>
@@ -175,19 +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='https://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='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='https://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
@@ -195,43 +197,42 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/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 b4cd5c552cde5c77817eabc7f51f067afcc1a465..8d3283b24e3265b0ffd2de2311c3d24fe51f20b0 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -8,21 +8,25 @@
<title>Set a parameter — setParam • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,20 +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>)
@@ -145,6 +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>)
@@ -165,7 +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>
@@ -182,59 +189,61 @@
<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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SimpleParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> (Cells) </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 100</span><span> 100 848036
+#> Global:
+#> (GENES) (Cells) [Seed]
+#> 100 100 955861
#>
#> 3 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
+#> Mean:
#> (Rate) (Shape)
#> 0.3 0.4
#>
-#> </span><span style='font-weight: bold;'>Counts:</span><span>
-#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
+#> Counts:
+#> [Dispersion]
#> 0.1
#> </div><div class='input'>
-</div></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="#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> 1.3.0.</p>
+ <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/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index f92a6d9803ae4ea46a09d699dd35b309c396a253..4e5f5ac87b438b86346153d139ecea153888cab4 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -8,21 +8,25 @@
<title>Set a parameter UNCHECKED — setParamUnchecked • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ VALIDITY!" />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ VALIDITY!" />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ VALIDITY!" />
<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>
@@ -125,6 +130,7 @@ VALIDITY!" />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,17 +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>
@@ -163,37 +167,39 @@ VALIDITY!</p>
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/setParams.html b/docs/reference/setParams.html
index 293e90fcb3701956a0cef85dbf71b20249676e03..343a2428a7465ddcc16ff0f494ab753e382b4a7e 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -8,21 +8,25 @@
<title>Set parameters — setParams • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,30 +129,32 @@
</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/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/Params-methods.R'><code>R/Params-methods.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/SplatParams-methods.R'><code>R/SplatParams-methods.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'>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>
@@ -157,7 +164,7 @@
</tr>
<tr>
<th>update</th>
- <td><p>list of parameters to set where <code><a href='https://www.rdocumentation.org/packages/base/topics/names'>names(update)</a></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>
@@ -166,11 +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
@@ -178,93 +184,96 @@ 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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SimpleParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> (Genes) (Cells) </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> 10000 100 848036
+#> Global:
+#> (Genes) (Cells) [Seed]
+#> 10000 100 955861
#>
#> 3 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
+#> Mean:
#> (Rate) (Shape)
#> 0.3 0.4
#>
-#> </span><span style='font-weight: bold;'>Counts:</span><span>
-#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
+#> Counts:
+#> [Dispersion]
#> 0.1
#> </div><div class='input'><span class='co'># Set individually</span>
<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 </span><span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SimpleParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 1000</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 50</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 1000 50 955861
#>
#> 3 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
+#> Mean:
#> (Rate) (Shape)
#> 0.3 0.4
#>
-#> </span><span style='font-weight: bold;'>Counts:</span><span>
-#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
+#> Counts:
+#> [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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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 </span><span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SimpleParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 1000</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 50</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 1000 50 955861
#>
#> 3 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
-#> </span><span style='font-weight: bold;'> (RATE)</span><span> </span><span style='font-weight: bold;'>(SHAPE)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 0.2</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0.8</span><span>
+#> Mean:
+#> (RATE) (SHAPE)
+#> 0.2 0.8
#>
-#> </span><span style='font-weight: bold;'>Counts:</span><span>
-#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
+#> Counts:
+#> [Dispersion]
#> 0.1
#> </div><div class='input'>
-</div></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
index d3b1f12a2fcbac817a60f768b132aacab1fc44cb..06025321e954ad312c36980d04215bea8a1699cc 100644
--- a/docs/reference/setParamsUnchecked.html
+++ b/docs/reference/setParamsUnchecked.html
@@ -8,21 +8,25 @@
<title>Set parameters UNCHECKED — setParamsUnchecked • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -151,7 +155,7 @@
</tr>
<tr>
<th>update</th>
- <td><p>list of parameters to set where <code><a href='https://www.rdocumentation.org/packages/base/topics/names'>names(update)</a></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>
@@ -160,11 +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
@@ -172,35 +175,36 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/showDFs.html b/docs/reference/showDFs.html
index 4a8797e324de71b573ebf1c5da8e7ef659761de4..ca9b8f3426dc40300d605767a2d18a46d4606c3b 100644
--- a/docs/reference/showDFs.html
+++ b/docs/reference/showDFs.html
@@ -8,21 +8,25 @@
<title>Show data.frame — showDFs • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -154,31 +158,39 @@
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/showPP.html b/docs/reference/showPP.html
index 72281fc74bfa8690dbae95462837ec072d6bdfbd..0b34baaa40e532f1fbd6daf2f5499ab1e8d9ae97 100644
--- a/docs/reference/showPP.html
+++ b/docs/reference/showPP.html
@@ -8,21 +8,25 @@
<title>Show pretty print — showPP • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -154,37 +158,39 @@
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/showValues.html b/docs/reference/showValues.html
index f4333054351681674fdc34ba5076a839b2c9df29..12794a6f74b4689692a5d6a322fb67cb1adca669 100644
--- a/docs/reference/showValues.html
+++ b/docs/reference/showValues.html
@@ -6,23 +6,27 @@
<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://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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,24 +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>
@@ -154,31 +158,39 @@
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 1df5da041e00831acc3dfe9b53917a00eb292452..ea36ff15c0b56b6b74490ad6004ad0f197d413b7 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate simple simulation parameters — simpleEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,9 +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>())
@@ -148,7 +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>
@@ -162,73 +166,73 @@ 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='https://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'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
-<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>mockSCE</a></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'>sce</span>)
-<span class='no'>params</span></div><div class='output co'>#> A <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SimpleParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 2000</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 200</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 200 955861
#>
#> 3 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
-#> </span><span style='font-weight: bold;'> (RATE)</span><span> </span><span style='font-weight: bold;'> (SHAPE)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'>0.00315146081285586</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0.562634238245172</span><span>
+#> Mean:
+#> (RATE) (SHAPE)
+#> 0.00315146081285586 0.562634238245172
#>
-#> </span><span style='font-weight: bold;'>Counts:</span><span>
-#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
+#> Counts:
+#> [Dispersion]
#> 0.1
-#> </div></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/simpleSimulate.html b/docs/reference/simpleSimulate.html
index 9892d217623484e5aeab2bfb87df3c2a1cfea386..f24d66a9525703e416eed19872199283b1becec5 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -8,21 +8,25 @@
<title>Simple simulation — simpleSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -60,6 +65,7 @@ simulated library sizes, differential expression etc." />
gtag('config', 'UA-52309538-4');
</script>
+
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<body>
@@ -76,7 +82,7 @@ simulated library sizes, differential expression etc." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ simulated library sizes, differential expression etc." />
<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>
@@ -125,6 +130,7 @@ simulated library sizes, differential expression etc." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -161,11 +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
@@ -173,7 +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>
@@ -183,30 +185,31 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index 84a2dfcde512fdde229136e00dbbb896b708f07e..3da07e87ab34a681a5e3cc2082127834c6fb53f6 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate SparseDC simulation parameters — sparseDCEstimate • 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>
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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" />
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-<!-- sticky kit -->
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+<!-- 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>
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<link href="../pkgdown.css" rel="stylesheet">
@@ -32,14 +36,15 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -60,6 +65,7 @@ dataset." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ dataset." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ dataset." />
<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>
@@ -125,6 +130,7 @@ dataset." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,10 +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>,
@@ -152,7 +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>
@@ -179,83 +183,83 @@ 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='https://www.rdocumentation.org/packages/SparseDC/topics/pre_proc_data'>pre_proc_data</a></code> and then parameters are estimated using
-<code><a href='https://www.rdocumentation.org/packages/SparseDC/topics/sparsedc_cluster'>sparsedc_cluster</a></code> using lambda values calculated using
-<code><a href='https://www.rdocumentation.org/packages/SparseDC/topics/lambda1_calculator'>lambda1_calculator</a></code> and
-<code><a href='https://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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"SparseDC"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
- <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>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'><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'>conditions</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sample'>sample</a></span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/nrow'>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'>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'>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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SparseDCParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 100</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 10</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 100 10 955861
#>
#> 7 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Markers:</span><span>
-#> </span><span style='font-weight: bold;'>(NUMBER)</span><span> </span><span style='font-weight: bold;'>(SHARED)</span><span> </span><span style='color: #0000BB;'> [Same]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 1</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 1</span><span> FALSE
+#> Markers:
+#> (NUMBER) (SHARED) [Same]
+#> 1 1 FALSE
#>
-#> </span><span style='font-weight: bold;'>Clusters:</span><span>
-#> </span><span style='font-weight: bold;'>(CONDITION 1)</span><span> </span><span style='font-weight: bold;'>(CONDITION 2)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 2, 3</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 1, 2, 3</span><span>
+#> Clusters:
+#> (CONDITION 1) (CONDITION 2)
+#> 2, 3 1, 2, 3
#>
-#> </span><span style='font-weight: bold;'>Means:</span><span>
-#> </span><span style='color: #0000BB;'>[Lower]</span><span> </span><span style='color: #0000BB;'>[Upper]</span><span>
+#> Means:
+#> [Lower] [Upper]
#> 1 2
-#> </div></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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+
</footer>
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+
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+
diff --git a/docs/reference/sparseDCSimulate.html b/docs/reference/sparseDCSimulate.html
index 91c9431184f9b4ee01e6a264ec3a0c139ab8a40f..e88c3a28ca749f0b70959e1ee29e76cd17059607 100644
--- a/docs/reference/sparseDCSimulate.html
+++ b/docs/reference/sparseDCSimulate.html
@@ -8,21 +8,25 @@
<title>SparseDC simulation — sparseDCSimulate • 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" />
+
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+<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" />
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+<!-- 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>
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<link href="../pkgdown.css" rel="stylesheet">
@@ -32,13 +36,14 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -159,22 +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='https://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='https://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='https://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
@@ -184,10 +186,9 @@ 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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"SparseDC"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='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>
@@ -195,32 +196,32 @@ Nucleic Acids Research (2017).</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatEstBCV.html b/docs/reference/splatEstBCV.html
index 892d553ddfbdc0faf732bf2b21e12b4092615cba..e6b74cfad44ff07301b1250bd11f754f637a47e8 100644
--- a/docs/reference/splatEstBCV.html
+++ b/docs/reference/splatEstBCV.html
@@ -8,21 +8,25 @@
<title>Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ in the edgeR package." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ in the edgeR package." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ in the edgeR package." />
<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>
@@ -125,6 +130,7 @@ in the edgeR package." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +142,12 @@ in the edgeR package." />
</div>
<div class="ref-description">
-
- <p>Parameters are estimated using the <code><a href='https://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>
@@ -156,48 +160,48 @@ 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='https://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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatEstDropout.html b/docs/reference/splatEstDropout.html
index 3d55190b1e19361d5ecb93a2e91694ef8739bb9e..f7f7930cbdc79a1cbc1f5fa3dce6a3c7cb8860bd 100644
--- a/docs/reference/splatEstDropout.html
+++ b/docs/reference/splatEstDropout.html
@@ -8,21 +8,25 @@
<title>Estimate Splat dropout parameters — splatEstDropout • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ when simulating dropout." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ when simulating dropout." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ when simulating dropout." />
<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>
@@ -125,6 +130,7 @@ when simulating dropout." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -156,47 +160,47 @@ 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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatEstLib.html b/docs/reference/splatEstLib.html
index 0d9bce3a37927b0224487b107795626df2f714ad..9bebff74c085f30e42657518744faef88ee69d8a 100644
--- a/docs/reference/splatEstLib.html
+++ b/docs/reference/splatEstLib.html
@@ -8,21 +8,25 @@
<title>Estimate Splat library size parameters — splatEstLib • 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>
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
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+<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" />
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<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
@@ -43,6 +47,7 @@ fitdist for details on the fitting." />
+
<!-- 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>
@@ -63,6 +68,7 @@ fitdist for details on the fitting." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -79,7 +85,7 @@ fitdist for details on the fitting." />
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -87,7 +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>
@@ -113,11 +119,10 @@ fitdist for details on the fitting." />
<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>
@@ -128,6 +133,7 @@ fitdist for details on the fitting." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -139,17 +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='https://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>
@@ -162,37 +166,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatEstMean.html b/docs/reference/splatEstMean.html
index 5c74ce2832455db46c9a54265dc1facf20ef4a4e..f2a15d684104cb94958e3b56560fd9e1a8239480 100644
--- a/docs/reference/splatEstMean.html
+++ b/docs/reference/splatEstMean.html
@@ -8,21 +8,25 @@
<title>Estimate Splat mean parameters — splatEstMean • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ simulate gene expression means." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ simulate gene expression means." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ simulate gene expression means." />
<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>
@@ -125,6 +130,7 @@ simulate gene expression means." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -156,49 +160,49 @@ 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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
index edd15aae5bf6e3b459e84d291d84f4512ba3b41d..c99279fdae4c701d0d2b8876777d6313b8df0b8d 100644
--- a/docs/reference/splatEstOutlier.html
+++ b/docs/reference/splatEstOutlier.html
@@ -8,21 +8,25 @@
<title>Estimate Splat expression outlier parameters — splatEstOutlier • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ median mean expression level." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ median mean expression level." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ median mean expression level." />
<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>
@@ -125,6 +130,7 @@ median mean expression level." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -156,11 +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
@@ -170,36 +173,37 @@ 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='https://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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatEstimate.html b/docs/reference/splatEstimate.html
index b856b51dbdaf535e63b4a27af472f2169fb60f59..3fab8c36e9ed966d43cb3bc78327ff0008ec1961 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate Splat simulation parameters — splatEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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-<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." />
@@ -41,6 +45,7 @@ is done." />
+
<!-- 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>
@@ -61,6 +66,7 @@ is done." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ is done." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ is done." />
<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>
@@ -126,6 +131,7 @@ is done." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,11 +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>())
@@ -152,7 +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>
@@ -166,98 +170,98 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
-<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>mockSCE</a></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'>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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>SplatParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><span>
+<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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 2000</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 200</span><span> 848036
+#> Global:
+#> (GENES) (CELLS) [Seed]
+#> 2000 200 955861
#>
#> 28 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Batches:</span><span>
-#> </span><span style='color: #0000BB;font-weight: bold;'> [BATCHES]</span><span> </span><span style='color: #0000BB;font-weight: bold;'>[BATCH CELLS]</span><span> </span><span style='color: #0000BB;'> [Location]</span><span> </span><span style='color: #0000BB;'> [Scale]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 1</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 200</span><span> 0.1 0.1
+#> Batches:
+#> [BATCHES] [BATCH CELLS] [Location] [Scale]
+#> 1 200 0.1 0.1
#>
-#> </span><span style='font-weight: bold;'>Mean:</span><span>
-#> </span><span style='font-weight: bold;'> (RATE)</span><span> </span><span style='font-weight: bold;'> (SHAPE)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'>0.002962686167343</span><span> </span><span style='color: #00BB00;font-weight: bold;'>0.496997730070513</span><span>
+#> Mean:
+#> (RATE) (SHAPE)
+#> 0.002962686167343 0.496997730070513
#>
-#> </span><span style='font-weight: bold;'>Library size:</span><span>
-#> </span><span style='font-weight: bold;'> (LOCATION)</span><span> </span><span style='font-weight: bold;'> (SCALE)</span><span> </span><span style='font-weight: bold;'> (NORM)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 357331.235</span><span> </span><span style='color: #00BB00;font-weight: bold;'>11607.2332293176</span><span> </span><span style='color: #00BB00;font-weight: bold;'> TRUE</span><span>
+#> Library size:
+#> (LOCATION) (SCALE) (NORM)
+#> 357331.235 11607.2332293176 TRUE
#>
-#> </span><span style='font-weight: bold;'>Exprs outliers:</span><span>
-#> </span><span style='font-weight: bold;'>(PROBABILITY)</span><span> (Location) (Scale)
-#> </span><span style='color: #00BB00;font-weight: bold;'> 0</span><span> 4 0.5
+#> Exprs outliers:
+#> (PROBABILITY) (Location) (Scale)
+#> 0 4 0.5
#>
-#> </span><span style='font-weight: bold;'>Groups:</span><span>
-#> </span><span style='color: #0000BB;'> [Groups]</span><span> </span><span style='color: #0000BB;'>[Group Probs]</span><span>
+#> Groups:
+#> [Groups] [Group Probs]
#> 1 1
#>
-#> </span><span style='font-weight: bold;'>Diff expr:</span><span>
-#> </span><span style='color: #0000BB;'>[Probability]</span><span> </span><span style='color: #0000BB;'> [Down Prob]</span><span> </span><span style='color: #0000BB;'> [Location]</span><span> </span><span style='color: #0000BB;'> [Scale]</span><span>
+#> Diff expr:
+#> [Probability] [Down Prob] [Location] [Scale]
#> 0.1 0.5 0.1 0.4
#>
-#> </span><span style='font-weight: bold;'>BCV:</span><span>
-#> </span><span style='font-weight: bold;'> (COMMON DISP)</span><span> </span><span style='font-weight: bold;'> (DOF)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'>0.752043426792845</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 11211.8933424157</span><span>
+#> BCV:
+#> (COMMON DISP) (DOF)
+#> 0.752043426792845 11211.8933424157
#>
-#> </span><span style='font-weight: bold;'>Dropout:</span><span>
-#> </span><span style='color: #0000BB;'> [Type]</span><span> </span><span style='font-weight: bold;'> (MIDPOINT)</span><span> </span><span style='font-weight: bold;'> (SHAPE)</span><span>
-#> none </span><span style='color: #00BB00;font-weight: bold;'> 2.71153535179343</span><span> </span><span style='color: #00BB00;font-weight: bold;'>-1.37209356733765</span><span>
+#> Dropout:
+#> [Type] (MIDPOINT) (SHAPE)
+#> none 2.71153535179343 -1.37209356733765
#>
-#> </span><span style='font-weight: bold;'>Paths:</span><span>
-#> </span><span style='color: #0000BB;'> [From]</span><span> </span><span style='color: #0000BB;'> [Steps]</span><span> </span><span style='color: #0000BB;'> [Skew]</span><span> </span><span style='color: #0000BB;'> [Non-linear]</span><span> </span><span style='color: #0000BB;'>[Sigma Factor]</span><span>
+#> Paths:
+#> [From] [Steps] [Skew] [Non-linear] [Sigma Factor]
#> 0 100 0.5 0.1 0.8
-#> </div></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="#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> 1.3.0.</p>
+ <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/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index 09b53f454e7baa58952e41fc92d1e85b7d775968..df9fc4d3a74f952a26e761f70323268c79178248 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -8,21 +8,25 @@
<title>Simulate BCV means — splatSimBCVMeans • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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." />
@@ -41,6 +45,7 @@ and inverse gamma distribution." />
+
<!-- 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>
@@ -61,6 +66,7 @@ and inverse gamma distribution." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ and inverse gamma distribution." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ and inverse gamma distribution." />
<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>
@@ -126,6 +131,7 @@ and inverse gamma distribution." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,15 +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>
@@ -158,37 +162,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index af9b6f8b082afaed04de5954816595a4f6666886..242767dd717b3aa73d69db2481dbcfedef7f67f3 100644
--- a/docs/reference/splatSimBatchCellMeans.html
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -8,21 +8,25 @@
<title>Simulate batch means — splatSimBatchCellMeans • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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" />
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-<!-- sticky kit -->
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+<!-- 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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ factors." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ factors." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ factors." />
<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>
@@ -125,6 +130,7 @@ factors." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,14 +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>
@@ -156,37 +160,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index e00a7b479ea7c5de030928faee8a2bae6fe260ff..f62b51a237ff7553b0a03cda40d905c2fdab2764 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -8,21 +8,25 @@
<title>Simulate batch effects — splatSimBatchEffects • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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" />
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<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." />
@@ -41,6 +45,7 @@ means for each batch." />
+
<!-- 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>
@@ -61,6 +66,7 @@ means for each batch." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ means for each batch." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ means for each batch." />
<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>
@@ -126,6 +131,7 @@ means for each batch." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,15 +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>
@@ -158,37 +162,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index fb5916dade26e1ba36740a82a6281d7d7f001221..b025f346184d7e5d3dc18aa692497c07a9926126 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -8,21 +8,25 @@
<title>Simulate cell means — splatSimCellMeans • 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 -->
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+<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" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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+<!-- 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
@@ -43,6 +47,7 @@ means are adjusted for each cell's expected library size." />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -63,6 +68,7 @@ means are adjusted for each cell's expected library size." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -79,7 +85,7 @@ means are adjusted for each cell's expected library size." />
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -87,7 +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>
@@ -113,11 +119,10 @@ means are adjusted for each cell's expected library size." />
<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>
@@ -128,6 +133,7 @@ means are adjusted for each cell's expected library size." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -139,13 +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>)
@@ -153,7 +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>
@@ -166,37 +170,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimDE.html b/docs/reference/splatSimDE.html
index 193af090dd2462b36449acb1c30b7bf8d10adeba..72a3889076a6b65f035a3e003435923801f71bd9 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -8,21 +8,25 @@
<title>Simulate group differential expression — splatSimDE • Splatter</title>
+
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<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 -->
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+<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" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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+<!-- 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 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 taken to make sure
@@ -42,6 +46,7 @@ they are simulated in the correct order." />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -62,6 +67,7 @@ they are simulated in the correct order." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -78,7 +84,7 @@ they are simulated in the correct order." />
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -86,7 +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>
@@ -112,11 +118,10 @@ they are simulated in the correct order." />
<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>
@@ -127,6 +132,7 @@ they are simulated in the correct order." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -138,18 +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 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>
@@ -162,37 +166,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimDropout.html b/docs/reference/splatSimDropout.html
index a1a19e712cc043357fb51c67febf6cf43e708763..c07cd8c6b6a0843bc1cb61a432f511479dcc005d 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -8,21 +8,25 @@
<title>Simulate dropout — splatSimDropout • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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 dropout — splatSimDropout" />
+<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
@@ -42,6 +46,7 @@ to decide which counts should be dropped." />
+
<!-- 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>
@@ -62,6 +67,7 @@ to decide which counts should be dropped." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -78,7 +84,7 @@ to decide which counts should be dropped." />
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -86,7 +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>
@@ -112,11 +118,10 @@ to decide which counts should be dropped." />
<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>
@@ -127,6 +132,7 @@ to decide which counts should be dropped." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -138,16 +144,14 @@ to decide which counts should be dropped." />
</div>
<div class="ref-description">
-
<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>
@@ -160,37 +164,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index edb19ad0e099493f0b8a0ee66619aac24bb3158e..afd1d9009617d8b08952d16cb60e35653a6f13d8 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -8,21 +8,25 @@
<title>Simulate gene means — splatSimGeneMeans • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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." />
@@ -41,6 +45,7 @@ with the median mean expression multiplied by the outlier factor." />
+
<!-- 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>
@@ -61,6 +66,7 @@ with the median mean expression multiplied by the outlier factor." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ with the median mean expression multiplied by the outlier factor." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ with the median mean expression multiplied by the outlier factor." />
<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>
@@ -126,6 +131,7 @@ with the median mean expression multiplied by the outlier factor." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,15 +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>
@@ -158,37 +162,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index e9fa3ddd90075bf44e413bee03b558c4d7887d2d..56b61da064b03bc76788d9dbcf7cfc22d0f5563b 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -8,21 +8,25 @@
<title>Simulate library sizes — splatSimLibSizes • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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." />
@@ -41,6 +45,7 @@ negative values are set to half the minimum non-zero value." />
+
<!-- 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>
@@ -61,6 +66,7 @@ negative values are set to half the minimum non-zero value." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ negative values are set to half the minimum non-zero value." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ negative values are set to half the minimum non-zero value." />
<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>
@@ -126,6 +131,7 @@ negative values are set to half the minimum non-zero value." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,15 +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>
@@ -158,37 +162,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 42cb24ee0353aca7dbd2f485af923ddf99f99113..871df99cf8e05bbdc53a9f6c1cb3e987e46a23bb 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -8,21 +8,25 @@
<title>Simulate true counts — splatSimTrueCounts • 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>
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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." />
@@ -41,6 +45,7 @@ group (or path position), expected library size and BCV." />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -61,6 +66,7 @@ group (or path position), expected library size and BCV." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -77,7 +83,7 @@ group (or path position), expected library size and BCV." />
</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">1.9.4</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 +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>
@@ -111,11 +117,10 @@ group (or path position), expected library size and BCV." />
<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>
@@ -126,6 +131,7 @@ group (or path position), expected library size and BCV." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -137,15 +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>
@@ -158,37 +162,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatSimulate.html b/docs/reference/splatSimulate.html
index 65bb33a560262440e7f874bbf83c012f979173da..511d15c2a8be23997eb91131f38919aaf97edb6e 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -8,21 +8,25 @@
<title>Splat simulation — splatSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,14 +36,15 @@
<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://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>
@@ -60,6 +65,7 @@ the Splat method." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ the Splat method." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ the Splat method." />
<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>
@@ -125,6 +130,7 @@ the Splat method." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,13 +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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>)
@@ -150,7 +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>
@@ -176,12 +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
@@ -201,8 +204,9 @@ 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='https://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
@@ -212,8 +216,7 @@ information includes:</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>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>
@@ -226,8 +229,7 @@ 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>
+ 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>
@@ -240,20 +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>,
@@ -261,11 +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>
@@ -277,40 +277,39 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/splatter.html b/docs/reference/splatter.html
index 059361640781a4a1ba567c207b1b7de57ca26bb7..f36ada1d7abf1dbe02bb4b1eec9f777f1fa229b2 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -8,21 +8,25 @@
<title>splatter. — splatter • 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 -->
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+<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" />
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-<!-- sticky kit -->
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+<!-- 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">
@@ -32,14 +36,15 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -60,6 +65,7 @@ simulation of single-cell RNA-seq count data." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ simulation of single-cell RNA-seq count data." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ simulation of single-cell RNA-seq count data." />
<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>
@@ -125,6 +130,7 @@ simulation of single-cell RNA-seq count data." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,50 +142,49 @@ 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/summariseDiff.html b/docs/reference/summariseDiff.html
index 731f6d47d224a28eed78e48b205b13414158af90..841f0d7628b386b25342c5c833e77deaa3a0511a 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -6,23 +6,27 @@
<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://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>
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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" />
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<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="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), Root Mean Squared
Error (RMSE) and Kolmogorov-Smirnov (KS) statistics for the various
@@ -42,6 +46,7 @@ properties and ranks them." />
+
<!-- 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>
@@ -62,6 +67,7 @@ properties and ranks them." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -78,7 +84,7 @@ properties and ranks them." />
</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">1.9.4</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.7.9019</span>
</span>
</div>
@@ -86,7 +92,7 @@ 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>
@@ -112,11 +118,10 @@ properties and ranks them." />
<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>
@@ -127,27 +132,26 @@ 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), 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>
@@ -156,56 +160,57 @@ 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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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>)
+ <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://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
-#> 1 Splat Mean 2.288933 NaN 1 2.375445 NaN
-#> 2 Splat Variance 11.025042 NaN 1 9.969259 NaN
-#> 3 Splat ZerosGene 30.000000 NaN 1 40.500000 NaN
-#> 4 Splat MeanVar 9.509015 NaN 1 11.819818 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 42.780000 NaN
-#> 6 Splat LibSize 59367.000000 NaN 1 59618.300000 NaN
-#> MAERank RMSE RMSEScaled RMSERank KS KSPVal KSRank
-#> 1 1 2.85907 NaN 1 0.334 0.000000e+00 1
-#> 2 1 12.57383 NaN 1 0.573 0.000000e+00 1
-#> 3 1 45.84158 NaN 1 0.542 0.000000e+00 1
-#> 4 1 14.92356 NaN 1 NA NA NA
-#> 5 1 51.94324 NaN 1 NA NA NA
-#> 6 1 61010.54295 NaN 1 1.000 1.450928e-11 1</div></pre>
+<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/summariseKS.html b/docs/reference/summariseKS.html
index b246c24d23f9a905043d4ac5900a0148cbe76f9c..9aab82fc877b85f2e9f51f24feb9d2cd07efdfd0 100644
--- a/docs/reference/summariseKS.html
+++ b/docs/reference/summariseKS.html
@@ -8,21 +8,25 @@
<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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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 referenc using the KS test." />
+<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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +141,11 @@
</div>
<div class="ref-description">
-
- <p>Summarise columns of a data.frame compared to a referenc using the KS test.</p>
-
+ <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>
@@ -163,37 +167,39 @@
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>
+ </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> 1.3.0.</p>
+ <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
index 46c595c91b22bd8ab3a555110b853b461dab1856..33cc0a8b61ef9a6ce1fea985aac3a59764487704 100644
--- a/docs/reference/summariseStats.html
+++ b/docs/reference/summariseStats.html
@@ -8,21 +8,25 @@
<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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Summarise statistics — summariseStats" />
+<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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,14 +141,12 @@
</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://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"MAD"</span>, <span class='st'>"MAE"</span>,
+ <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>
@@ -164,37 +168,39 @@ those names will be used in the output.</p></td>
<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>
+ </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> 1.3.0.</p>
+ <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
index a381746263cd0c2e9651ba2f639e0136c8c6840e..375ee92915c448f593942cd9f4c3da72138ddcf7 100644
--- a/docs/reference/tidyStatSumm.html
+++ b/docs/reference/tidyStatSumm.html
@@ -8,21 +8,25 @@
<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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<link href="../extra.css" rel="stylesheet">
-<meta property="og:title" content="Tidy summarised statistics — tidyStatSumm" />
+<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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +141,11 @@
</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://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"MAD"</span>, <span class='st'>"MAE"</span>, <span class='st'>"RMSE"</span>))</pre>
-
+ <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>
@@ -154,37 +158,39 @@
<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>
+ </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> 1.3.0.</p>
+ <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 a3e57d92ddf1a0f9fccbb49e5a22ffa93806e292..88d989c74485af377ba52e0b20667775b6074124 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -8,21 +8,25 @@
<title>Winsorize vector — winsorize • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -154,37 +158,39 @@
<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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/zinbEstimate.html b/docs/reference/zinbEstimate.html
index d770a8bee476c5de26c84e88809e7c4688984c1d..8eaa6e888d68e98215cc88634c2b8ce2e0d2cf1d 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -8,21 +8,25 @@
<title>Estimate ZINB-WaVE simulation parameters — zinbEstimate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-<!-- sticky kit -->
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+<!-- 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">
@@ -32,14 +36,15 @@
<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -60,6 +65,7 @@ dataset." />
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -76,7 +82,7 @@ dataset." />
</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">1.9.4</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 +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>
@@ -110,11 +116,10 @@ dataset." />
<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>
@@ -125,6 +130,7 @@ dataset." />
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -136,10 +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>,
@@ -159,7 +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>
@@ -209,110 +213,110 @@ single core.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>additional arguments passes to <code><a href='https://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='https://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='https://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"><div class='input'><span class='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>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://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>scater</span>)
- <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</span>)
- <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/scater/topics/mockSCE'>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>)
+ <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
-#> 0.304 0.010 0.319 </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
-#> 0.044 0.001 0.045 </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
-#> 0.214 0.007 0.225 </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
-#> 0.070 0.008 0.078 </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
-#> 0.157 0.002 0.161 </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 <span style='font-weight: bold;'>Params</span><span> object of class </span><span style='font-weight: bold;'>ZINBParams</span><span>
-#> Parameters can be (estimable) or </span><span style='color: #0000BB;'>[not estimable],</span><span> 'Default' or </span><span style='color: #00BB00;font-weight: bold;'>'NOT DEFAULT'</span><span>
+#> 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
#>
-#> </span><span style='font-weight: bold;'>Global:</span><span>
-#> </span><span style='font-weight: bold;'>(GENES)</span><span> </span><span style='font-weight: bold;'>(CELLS)</span><span> </span><span style='color: #0000BB;'> [Seed]</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'> 100</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 20</span><span> 848036
+#> Global:
+#> (Genes) (CELLS) [Seed]
+#> 100 20 955861
#>
#> 1 additional parameters
#>
-#> </span><span style='font-weight: bold;'>Model:</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'>ZinbModel with 100 features, 20 samples, 0 latent factors and 241 parameters</span><span>
+#> Model:
+#> ZinbModel with 100 features, 20 samples, 0 latent factors and 241 parameters
#>
-#> </span><span style='font-weight: bold;'>Parameters of the ZinbModel</span><span>
+#> Parameters of the ZinbModel
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Design:</span><span>
-#> </span><span style='font-weight: bold;'> (SAMPLES)</span><span> (Genes)
-#> </span><span style='color: #00BB00;font-weight: bold;'>1, 1, 1, 1,...</span><span> 1, 1, 1, 1,...
+#> Model Design:
+#> (SAMPLES) (Genes)
+#> 1, 1, 1, 1,... 1, 1, 1, 1,...
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Offsets:</span><span>
-#> </span><span style='font-weight: bold;'> (MU)</span><span> </span><span style='font-weight: bold;'> (PI)</span><span>
-#> </span><span style='color: #00BB00;font-weight: bold;'>20 x 100 matrix</span><span> </span><span style='color: #00BB00;font-weight: bold;'>20 x 100 matrix</span><span>
+#> Model Offsets:
+#> (MU) (PI)
+#> 20 x 100 matrix 20 x 100 matrix
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Indices:</span><span>
+#> Model Indices:
#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
#> 1 1 1 1
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Intercepts:</span><span>
+#> Model Intercepts:
#> (Sample Mu) (Gene Mu) (Sample Pi) (Gene Pi)
#> TRUE TRUE TRUE TRUE
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Latent factors:</span><span>
+#> Model Latent factors:
#> (W)
#> 20 x 0 matrix
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Coefficients:</span><span>
-#> </span><span style='font-weight: bold;'> (SAMPLE MU)</span><span> </span><span style='font-weight: bold;'> (GENE MU)</span><span> (Latent Mu) </span><span style='font-weight: bold;'> (SAMPLE PI)</span><span> </span><span style='font-weight: bold;'> (GENE PI)</span><span> (Latent Pi)
-#> </span><span style='color: #00BB00;font-weight: bold;'>-0.459768269108686, 1.62119422809804, -0.223102757788152, 0.0429479357333727,...</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 4.26299872242102, 4.29178871361806, 4.44953744138558, 3.86260697728158,...</span><span> 0 x 100 matrix </span><span style='color: #00BB00;font-weight: bold;'> 1.90228646100659, -6.94249109253294, -1.07943871883735, -0.430729773518204,...</span><span> </span><span style='color: #00BB00;font-weight: bold;'> -0.983749678057473, -1.35076635474983, -1.23286376482938, -1.26061065393089,...</span><span> 0 x 100 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
#>
-#> </span><span style='font-weight: bold;'>Model</span><span> </span><span style='font-weight: bold;'>Regularisation:</span><span>
-#> (Sample Mu) </span><span style='font-weight: bold;'> (GENE MU)</span><span> (Sample Pi) </span><span style='font-weight: bold;'> (GENE PI)</span><span>
-#> 1 </span><span style='color: #00BB00;font-weight: bold;'> 5</span><span> 1 </span><span style='color: #00BB00;font-weight: bold;'> 5</span><span>
-#> </span><span style='font-weight: bold;'> (LATENT)</span><span> (Latent coeffs) (Zeta) (Logit)
-#> </span><span style='color: #00BB00;font-weight: bold;'> 5</span><span> 1 100 0.001
+#> 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></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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/zinbSimulate.html b/docs/reference/zinbSimulate.html
index 1c1eea1af5563619c27643908905b6c1922cf6e3..e0b3919a918347769eac4f0431f53e7c14363608 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -8,21 +8,25 @@
<title>ZINB-WaVE simulation — zinbSimulate • 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/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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/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">
@@ -32,13 +36,14 @@
<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://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>
@@ -59,6 +64,7 @@
gtag('config', 'UA-52309538-4');
</script>
+
</head>
<body>
@@ -75,7 +81,7 @@
</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">1.9.4</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 +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>
@@ -109,11 +115,10 @@
<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>
@@ -124,6 +129,7 @@
</div><!--/.navbar -->
+
</header>
<div class="row">
@@ -135,13 +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>
@@ -159,19 +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='https://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='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='https://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
@@ -182,10 +184,9 @@ 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='kw'>if</span> (<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ns-load'>requireNamespace</a></span>(<span class='st'>"zinbwave"</span>, <span class='kw'>quietly</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>"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>
@@ -194,32 +195,32 @@ bioRxiv (2017).</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+ <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/sitemap.xml b/docs/sitemap.xml
index 4fa3ad447753f11873f74792a1c518782bc0041d..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>
@@ -63,6 +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>
@@ -75,6 +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>
@@ -120,12 +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>
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/WORDLIST b/inst/WORDLIST
index c90a07c1acb75ab19822628bbea9cae3d6674a17..8c3439ae0093d36e1e09b40f8269d19a600e84af 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -5,6 +5,7 @@ AppVeyor
BASiCS
BASiCSEstimate
BASiCSParams
+BASiCSSimulate
bcv
BCV
Bioc
@@ -13,12 +14,13 @@ biocViews
bioRxiv
BPPARAM
Chu
+compareSCEs
compareSCESets
cpm
cutoff
df
+diffSCEs
diffSCESets
-diffSCESs
DM
doi
DP
@@ -28,6 +30,7 @@ eg
etc
fpkm
FPKM
+gam
getLNormFactors
Github
Gribkova
@@ -35,6 +38,8 @@ ImmunoOncology
ingroup
JC
KD
+Kersplat
+KersplatParams
Korthauer
KR
len
@@ -54,25 +59,30 @@ 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
@@ -81,13 +91,16 @@ SCDDParams
scDDSimulate
SCE
SCESets
+scRNA
sd
sdlog
+selectFit
seq
SimpleParams
SingleCellExperiment
SingleCellExperiments
SNE
+Söding
SparseDC
sparseDCEstimate
SparseDCParams
@@ -99,6 +112,9 @@ SplatParams
splatSimulate
splatSimulatePaths
Splatter's
+splotchEstimate
+SplotchParams
+splotchSimulate
summariseDiff
SummarizedExperiment
th
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/SplatParams.Rd b/man/SplatParams.Rd
index bb906f959b313a7dcee5dfd3b5f1d2797f3307a6..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.}
@@ -133,7 +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/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/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/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/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/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 e144b4055269240d5999c4f4376b4532359acc9c..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)
diff --git a/man/setParams.Rd b/man/setParams.Rd
index b7265f0f52cfe27d453ae75d94eea37fe400797f..0e62af22920d3b2e02fdd886d767827fdb8e5621 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -1,15 +1,18 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/AllGenerics.R, R/Params-methods.R,
-% R/SplatParams-methods.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(object, update = NULL, ...)
+\S4method{setParams}{KersplatParams}(object, update = NULL, ...)
+
\S4method{setParams}{Params}(object, update = NULL, ...)
\S4method{setParams}{SplatParams}(object, update = NULL, ...)
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/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/summariseDiff.Rd b/man/summariseDiff.Rd
index bcc11be13f32a63ec5ae38701145ea381afec393..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)
}
diff --git a/man/summariseKS.Rd b/man/summariseKS.Rd
index f424f42aede6f35c03ea24e6bbcbb52873f50518..7e8f43a1ac47e5247bb2dedc11f6a9911ecee419 100644
--- a/man/summariseKS.Rd
+++ b/man/summariseKS.Rd
@@ -20,5 +20,5 @@ those names will be used in the output.}
data.frame with the summarised measure, scaled and ranked
}
\description{
-Summarise columns of a data.frame compared to a referenc using the KS test.
+Summarise columns of a data.frame compared to a reference using the KS test.
}
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/vignettes/splat_params.Rmd b/vignettes/splat_params.Rmd
index 5b72b8f319a128fb673e9e595a739bbcf869aa17..f8639d29cc71d5da3c11bffaa46f7b414853491a 100644
--- a/vignettes/splat_params.Rmd
+++ b/vignettes/splat_params.Rmd
@@ -380,7 +380,8 @@ plotPCA(sim2, colour_by = "Group") +
"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"))
+ "Group 5 has bigger factors with moderate",
+ "variability"))
# Combination of everything
sim3 <- splatSimulateGroups(params.groups,
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index 44255b4be91fd927777156da55980da210045a24..8bb64af30582846ec389c7dd34195d3a7a69b371 100644
--- a/vignettes/splatter.Rmd
+++ b/vignettes/splatter.Rmd
@@ -45,7 +45,7 @@ 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 a mock dataset generted with the `scater` package:
+Splatter. Here is an example a mock dataset generated with the `scater` package:
```{r quickstart}
# Load package