diff --git a/.Rbuildignore b/.Rbuildignore
index 5c7dbad65f33379850f6c86bc7b0c8cde6549c57..708610f47beec04f16f9dfe7f49791ded3b7bfb9 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@
^index\.md$
^_pkgdown\.yml$
^pkgdown$
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
index c141603ff53809e900bb7dc49ab0e47884c6838f..c0399849fba9b381c6fbd18b712e68c9df48ee87 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,3 +26,5 @@ vignettes/*.pdf
*.knit.md
.Rproj.user
inst/doc
+doc
+Meta
diff --git a/DESCRIPTION b/DESCRIPTION
index 0218c77fb0498d1321fd9cde2f1ba60e3d473448..1e914184587198407c5c91f62a4a860740a8ae06 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.7.4
-Date: 2019-04-17
+Version: 1.7.5
+Date: 2019-04-18
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -61,7 +61,8 @@ Suggests:
BASiCS,
zinbwave,
SparseDC,
- BiocManager
+ BiocManager,
+ spelling
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
@@ -69,3 +70,4 @@ BugReports: https://github.com/Oshlack/splatter/issues
RoxygenNote: 6.1.1
Encoding: UTF-8
VignetteBuilder: knitr
+Language: en-GB
diff --git a/NEWS.md b/NEWS.md
index ebbb84d94ad83c8620e2fb7d255004e6e1b95154..8cac20920dbf35b542bcc684f95ba0450ad0f82b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+## Version 1.7.5 (2018-04-18)
+
+* Add Splat parameters vignette
+* Fix spelling
+
## Version 1.7.4 (2018-04-17)
* Allow SplatParams parameters to be set in any order
@@ -53,7 +58,7 @@
* Fix bug in getLNormFactors when reversing factors less than one
* Update documentation to new Roxygen version (6.1.0)
-* Change varible name in vignette for compatibility with scater
+* Change variable name in vignette for compatibility with scater
* Add suggested package checks to tests
## Version 1.5.1 (2018-06-12)
@@ -226,7 +231,7 @@
## Version 0.99.13 (2017-03-25)
-* Modify how Lun2Params stores gene paramters to use data.frame
+* Modify how Lun2Params stores gene parameters to use data.frame
* Move sampling of genes/cells to lun2Simulate
* Return to old Lun2 nGenes estimate
@@ -236,7 +241,7 @@
* Update compareSCESets plots
* Modify Lun2 nGenes estimate
* Modify how addFeatureStats names columns
-* Add infinte bcv.df warning to splatSimulate
+* Add infinite bcv.df warning to splatSimulate
## Version 0.99.11 (2017-03-20)
@@ -338,7 +343,7 @@
* Redesign how parameters are stored
* Each simulation now has it's own S4 Params class
-* Modify exisiting simulations to use new parameter objects
+* Modify existing simulations to use new parameter objects
## Version 0.6.0 (2016-10-12)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 32f13df826437fc10230d9591df6f8faa580398f..1da947a4586fee93e38cf7b87ae43d95ec4c86ed 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -332,10 +332,10 @@ setClass("LunParams",
#' \item{\emph{Gene parameters}}{
#' \describe{
#' \item{\code{gene.params}}{A \code{data.frame} containing gene
-#' parameters with two coloumns: \code{Mean} (mean expression for
+#' parameters with two columns: \code{Mean} (mean expression for
#' each gene) and \code{Disp} (dispersion for each gene).}
#' \item{\code{zi.params}}{A \code{data.frame} containing
-#' zero-inflated gene parameters with three coloumns: \code{Mean}
+#' zero-inflated gene parameters with three columns: \code{Mean}
#' (mean expression for each gene), \code{Disp} (dispersion for
#' each, gene), and \code{Prop} (zero proportion for each gene).}
#' }
@@ -343,7 +343,7 @@ setClass("LunParams",
#' \item{\code{[nPlates]}}{The number of plates to simulate.}
#' \item{\emph{Plate parameters}}{
#' \describe{
-#' \item{\code{plate.ingroup}}{Character vecotor giving the plates
+#' \item{\code{plate.ingroup}}{Character vector giving the plates
#' considered to be part of the "ingroup".}
#' \item{\code{plate.mod}}{Plate effect modifier factor. The plate
#' effect variance is divided by this value.}
@@ -492,7 +492,7 @@ setClass("SCDDParams",
#' \item{\emph{Gene parameters}}{
#' \describe{
#' \item{\code{gene.params}}{A \code{data.frame} containing gene
-#' parameters with two coloumns: \code{Mean} (mean expression for
+#' parameters with two columns: \code{Mean} (mean expression for
#' each biological gene) and \code{Delta} (cell-to-cell
#' heterogeneity for each biological gene).}
#' }
@@ -506,7 +506,7 @@ setClass("SCDDParams",
#' \item{\emph{Cell parameters}}{
#' \describe{
#' \item{\code{cell.params}}{A \code{data.frame} containing gene
-#' parameters with two coloumns: \code{Phi} (mRNA content factor for
+#' parameters with two columns: \code{Phi} (mRNA content factor for
#' each cell, scaled to sum to the number of cells in each batch)
#' and \code{S} (capture efficient for each cell).}
#' }
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index d7f0ceca4f75a9f1f7b14dfb23d77b6d3eed70e3..4c8d46c004c713bdb19beca478df29bf01f832ed 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -36,7 +36,7 @@ setGeneric("getParam", function(object, name) {standardGeneric("getParam")})
#'
#' @param object object to set parameter in.
#' @param name name of the parameter to set.
-#' @param value value to set the paramter to.
+#' @param value value to set the parameter to.
#'
#' @return Object with new parameter value.
#'
@@ -57,7 +57,7 @@ setGeneric("setParam", function(object, name, value) {
#'
#' @param object object to set parameter in.
#' @param name name of the parameter to set.
-#' @param value value to set the paramter to.
+#' @param value value to set the parameter to.
#'
#' @return Object with new parameter value.
#'
diff --git a/R/BASiCS-simulate.R b/R/BASiCS-simulate.R
index 66cc4242aa349b2c58d62fe6ffd0c6b1a88f33ef..743f48f11b47bbcbd29789b83d78348bba95e0cb 100644
--- a/R/BASiCS-simulate.R
+++ b/R/BASiCS-simulate.R
@@ -18,7 +18,7 @@
#'
#' @references
#' Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
-#' Single-Cell Sequencing data. PLoS Comput. Biol. (2015).
+#' Single-Cell Sequencing data. PLoS Computational Biology (2015).
#'
#' Paper: \url{10.1371/journal.pcbi.1004333}
#'
diff --git a/R/compare.R b/R/compare.R
index 88fede5dceadce42e320eb338c5ddfe33eaa4f9b..cad0a775581296f4fce63e7183d4d0290d5b5c6d 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -24,7 +24,7 @@
#' \item{\code{Variances}}{Boxplot of variance distribution.}
#' \item{\code{MeanVar}}{Scatter plot with fitted lines showing the
#' mean-variance relationship.}
-#' \item{\code{LibraySizes}}{Boxplot of the library size
+#' \item{\code{LibrarySizes}}{Boxplot of the library size
#' distribution.}
#' \item{\code{ZerosGene}}{Boxplot of the percentage of each gene
#' that is zero.}
@@ -227,7 +227,7 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
#' \item{\code{Variances}}{Boxplot of variance differences.}
#' \item{\code{MeanVar}}{Scatter plot showing the difference from
#' the reference variance across expression ranks.}
-#' \item{\code{LibraySizes}}{Boxplot of the library size
+#' \item{\code{LibraeySizes}}{Boxplot of the library size
#' differences.}
#' \item{\code{ZerosGene}}{Boxplot of the differences in the
#' percentage of each gene that is zero.}
@@ -411,7 +411,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
geom_hline(yintercept = 0, colour = "red") +
geom_boxplot() +
scale_colour_manual(values = colours) +
- ylab(paste("Rank difference libray size")) +
+ ylab(paste("Rank difference library size")) +
ggtitle("Difference in library sizes") +
theme_minimal()
diff --git a/R/lun2-simulate.R b/R/lun2-simulate.R
index ec5ff3b11545cb519bda2c2f64405cbfcc3eb13c..68cc68471f5f06d92ac3fa3e23e302077f3ca731 100644
--- a/R/lun2-simulate.R
+++ b/R/lun2-simulate.R
@@ -19,9 +19,9 @@
#' Library size factors are also applied and optionally a zero-inflated
#' negative-binomial can be used.
#'
-#' If the number of genes to simulate differs from the number of provied gene
+#' If the number of genes to simulate differs from the number of provided gene
#' parameters or the number of cells to simulate differs from the number of
-#' library sizes the relevant paramters will be sampled with a warning. This
+#' library sizes the relevant parameters will be sampled with a warning. This
#' allows any number of genes or cells to be simulated regardless of the
#' number in the dataset used in the estimation step but has the downside that
#' some genes or cells may be simulated multiple times.
@@ -145,7 +145,7 @@ lun2Simulate <- function(params = newLun2Params(), zinb = FALSE,
}
}
- if (verbose) {message("Simulating libray size factors...")}
+ if (verbose) {message("Simulating library size factors...")}
lib.facs <- lib.sizes / mean(lib.sizes)
lib.facs <- sample(lib.facs, nCells, replace = TRUE) * lib.mod
cells$LibSizeFac <- lib.facs
diff --git a/R/sparseDC-estimate.R b/R/sparseDC-estimate.R
index 0c0f793f38b6c71d0e8ec68ae034063e36c78eca..b4b02eaa35aec14df70db929ac8581f5fb65f55c 100644
--- a/R/sparseDC-estimate.R
+++ b/R/sparseDC-estimate.R
@@ -7,7 +7,7 @@
#' containing count data to estimate parameters from.
#' @param conditions numeric vector giving the condition each cell belongs to.
#' @param nclusters number of cluster present in the dataset.
-#' @param norm logical, whether to libray size normalise counts before
+#' @param norm logical, whether to library size normalise counts before
#' estimation. Set this to FALSE if counts is already normalised.
#' @param params PhenoParams object to store estimated values in.
#'
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index efa087fdd0a07116e920b8d2b82cf1a1649b1425..8063afe5424927e29f45a6c7c4b4fe365e6ba367 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -396,7 +396,7 @@ splatSimBatchCellMeans <- function(sim, params) {
#'
#' Simulate differential expression. Differential expression factors for each
#' group are produced using \code{\link{getLNormFactors}} and these are added
-#' along with updated means for each group. For paths care is taked to make sure
+#' along with updated means for each group. For paths care is taken to make sure
#' they are simulated in the correct order.
#'
#' @param sim SingleCellExperiment to add differential expression to.
@@ -696,7 +696,7 @@ splatSimTrueCounts <- function(sim, params) {
#' Simulate dropout
#'
-#' A logistic function is used to form a relationshop between the expression
+#' A logistic function is used to form a relationship between the expression
#' level of a gene and the probability of dropout, giving a probability for each
#' gene in each cell. These probabilities are used in a Bernoulli distribution
#' to decide which counts should be dropped.
@@ -773,7 +773,7 @@ splatSimDropout <- function(sim, params) {
if (dropout.type != "none") {
- # Generate probabilites based on expression
+ # Generate probabilities based on expression
drop.prob <- sapply(seq_len(nCells), function(idx) {
eta <- log(cell.means[, idx])
return(logistic(eta, x0 = dropout.mid[idx], k = dropout.shape[idx]))
@@ -834,7 +834,7 @@ getLNormFactors <- function(n.facs, sel.prob, neg.prob, fac.loc, fac.scale) {
#' Identify the correct order to process paths so that preceding paths have
#' already been simulated.
#'
-#' @param path.from vector giving the path endpoints that each path orginates
+#' @param path.from vector giving the path endpoints that each path originates
#' from.
#'
#' @return Vector giving the order to process paths in.
diff --git a/R/utils.R b/R/utils.R
index 85400dab7c13c9b447bc5eb7433ebae17e81a97d..96fec570540fa8669b4b7436820720aecbf32441 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -6,7 +6,7 @@
#' @param x0 midpoint parameter. Gives the centre of the function.
#' @param k shape parameter. Gives the slope of the function.
#'
-#' @return Value of logistic funciton with given parameters
+#' @return Value of logistic function with given parameters
logistic <- function(x, x0, k) {
1 / (1 + exp(-k * (x - x0)))
}
diff --git a/R/zinb-estimate.R b/R/zinb-estimate.R
index 866c3505762cfca877f2e08cddf8efb0ed515ba9..524b2c4e648266fb18104f70e1f3d502428f2d37 100644
--- a/R/zinb-estimate.R
+++ b/R/zinb-estimate.R
@@ -9,7 +9,7 @@
#' @param design.genes design matrix of gene-level covariates.
#' @param common.disp logical. Whether or not a single dispersion for all
#' features is estimated.
-#' @param iter.init number of iterations to use for initalization.
+#' @param iter.init number of iterations to use for initialization.
#' @param iter.opt number of iterations to use for optimization.
#' @param stop.opt stopping criterion for optimization.
#' @param params ZINBParams object to store estimated values in.
diff --git a/README.md b/README.md
index 7b85bef86d225e7da1c40529f05fc5cbb8334bbc..33b0ac2075b504d11ab290a9fcbbc7044bde6edd 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@ aren't required for core functionality).
## Getting started
Once installed the best place to get started is the vignette. For most users
-the most convient way to access this is online [here][vignette].
+the most convenient way to access this is online [here][vignette].
Alternatively, if you chose to build the vignette, you can load Splatter, then
browse the vignettes:
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 8bd38ffb016a9718c3ca5ce21ad107b9fa9d4717..72343163485020e54a4e6336a22316d66506dbde 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>License • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -37,7 +37,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -63,14 +64,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -88,6 +90,18 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
@@ -802,9 +816,8 @@ Public License instead of this License. But first, please read
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 043ae7079c1c83274d04e2359a79afb0cb37e0cc..f7e8aba33eb5b9644ac734d72cc4e785ce27e93e 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Articles • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -37,7 +37,8 @@
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+ <h1>Splat simulation parameters</h1>
+
+ <h4 class="date">Last updated: 18 April 2019</h4>
+
+ <small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splat_params.Rmd"><code>vignettes/splat_params.Rmd</code></a></small>
+ <div class="hidden name"><code>splat_params.Rmd</code></div>
+
+ </div>
+
+
+
+<p>This vignette describes the Splat simulation model and the parameters it uses in more detail.</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://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">#> Loading required package: SingleCellExperiment</span></a>
+<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co">#> Loading required package: SummarizedExperiment</span></a>
+<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">#> Loading required package: GenomicRanges</span></a>
+<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">#> Loading required package: stats4</span></a>
+<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">#> Loading required package: BiocGenerics</span></a>
+<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co">#> Loading required package: parallel</span></a>
+<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co">#> Attaching package: 'BiocGenerics'</span></a>
+<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co">#> The following objects are masked from '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">#> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,</span></a>
+<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co">#> clusterExport, clusterMap, parApply, parCapply, parLapply,</span></a>
+<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="co">#> parLapplyLB, parRapply, parSapply, parSapplyLB</span></a>
+<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="co">#> The following objects are masked from 'package:stats':</span></a>
+<a class="sourceLine" id="cb1-16" data-line-number="16"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-17" data-line-number="17"><span class="co">#> IQR, mad, sd, var, xtabs</span></a>
+<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co">#> The following objects are masked from 'package:base':</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">#> anyDuplicated, append, as.data.frame, basename, cbind,</span></a>
+<a class="sourceLine" id="cb1-21" data-line-number="21"><span class="co">#> colnames, dirname, do.call, duplicated, eval, evalq, Filter,</span></a>
+<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co">#> Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,</span></a>
+<a class="sourceLine" id="cb1-23" data-line-number="23"><span class="co">#> mapply, match, mget, order, paste, pmax, pmax.int, pmin,</span></a>
+<a class="sourceLine" id="cb1-24" data-line-number="24"><span class="co">#> pmin.int, Position, rank, rbind, Reduce, rownames, sapply,</span></a>
+<a class="sourceLine" id="cb1-25" data-line-number="25"><span class="co">#> setdiff, sort, table, tapply, union, unique, unsplit, which,</span></a>
+<a class="sourceLine" id="cb1-26" data-line-number="26"><span class="co">#> which.max, which.min</span></a>
+<a class="sourceLine" id="cb1-27" data-line-number="27"><span class="co">#> Loading required package: S4Vectors</span></a>
+<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-29" data-line-number="29"><span class="co">#> Attaching package: 'S4Vectors'</span></a>
+<a class="sourceLine" id="cb1-30" data-line-number="30"><span class="co">#> The following object is masked from 'package:base':</span></a>
+<a class="sourceLine" id="cb1-31" data-line-number="31"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-32" data-line-number="32"><span class="co">#> expand.grid</span></a>
+<a class="sourceLine" id="cb1-33" data-line-number="33"><span class="co">#> Loading required package: IRanges</span></a>
+<a class="sourceLine" id="cb1-34" data-line-number="34"><span class="co">#> Loading required package: GenomeInfoDb</span></a>
+<a class="sourceLine" id="cb1-35" data-line-number="35"><span class="co">#> Loading required package: Biobase</span></a>
+<a class="sourceLine" id="cb1-36" data-line-number="36"><span class="co">#> Welcome to Bioconductor</span></a>
+<a class="sourceLine" id="cb1-37" data-line-number="37"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-38" data-line-number="38"><span class="co">#> Vignettes contain introductory material; view with</span></a>
+<a class="sourceLine" id="cb1-39" data-line-number="39"><span class="co">#> 'browseVignettes()'. To cite Bioconductor, see</span></a>
+<a class="sourceLine" id="cb1-40" data-line-number="40"><span class="co">#> 'citation("Biobase")', and for packages 'citation("pkgname")'.</span></a>
+<a class="sourceLine" id="cb1-41" data-line-number="41"><span class="co">#> Loading required package: DelayedArray</span></a>
+<a class="sourceLine" id="cb1-42" data-line-number="42"><span class="co">#> Loading required package: matrixStats</span></a>
+<a class="sourceLine" id="cb1-43" data-line-number="43"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-44" data-line-number="44"><span class="co">#> Attaching package: 'matrixStats'</span></a>
+<a class="sourceLine" id="cb1-45" data-line-number="45"><span class="co">#> The following objects are masked from 'package:Biobase':</span></a>
+<a class="sourceLine" id="cb1-46" data-line-number="46"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-47" data-line-number="47"><span class="co">#> anyMissing, rowMedians</span></a>
+<a class="sourceLine" id="cb1-48" data-line-number="48"><span class="co">#> Loading required package: BiocParallel</span></a>
+<a class="sourceLine" id="cb1-49" data-line-number="49"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-50" data-line-number="50"><span class="co">#> Attaching package: 'DelayedArray'</span></a>
+<a class="sourceLine" id="cb1-51" data-line-number="51"><span class="co">#> The following objects are masked from '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">#> colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</span></a>
+<a class="sourceLine" id="cb1-54" data-line-number="54"><span class="co">#> The following objects are masked from 'package:base':</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">#> aperm, apply, rowsum</span></a>
+<a class="sourceLine" id="cb1-57" data-line-number="57"><span class="co">#> Registered S3 methods overwritten by 'ggplot2':</span></a>
+<a class="sourceLine" id="cb1-58" data-line-number="58"><span class="co">#> method from </span></a>
+<a class="sourceLine" id="cb1-59" data-line-number="59"><span class="co">#> [.quosures rlang</span></a>
+<a class="sourceLine" id="cb1-60" data-line-number="60"><span class="co">#> c.quosures rlang</span></a>
+<a class="sourceLine" id="cb1-61" data-line-number="61"><span class="co">#> print.quosures rlang</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">#> Loading required package: ggplot2</span></a>
+<a class="sourceLine" id="cb1-64" data-line-number="64"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-65" data-line-number="65"><span class="co">#> Attaching package: 'scater'</span></a>
+<a class="sourceLine" id="cb1-66" data-line-number="66"><span class="co">#> The following object is masked from 'package:S4Vectors':</span></a>
+<a class="sourceLine" id="cb1-67" data-line-number="67"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-68" data-line-number="68"><span class="co">#> rename</span></a>
+<a class="sourceLine" id="cb1-69" data-line-number="69"><span class="co">#> The following object is masked from 'package:stats':</span></a>
+<a class="sourceLine" id="cb1-70" data-line-number="70"><span class="co">#> </span></a>
+<a class="sourceLine" id="cb1-71" data-line-number="71"><span class="co">#> filter</span></a>
+<a class="sourceLine" id="cb1-72" data-line-number="72"><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>
+<div id="the-base-splat-model" class="section level1">
+<h1 class="hasAnchor">
+<a href="#the-base-splat-model" class="anchor"></a>The base Splat model</h1>
+<p>This figure, taken from the Splatter publication, describes the core of the Splat simulation model.</p>
+<div class="figure">
+<img src="splat-model.png" alt="Splat simulation model"><p class="caption">Splat simulation model</p>
+</div>
+<p>The Splat simulation uses a hierarchical probabilistic where different aspects of a dataset are generated from appropriate statistical distributions. The first stage generates a mean expression level for each gene. These are originally chosen from a Gamma distribution. For some genes that are selected to be outliers with high expression a factor is generated from a log-normal distribution. These factors are then multiplied by the median gene mean to create new means for those genes.</p>
+<p>The next stage incorporates variation in the counts per cell. An expected library size (total counts) is chosen for each cell from a log-normal distribution. The library sizes are then used to scale the gene means for each cell, resulting in a range a counts per cell in the simulated dataset. The gene means are then further adjusted to enforce a relationship between the mean expression level and the variability.</p>
+<p>The final cell by gene matrix of gene means is then used to generate a count matrix using a Poisson distribution. The result is a synthetic dataset consisting of counts from a Gamma-Poisson (or negative-binomial) distribution. An additional optional step can be used to replicate a “dropout†effect. A probability of dropout is generated using a logistic function based on the underlying mean expression level. A Bernoulli distribution is then used to create a dropout matrix which sets some of the generated counts to zero.</p>
+<p>The model described here will generate a single population of cells but the Splat simulation has been designed to be as flexible as possible and can create scenarios including multiple groups of cells (cell types), continuous paths between cell types and multiple experimental batches. The parameters used to create these types of simulations and how they interact with the model are described below.</p>
+</div>
+<div id="splat-simulation-parameters" class="section level1">
+<h1 class="hasAnchor">
+<a href="#splat-simulation-parameters" class="anchor"></a>Splat simulation parameters</h1>
+<p>Within Splatter the parameters for the Splat simulation model are held in the <code>SplatParams</code> object. Let’s create one of these objects and see what it looks like.</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
+<a class="sourceLine" id="cb2-2" data-line-number="2">params</a>
+<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co">#> A Params object of class SplatParams </span></a>
+<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT' </span></a>
+<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#> </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 700433 </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>
+<p>Like all the parameter objects in Splatter printing this object displays all the parameters required for this simulation. As we haven’t set any of the parameters the default values are shown but if we were to change any of them they would be highlighted. We can also see which parameters can be estimated by the Splat estimation procedure and which can’t. The default values have been chosen to be fairly realistic but it is recommended that estimation is used to get a simulation that is more like the data you are interested in. Parameters can be modified by setting them in the <code>SplatParams</code> object or by providing them directly to the simulation function.</p>
+<p>The rest of this section provides details of all this parameters and explains how they can be used with examples.</p>
+<div id="global-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#global-parameters" class="anchor"></a>Global parameters</h2>
+<p>These parameters are used in every simulation model and control global features of the dataset produced.</p>
+<div id="ngenes---number-of-genes" class="section level3">
+<h3 class="hasAnchor">
+<a href="#ngenes---number-of-genes" class="anchor"></a><code>nGenes</code> - Number of genes</h3>
+<p>The number of genes to simulate.</p>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># Set the number of genes to 1000</span></a>
+<a class="sourceLine" id="cb3-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">1000</span>)</a>
+<a class="sourceLine" id="cb3-3" data-line-number="3"></a>
+<a class="sourceLine" id="cb3-4" data-line-number="4">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(sim)</a>
+<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#> [1] 1000 100</span></a></code></pre></div>
+</div>
+<div id="ncells---number-of-cells" class="section level3">
+<h3 class="hasAnchor">
+<a href="#ncells---number-of-cells" class="anchor"></a><code>nCells</code> - Number of cells</h3>
+<p>The number of genes to simulate. In the Splat simulation this cannot be set directly but must be controlled using the <code>batchCells</code> parameter.</p>
+</div>
+<div id="seed---random-seed" class="section level3">
+<h3 class="hasAnchor">
+<a href="#seed---random-seed" class="anchor"></a><code>seed</code> - Random seed</h3>
+<p>Seed to use for generating random numbers including selecting values from distributions. By changing this value multiple simulated datasets with the same parameters can be produced. Simulations produced using the same set of parameters and random seed should be identical but there may be differences between operating systems, software versions etc.</p>
+</div>
+</div>
+<div id="batch-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#batch-parameters" class="anchor"></a>Batch parameters</h2>
+<p>These parameters control experimental batches in the simulated dataset. The overall effect of how batch effects are included in the model is similar to technical replicates (i.e. the same biological sample sequenced multiple times). This means that the underlying structure is consistent between batches but a global technical signature is added may separate them.</p>
+<div id="nbatches---number-of-batches" class="section level3">
+<h3 class="hasAnchor">
+<a href="#nbatches---number-of-batches" class="anchor"></a><code>nBatches</code> - Number of batches</h3>
+<p>The number of batches in the simulation. This cannot be set directly but is controlled by setting <code>batchCells</code>.</p>
+</div>
+<div id="batchcells---cells-per-batch" class="section level3">
+<h3 class="hasAnchor">
+<a href="#batchcells---cells-per-batch" class="anchor"></a><code>batchCells</code> - Cells per batch</h3>
+<p>A vector specifying the number of cells in each batch. The number of batches (<code>nBatches</code>) is equal to the length of the vector and the number of cells (<code>nCells</code>) is equal to the sum.</p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># Simulation with two batches of 100 cells</span></a>
+<a class="sourceLine" id="cb4-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">batchCells =</span> <span class="kw"><a href="https://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="cb4-3" 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="cb4-6" 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="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></code></pre></div>
+<p><img src="splat_params_files/figure-html/batches-1.png" width="700"></p>
+</div>
+<div id="batch-facloc---batch-factor-location-and-batch-facscale---batch-factor-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#batch-facloc---batch-factor-location-and-batch-facscale---batch-factor-scale" class="anchor"></a><code>batch.facLoc</code> - Batch factor location and <code>batch.facScale</code> - Batch factor scale</h3>
+<p>Batches are specified by generating a small scaling factor for each gene in each batch from a log-normal distribution. These factors are then applied to the underlying gene means in each batch. Modifying these parameters affects how different the batches are from each other by generating bigger or smaller factors.</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># Simulation with small batch effects</span></a>
+<a class="sourceLine" id="cb5-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">batchCells =</span> <span class="kw"><a href="https://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="cb5-3" 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="cb5-6" 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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Small batch effects"</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="cb6-4" 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="cb6-7" 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"><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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Big batch effects"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/batch-factors-2.png" width="700"></p>
+</div>
+</div>
+<div id="mean-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#mean-parameters" class="anchor"></a>Mean parameters</h2>
+<p>These parameters control the distribution that is used to generate the underlying original gene means.</p>
+<div id="mean-shape---mean-shape-and-mean-rate---mean-rate" class="section level3">
+<h3 class="hasAnchor">
+<a href="#mean-shape---mean-shape-and-mean-rate---mean-rate" class="anchor"></a><code>mean.shape</code> - Mean shape and <code>mean.rate</code> - Mean rate</h3>
+<p>These parameters control the Gamma distribution that gene means are drawn from. The relationship between shape and rate can be complex and it is often better to use values estimated from a real dataset than to try and manually set them. Although these parameters control the base gene means the means in the final simulation will depend upon other parts of the model, particularly the simulated total counts per cell (library sizes).</p>
+</div>
+</div>
+<div id="library-size-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#library-size-parameters" class="anchor"></a>Library size parameters</h2>
+<p>These parameters control the expected number of counts for each cell. Note that because of sampling the actual counts per cell in the final simulation may be different. Turning on the dropout effect will also effect this. We use the term “library size†here for consistency but expected total counts would be more appropriate.</p>
+<div id="lib-loc---library-size-location-and-lib-scale---library-size-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#lib-loc---library-size-location-and-lib-scale---library-size-scale" class="anchor"></a><code>lib.loc</code> - Library size location and <code>lib.scale</code> - Library size scale</h3>
+<p>These parameters control the shape of the distribution that is used to generate library sizes for each cell. Increasing <code>lib.loc</code> will lead to more counts per cell and increasing <code>lib.scale</code> will result in more variability in the counts per cell.</p>
+</div>
+<div id="lib-norm---library-size-distribution" class="section level3">
+<h3 class="hasAnchor">
+<a href="#lib-norm---library-size-distribution" class="anchor"></a><code>lib.norm</code> - Library size distribution</h3>
+<p>The default (and recommended) distribution used for library sizes in the Splat simulation is a log-normal. However, in rare cases a normal distribution might be more appropriate. Setting <code>lib.norm</code> to <code>TRUE</code> will use a normal distribution instead of a log-normal.</p>
+</div>
+</div>
+<div id="expression-outlier-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#expression-outlier-parameters" class="anchor"></a>Expression outlier parameters</h2>
+<p>When developing the Splat simulation we found that while the Gamma distribution was generally a good match for gene means for some datasets it did not properly capture highly expressed genes. For this reason we added expression outliers to the Splat model.</p>
+<div id="out-prob---expression-outlier-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#out-prob---expression-outlier-probability" class="anchor"></a><code>out.prob</code> - Expression outlier probability</h3>
+<p>This parameter controls the probability that genes will be selected to be expression outliers. Higher values will results in more outlier genes.</p>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="co"># Few outliers</span></a>
+<a class="sourceLine" id="cb7-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">out.prob =</span> <span class="fl">0.001</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">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://www.rdocumentation.org/packages/ggplot2/topics/aes">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="cb7-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/geom_histogram">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://www.rdocumentation.org/packages/ggplot2/topics/labs">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://www.rdocumentation.org/packages/ggplot2/topics/ggplot">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://www.rdocumentation.org/packages/ggplot2/topics/aes">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="cb8-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/geom_histogram">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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Lots of outliers"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/outlier-prob-2.png" width="700"></p>
+</div>
+<div id="out-facloc---expression-outlier-factor-location-and-out-facscale---expression-outlier-factor-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#out-facloc---expression-outlier-factor-location-and-out-facscale---expression-outlier-factor-scale" class="anchor"></a><code>out.facLoc</code> - Expression outlier factor location and <code>out.facScale</code> - Expression outlier factor scale</h3>
+<p>The expression outlier factors are drawn from a log-normal distribution controlled by these parameters. The generated factors are applied to the median mean expression rather than the existing mean for the selected genes. This is to be consistent with the estimation procedure for these factors and to make sure that the final means are outliers. For example to avoid the situation where a factor is applied to a lowly expressed gene, making it just moderately expressed rather than an expression outlier.</p>
+</div>
+<div id="group-parameters" class="section level3">
+<h3 class="hasAnchor">
+<a href="#group-parameters" class="anchor"></a>Group parameters</h3>
+<p>Up until this stage of the simulation only a single population of cells is considered but we often want to simulate datasets with multiple kinds of cells. We do this by assigning cells to groups.</p>
+</div>
+<div id="ngroups---number-of-groups" class="section level3">
+<h3 class="hasAnchor">
+<a href="#ngroups---number-of-groups" class="anchor"></a><code>nGroups</code> - Number of groups</h3>
+<p>The number of groups to simulate. This parameter cannot be set directly and is controlled using <code>group.prob</code>.</p>
+</div>
+<div id="group-prob---group-probabilities" class="section level3">
+<h3 class="hasAnchor">
+<a href="#group-prob---group-probabilities" class="anchor"></a><code>group.prob</code> - Group probabilities</h3>
+<p>A vector giving the probability that cells will be assigned to groups. The length of the vector gives the number of groups (<code>nGroups</code>) and the probabilities must sum to 1. Adjusting the number and relative values of the probabilities changes the number and relative sizes of the groups. To simulate groups we also need to use the <code>splatSimulateGroups</code> function or set <code>method = "groups"</code>.</p>
+<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">params.groups <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">batchCells =</span> <span class="dv">500</span>, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a>
+<a class="sourceLine" id="cb9-2" data-line-number="2"></a>
+<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="co"># One small group, one big group</span></a>
+<a class="sourceLine" id="cb9-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://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="cb9-5" 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="cb9-7" 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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"One small group, one big group"</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="cb10-5" 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="cb10-7" 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"><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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Five groups"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/groups-2.png" width="700"></p>
+<p><strong>Note:</strong> Once there are more than three or four groups it becomes difficult to properly view them in PCA space. We use PCA here for simplicity but generally a non-linear dimensionality reduction such as t-SNE or UMAP is a more useful way to visualise the groups.</p>
+</div>
+<div id="differential-expression-parameters" class="section level3">
+<h3 class="hasAnchor">
+<a href="#differential-expression-parameters" class="anchor"></a>Differential expression parameters</h3>
+<p>Different groups are created by modifying the base expression levels of selected genes. The process for doing this is to simulate differential expression (DE) between each group and a fictional base cell. Altering the differential expression parameters controls how similar groups are to each other.</p>
+</div>
+<div id="de-prob---de-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#de-prob---de-probability" class="anchor"></a><code>de.prob</code> - DE probability</h3>
+<p>This parameter controls the probability that a gene will be selected to be differentially expressed.</p>
+<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="co"># Few DE genes</span></a>
+<a class="sourceLine" id="cb11-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://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="cb11-3" 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="cb11-5" 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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Few DE genes"</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="cb12-4" 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="cb12-6" 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"><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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Lots of DE genes"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/de-prob-2.png" width="700"></p>
+</div>
+<div id="de-downprob---down-regulation-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#de-downprob---down-regulation-probability" class="anchor"></a><code>de.downProb</code> - Down-regulation probability</h3>
+<p>A selected DE gene can be either down-regulated (has a factor less than one) or up-regulated (has a factor greater than one). This parameter controls the probability that a selected gene will be down-regulated.</p>
+</div>
+<div id="de-facloc---de-factor-location-and-de-facscale---de-factor-scale" class="section level3">
+<h3 class="hasAnchor">
+<a href="#de-facloc---de-factor-location-and-de-facscale---de-factor-scale" class="anchor"></a><code>de.facLoc</code> - DE factor location and <code>de.facScale</code> - DE factor scale</h3>
+<p>Differential expression factors are produced from a log-normal distribution in a similar way to batch effect factors and expression outlier factors. Changing these parameters can result in more or less extreme differences between groups.</p>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="co"># Small DE factors</span></a>
+<a class="sourceLine" id="cb13-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups, <span class="dt">group.prob =</span> <span class="kw"><a href="https://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="cb13-3" 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="cb13-5" 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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Small DE factors"</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="cb14-4" 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="cb14-6" 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"><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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Big DE factors"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/de-factors-2.png" width="700"></p>
+<p>Just looking at the PCA plots this effect seems similar to adjusting <code>de.prob</code> but the effect is achieved in a different way. A higher <code>de.prob</code> means that more genes are differentially expressed but changing the DE factors changes the level of DE for the same number of genes.</p>
+</div>
+<div id="complex-differential-expression" class="section level3">
+<h3 class="hasAnchor">
+<a href="#complex-differential-expression" class="anchor"></a>Complex differential expression</h3>
+<p>Each of the differential expression parameters can be specified for each group by providing a vector of values. These vectors must be the same length as <code>group.prob</code>. Specifying parameters as vectors allows more complex simulations where groups are more or less different to each other rather than being equally distinct. Here are some examples of different DE scenarios.</p>
+<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="co"># Different DE probs</span></a>
+<a class="sourceLine" id="cb15-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb15-3" data-line-number="3"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://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="cb15-5" 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="cb15-7" 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="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="cb15-9" data-line-number="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/labs">labs</a></span>(<span class="dt">title =</span> <span class="st">"Different DE probabilities"</span>,</a>
+<a class="sourceLine" id="cb15-10" data-line-number="10"> <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="cb15-11" data-line-number="11"> <span class="st">"Groups 3 and 4 have the default number,"</span>,</a>
+<a class="sourceLine" id="cb15-12" data-line-number="12"> <span class="st">"Group 5 has many DE genes"</span>))</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/complex-de-1.png" width="700"></p>
+<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"> </a>
+<a class="sourceLine" id="cb16-2" data-line-number="2"></a>
+<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="co"># Different DE factors</span></a>
+<a class="sourceLine" id="cb16-4" data-line-number="4">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulateGroups</a></span>(params.groups,</a>
+<a class="sourceLine" id="cb16-5" data-line-number="5"> <span class="dt">group.prob =</span> <span class="kw"><a href="https://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="cb16-8" 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="cb16-10" 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"><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="cb16-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/labs">labs</a></span>(<span class="dt">title =</span> <span class="st">"Different DE factors"</span>,</a>
+<a class="sourceLine" id="cb16-13" data-line-number="13"> <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="cb16-14" data-line-number="14"> <span class="st">"and scale (variability),"</span>,</a>
+<a class="sourceLine" id="cb16-15" data-line-number="15"> <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="cb16-16" data-line-number="16"> <span class="st">"Groups 3 and 4 have greater location with small,"</span>,</a>
+<a class="sourceLine" id="cb16-17" data-line-number="17"> <span class="st">"and large scales"</span>,</a>
+<a class="sourceLine" id="cb16-18" data-line-number="18"> <span class="st">"Group 5 has bigger factors with moderate variability"</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="cb17-9" 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="cb17-11" 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"><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="cb17-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/labs">labs</a></span>(<span class="dt">title =</span> <span class="st">"Different DE factors"</span>,</a>
+<a class="sourceLine" id="cb17-14" data-line-number="14"> <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="cb17-15" data-line-number="15"> <span class="st">"Group 1 is small with many very up-regulated DE genes,"</span>,</a>
+<a class="sourceLine" id="cb17-16" data-line-number="16"> <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="cb17-17" data-line-number="17"> <span class="st">"Group 3 has many down-regulated DE genes,"</span>,</a>
+<a class="sourceLine" id="cb17-18" data-line-number="18"> <span class="st">"Group 4 has very few DE genes,"</span>,</a>
+<a class="sourceLine" id="cb17-19" data-line-number="19"> <span class="st">"Group 5 is large with moderate DE factors"</span>)</a>
+<a class="sourceLine" id="cb17-20" data-line-number="20"> )</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/complex-de-3.png" width="700"></p>
+</div>
+</div>
+<div id="biological-coefficient-of-variation-bcv-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#biological-coefficient-of-variation-bcv-parameters" class="anchor"></a>Biological Coefficient of Variation (BCV) parameters</h2>
+<p>The BCV parameters control the variability of the genes in the simulated dataset.</p>
+<div id="bcv-common---common-bcv" class="section level3">
+<h3 class="hasAnchor">
+<a href="#bcv-common---common-bcv" class="anchor"></a><code>bcv.common</code> - Common BCV</h3>
+<p>The <code>bcv.common</code> parameter controls the underlying common variability across all genes in the dataset.</p>
+</div>
+<div id="bcv-df---bcv-degrees-of-freedom" class="section level3">
+<h3 class="hasAnchor">
+<a href="#bcv-df---bcv-degrees-of-freedom" class="anchor"></a><code>bcv.df</code> - BCV Degrees of Freedom</h3>
+<p>This parameter sets the degrees of freedom used in the BCV inverse chi-squared distribution. Changing this changes the effect of mean expression on the variability of a gene.</p>
+</div>
+</div>
+<div id="dropout-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#dropout-parameters" class="anchor"></a>Dropout parameters</h2>
+<p>These parameters control whether additional dropout is added to increase the number of zeros in the simulated dataset and if it is how that is applied.</p>
+<div id="dropout-type---dropout-type" class="section level3">
+<h3 class="hasAnchor">
+<a href="#dropout-type---dropout-type" class="anchor"></a><code>dropout.type</code> - Dropout type</h3>
+<p>This parameter determines the kind of dropout effect to simulate. Setting it to <code>"none"</code> means no dropout, “<code>experiment</code>†is global dropout using the same set of parameters for every cell, <code>"batch"</code> uses the same parameters for every cell in the same batch, <code>"group"</code> uses the same parameters for every cell in the same group and <code>"cell"</code> uses a different set of parameters for every cell.</p>
+</div>
+<div id="dropout-mid---dropout-mid-point-and-dropout-shape---dropout-shape" class="section level3">
+<h3 class="hasAnchor">
+<a href="#dropout-mid---dropout-mid-point-and-dropout-shape---dropout-shape" class="anchor"></a><code>dropout.mid</code> - Dropout mid point and <code>dropout.shape</code> - Dropout shape</h3>
+<p>The probability that a particular count in a particular cell is set to zero is related to the mean expression of that gene in that cell. This relationship is represented using a logistic function with these parameters. The <code>dropout.mid</code> parameter control the point at which the probability is equal to 0.5 and the <code>dropout.shape</code> controls how it changes with increasing expression. These parameters must be vectors of the appropriate length depending on the selected dropout type.</p>
+</div>
+</div>
+<div id="path-parameters" class="section level2">
+<h2 class="hasAnchor">
+<a href="#path-parameters" class="anchor"></a>Path parameters</h2>
+<p>For many uses simulating groups is sufficient but in some cases it is more appropriate to simulate continuous changes between cell types. The number of paths and the probability of assigning cells to them is still controlled by the <code>group.prob</code> parameter and the amount of change along a path is controlled by the DE parameters but other aspects of the <code>splatSimulatePaths</code> model are controlled by these parameters.</p>
+<div id="path-from---path-origin" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-from---path-origin" class="anchor"></a><code>path.from</code> - Path origin</h3>
+<p>This parameter controls the order of differentiation paths. It is a vector the same length as <code>group.prob</code> giving the starting position of each path. For example a <code>path.from</code> of <code><a href="https://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>
+<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="cb18-4" 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="cb18-6" 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="cb18-8" 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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Linear paths"</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="cb19-5" 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="cb19-7" 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="cb19-9" 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"><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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Branching path"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-2.png" width="700"></p>
+</div>
+<div id="path-nsteps---number-of-steps" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-nsteps---number-of-steps" class="anchor"></a><code>path.nSteps</code> - Number of steps</h3>
+<p>A path is created by using the same differential expression procedure as used for groups to generate an end point. Interpolation is then used to create a series of steps between the start and end points. This parameter controls the number of steps along a path and therefore how discrete or smooth it is.</p>
+<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="co"># Few steps</span></a>
+<a class="sourceLine" id="cb20-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups, <span class="dt">path.nSteps =</span> <span class="dv">3</span>,</a>
+<a class="sourceLine" id="cb20-3" data-line-number="3"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb20-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Few steps"</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="cb21-6" 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"><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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Lots of steps"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-steps-2.png" width="700"></p>
+</div>
+<div id="path-skew---path-skew" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-skew---path-skew" class="anchor"></a><code>path.skew</code> - Path skew</h3>
+<p>By default cells are evenly distributed along a path but it sometimes be useful to introduce a skew in the distribution, For example you may want to simulate a scenario with few stem-like cells and many differentiated cells. Setting <code>path.skew</code> to 0 will mean that all cells come from the end point while higher values up to 1 will skew them towards the start point.</p>
+<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="co"># Skew towards the end</span></a>
+<a class="sourceLine" id="cb22-2" data-line-number="2">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulatePaths</a></span>(params.groups, <span class="dt">path.skew =</span> <span class="fl">0.1</span>,</a>
+<a class="sourceLine" id="cb22-3" data-line-number="3"> <span class="dt">de.prob =</span> <span class="fl">0.5</span>, <span class="dt">de.facLoc =</span> <span class="fl">0.2</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb22-4" data-line-number="4">sim1 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/scater/topics/normalize">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="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://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Skewed towards the end"</span>)</a></code></pre></div>
+<p><img src="splat_params_files/figure-html/paths-skew-1.png" width="700"></p>
+</div>
+<div id="path-nonlinearprob---non-linear-probability" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-nonlinearprob---non-linear-probability" class="anchor"></a><code>path.nonlinearProb</code> - Non-linear probability</h3>
+<p>Most genes are interpolated in a linear way along a path but in reality this may not always be the case. For example it is easy to imagine a gene that is lowly-expressed at the start of a process, highly-expressed in the middle and lowly-expressed again at the end. The <code>path.nonlinearProb</code> parameter controls the probability that a gene will change in a non-linear way along a path.</p>
+</div>
+<div id="path-sigmafac---path-skew" class="section level3">
+<h3 class="hasAnchor">
+<a href="#path-sigmafac---path-skew" class="anchor"></a><code>path.sigmaFac</code> - Path skew</h3>
+<p>Non-linear changes along a path are achieved by building a Brownian bridge between the two end points. A Brownian bridge is Brownian motion controlled in such a way that the end points are fixed. The <code>path.sigmaFac</code> parameter controls how extreme each step in the Brownian motion is and therefore how much the interpolation differs from a linear path.</p>
+</div>
+</div>
+</div>
+ </div>
+
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <div id="tocnav">
+ <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+<li><a href="#the-base-splat-model">The base Splat model</a></li>
+ <li>
+<a href="#splat-simulation-parameters">Splat simulation parameters</a><ul class="nav nav-pills nav-stacked">
+<li><a href="#global-parameters">Global parameters</a></li>
+ <li><a href="#batch-parameters">Batch parameters</a></li>
+ <li><a href="#mean-parameters">Mean parameters</a></li>
+ <li><a href="#library-size-parameters">Library size parameters</a></li>
+ <li><a href="#expression-outlier-parameters">Expression outlier parameters</a></li>
+ <li><a href="#biological-coefficient-of-variation-bcv-parameters">Biological Coefficient of Variation (BCV) parameters</a></li>
+ <li><a href="#dropout-parameters">Dropout parameters</a></li>
+ <li><a href="#path-parameters">Path parameters</a></li>
+ </ul>
+</li>
+ </ul>
+</div>
+ </div>
+
+</div>
+
+
+ <footer><div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+</div>
+ </footer>
+</div>
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+</html>
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diff --git a/docs/articles/splatter-logo-small.png b/docs/articles/splatter-logo-small.png
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diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index a4b3f324eac313f90a96afff2f366e377afd4b9b..5af2d342cc2b65dabc5c53810d41536486fedcb3 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -1,19 +1,19 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<title>Introduction to Splatter • Splatter</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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+<!-- 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="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<meta property="og:title" content="Introduction to Splatter">
<meta property="og:description" content="">
<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script><script>
@@ -29,14 +29,15 @@
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -54,6 +55,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+<li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -80,7 +93,7 @@
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2018-11-02</h4>
+ <h4 class="date">2019-04-18</h4>
<small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splatter.Rmd"><code>vignettes/splatter.Rmd</code></a></small>
<div class="hidden name"><code>splatter.Rmd</code></div>
@@ -97,11 +110,11 @@
<h1 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h1>
<p>Splatter can be installed from Bioconductor:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="op">!</span><span class="kw">requireNamespace</span>(<span class="st">"BiocManager"</span>, <span class="dt">quietly=</span><span class="ot">TRUE</span>))</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2"> <span class="kw">install.packages</span>(<span class="st">"BiocManager"</span>)</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3">BiocManager<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="op">!</span><span class="kw"><a href="https://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>
<p>To install the most recent development version from Github use:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">BiocManager<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,</a>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">BiocManager<span class="op">::</span><span class="kw"><a href="https://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>
<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">
@@ -109,7 +122,7 @@
<a href="#quickstart" class="anchor"></a>Quickstart</h1>
<p>Assuming you already have a matrix of count data similar to that you wish to simulate there are two simple steps to creating a simulated data set with Splatter. Here is an example using the example dataset in the <code>scater</code> package:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># Load package</span></a>
-<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw">library</span>(splatter)</a></code></pre></div>
+<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(splatter)</a></code></pre></div>
<pre><code>## Loading required package: SingleCellExperiment</code></pre>
<pre><code>## Loading required package: SummarizedExperiment</code></pre>
<pre><code>## Loading required package: GenomicRanges</code></pre>
@@ -129,13 +142,12 @@
<pre><code>## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind,
-## colMeans, colnames, colSums, dirname, do.call, duplicated,
-## eval, evalq, Filter, Find, get, grep, grepl, intersect,
-## is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
-## paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
-## Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
-## table, tapply, union, unique, unsplit, which, which.max,
-## which.min</code></pre>
+## colnames, dirname, do.call, duplicated, eval, evalq, Filter,
+## Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
+## mapply, match, mget, order, paste, pmax, pmax.int, pmin,
+## pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
+## setdiff, sort, table, tapply, union, unique, unsplit, which,
+## which.max, which.min</code></pre>
<pre><code>## Loading required package: S4Vectors</code></pre>
<pre><code>##
## Attaching package: 'S4Vectors'</code></pre>
@@ -165,9 +177,14 @@
## colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</code></pre>
<pre><code>## The following objects are masked from 'package:base':
##
-## aperm, apply</code></pre>
-<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1"><span class="co"># Load example data</span></a>
-<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw">library</span>(scater)</a></code></pre></div>
+## aperm, apply, rowsum</code></pre>
+<pre><code>## Registered S3 methods overwritten by 'ggplot2':
+## method from
+## [.quosures rlang
+## c.quosures rlang
+## print.quosures rlang</code></pre>
+<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1"><span class="co"># Load example data</span></a>
+<a class="sourceLine" id="cb30-2" 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>
<pre><code>## Loading required package: ggplot2</code></pre>
<pre><code>##
## Attaching package: 'scater'</code></pre>
@@ -177,17 +194,17 @@
<pre><code>## The following object is masked from 'package:stats':
##
## filter</code></pre>
-<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)</a>
-<a class="sourceLine" id="cb34-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
-<a class="sourceLine" id="cb34-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a>
-<a class="sourceLine" id="cb34-4" data-line-number="4"><span class="co"># Simulate data using estimated parameters</span></a>
-<a class="sourceLine" id="cb34-5" data-line-number="5">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
+<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/data">data</a></span>(<span class="st">"sc_example_counts"</span>)</a>
+<a class="sourceLine" id="cb35-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
+<a class="sourceLine" id="cb35-3" data-line-number="3">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a>
+<a class="sourceLine" id="cb35-4" data-line-number="4"><span class="co"># Simulate data using estimated parameters</span></a>
+<a class="sourceLine" id="cb35-5" data-line-number="5">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params)</a></code></pre></div>
<pre><code>## Getting parameters...</code></pre>
<pre><code>## Creating simulation object...</code></pre>
<pre><code>## Simulating library sizes...</code></pre>
<pre><code>## Simulating gene means...</code></pre>
<pre><code>## Simulating BCV...</code></pre>
-<pre><code>## Simulating counts..</code></pre>
+<pre><code>## Simulating counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
<p>These steps will be explained in detail in the following sections but briefly the first step takes a dataset and estimates simulation parameters from it and the second step takes those parameters and simulates a new dataset.</p>
@@ -197,139 +214,19 @@
<a href="#the-splat-simulation" class="anchor"></a>The Splat simulation</h1>
<p>Before we look at how we estimate parameters let’s first look at how Splatter simulates data and what those parameters are. We use the term ‘Splat’ to refer to the Splatter’s own simulation and differentiate it from the package itself. The core of the Splat model is a gamma-Poisson distribution used to generate a gene by cell matrix of counts. Mean expression levels for each gene are simulated from a <a href="https://en.wikipedia.org/wiki/Gamma_distribution">gamma distribution</a> and the Biological Coefficient of Variation is used to enforce a mean-variance trend before counts are simulated from a <a href="https://en.wikipedia.org/wiki/Poisson_distribution">Poisson distribution</a>. Splat also allows you to simulate expression outlier genes (genes with mean expression outside the gamma distribution) and dropout (random knock out of counts based on mean expression). Each cell is given an expected library size (simulated from a log-normal distribution) that makes it easier to match to a given dataset.</p>
<p>Splat can also simulate differential expression between groups of different types of cells or differentiation paths between different cells types where expression changes in a continuous way. These are described further in the <a href="#simulating-counts">simulating counts</a> section.</p>
-<div id="parameters" class="section level2">
-<h2 class="hasAnchor">
-<a href="#parameters" class="anchor"></a>Parameters</h2>
-<p>The parameters required for the Splat simulation are briefly described here:</p>
-<ul>
-<li>
-<strong>Global parameters</strong>
-<ul>
-<li>
-<code>nGenes</code> - The number of genes to simulate.</li>
-<li>
-<code>nCells</code> - The number of cells to simulate.</li>
-<li>
-<code>seed</code> - Seed to use for generating random numbers.</li>
-</ul>
-</li>
-<li>
-<strong>Batch parameters</strong>
-<ul>
-<li>
-<code>nBatches</code> - The number of batches to simulate.</li>
-<li>
-<code>batchCells</code> - The number of cells in each batch.</li>
-<li>
-<code>batch.facLoc</code> - Location (meanlog) parameter for the batch effects factor log-normal distribution.</li>
-<li>
-<code>batch.facScale</code> - Scale (sdlog) parameter for the batch effects factor log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Mean parameters</strong>
-<ul>
-<li>
-<code>mean.shape</code> - Shape parameter for the mean gamma distribution.</li>
-<li>
-<code>mean.rate</code> - Rate parameter for the mean gamma distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Library size parameters</strong>
-<ul>
-<li>
-<code>lib.loc</code> - Location (meanlog) parameter for the library size log-normal distribution, or mean for the normal distribution.</li>
-<li>
-<code>lib.scale</code> - Scale (sdlog) parameter for the library size log-normal distribution, or sd for the normal distribution.</li>
-<li>
-<code>lib.norm</code> - Whether to use a normal distribution instead of the usual log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Expression outlier parameters</strong>
-<ul>
-<li>
-<code>out.prob</code> - Probability that a gene is an expression outlier.</li>
-<li>
-<code>out.facLoc</code> - Location (meanlog) parameter for the expression outlier factor log-normal distribution.</li>
-<li>
-<code>out.facScale</code> - Scale (sdlog) parameter for the expression outlier factor log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Group parameters</strong>
-<ul>
-<li>
-<code>nGroups</code> - The number of groups or paths to simulate.</li>
-<li>
-<code>group.prob</code> - The probabilities that cells come from particular groups.</li>
-</ul>
-</li>
-<li>
-<strong>Differential expression parameters</strong>
-<ul>
-<li>
-<code>de.prob</code> - Probability that a gene is differentially expressed in each group or path.</li>
-<li>
-<code>de.loProb</code> - Probability that a differentially expressed gene is down-regulated.</li>
-<li>
-<code>de.facLoc</code> - Location (meanlog) parameter for the differential expression factor log-normal distribution.</li>
-<li>
-<code>de.facScale</code> - Scale (sdlog) parameter for the differential expression factor log-normal distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Biological Coefficient of Variation parameters</strong>
-<ul>
-<li>
-<code>bcv.common</code> - Underlying common dispersion across all genes.</li>
-<li>
-<code>bcv.df</code> - Degrees of Freedom for the BCV inverse chi-squared distribution.</li>
-</ul>
-</li>
-<li>
-<strong>Dropout parameters</strong>
-<ul>
-<li>
-<code>dropout.type</code> - Type of dropout to simulate.</li>
-<li>
-<code>dropout.mid</code> - Midpoint parameter for the dropout logistic function.</li>
-<li>
-<code>dropout.shape</code> - Shape parameter for the dropout logistic function.</li>
-</ul>
-</li>
-<li>
-<strong>Differentiation path parameters</strong>
-<ul>
-<li>
-<code>path.from</code> - Vector giving the originating point of each path.</li>
-<li>
-<code>path.length</code> - Vector giving the number of steps to simulate along each path.</li>
-<li>
-<code>path.skew</code> - Vector giving the skew of each path.</li>
-<li>
-<code>path.nonlinearProb</code> - Probability that a gene changes expression in a non-linear way along the differentiation path.</li>
-<li>
-<code>path.sigmaFac</code> - Sigma factor for non-linear gene paths.</li>
-</ul>
-</li>
-</ul>
-<p>While this may look like a lot of parameters Splatter attempts to make it easy for the user, both by providing sensible defaults and making it easy to estimate many of the parameters from real data. For more details on the parameters see <code><a href="../reference/SplatParams.html">?SplatParams</a></code>.</p>
-</div>
</div>
<div id="the-splatparams-object" class="section level1">
<h1 class="hasAnchor">
<a href="#the-splatparams-object" class="anchor"></a>The <code>SplatParams</code> object</h1>
<p>All the parameters for the Splat simulation are stored in a <code>SplatParams</code> object. Let’s create a new one and see what it looks like.</p>
-<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
-<a class="sourceLine" id="cb43-2" data-line-number="2">params</a></code></pre></div>
+<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" 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="cb44-2" 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'
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 477689
+## 10000 100 700433
##
## 28 additional parameters
##
@@ -366,26 +263,26 @@
## none 0 -1
##
## Paths:
-## [From] [Length] [Skew] [Non-linear]
+## [From] [Steps] [Skew] [Non-linear]
## 0 100 0.5 0.1
## [Sigma Factor]
## 0.8</code></pre>
-<p>As well as telling us what type of object we have (“A <code>Params</code> object of class <code>SplatParams</code>â€) and showing us the values of the parameter this output gives us some extra information. We can see which parameters can be estimated by the <code>splatEstimate</code> function (those in parentheses), which can’t be estimated (those in brackets) and which have been changed from their default values (those in ALL CAPS).</p>
+<p>As well as telling us what type of object we have (“A <code>Params</code> object of class <code>SplatParams</code>â€) and showing us the values of the parameter this output gives us some extra information. We can see which parameters can be estimated by the <code>splatEstimate</code> function (those in parentheses), which can’t be estimated (those in brackets) and which have been changed from their default values (those in ALL CAPS). For more details about the parameters of the Splat simulation refer to the <a href="splat_params.html">Splat parameters vignette</a>.</p>
<div id="getting-and-setting" class="section level2">
<h2 class="hasAnchor">
<a href="#getting-and-setting" class="anchor"></a>Getting and setting</h2>
<p>If we want to look at a particular parameter, for example the number of genes to simulate, we can extract it using the <code>getParam</code> function:</p>
-<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
<pre><code>## [1] 10000</code></pre>
<p>Alternatively, to give a parameter a new value we can use the <code>setParam</code> function:</p>
-<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
-<a class="sourceLine" id="cb47-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
+<div class="sourceCode" id="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/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
+<a class="sourceLine" id="cb48-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
<pre><code>## [1] 5000</code></pre>
<p>If we want to extract multiple parameters (as a list) or set multiple parameters we can use the <code>getParams</code> or <code>setParams</code> functions:</p>
-<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
-<a class="sourceLine" id="cb49-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))</a>
-<a class="sourceLine" id="cb49-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
-<a class="sourceLine" id="cb49-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
+<a class="sourceLine" id="cb50-2" 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="cb50-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
+<a class="sourceLine" id="cb50-4" 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>
<pre><code>## $nGenes
## [1] 8000
##
@@ -394,15 +291,15 @@
##
## $mean.shape
## [1] 0.6</code></pre>
-<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
-<a class="sourceLine" id="cb51-2" data-line-number="2">params <-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)</a>
-<a class="sourceLine" id="cb51-3" data-line-number="3">params</a></code></pre></div>
+<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
+<a class="sourceLine" id="cb52-2" 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="cb52-3" 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'
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 477689
+## 8000 100 700433
##
## 28 additional parameters
##
@@ -439,14 +336,14 @@
## none 0 -1
##
## Paths:
-## [From] [Length] [Skew] [Non-linear]
+## [From] [Steps] [Skew] [Non-linear]
## 0 100 0.5 0.1
## [Sigma Factor]
## 0.8</code></pre>
<p>The parameters with have changed are now shown in ALL CAPS to indicate that they been changed form the default.</p>
<p>We can also set parameters directly when we call <code>newSplatParams</code>:</p>
-<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)</a>
-<a class="sourceLine" id="cb53-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" 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="cb54-2" 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>
<pre><code>## $lib.loc
## [1] 12
##
@@ -458,23 +355,23 @@
<h1 class="hasAnchor">
<a href="#estimating-parameters" class="anchor"></a>Estimating parameters</h1>
<p>Splat allows you to estimate many of it’s parameters from a data set containing counts using the <code>splatEstimate</code> function.</p>
-<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
-<a class="sourceLine" id="cb55-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
+<a class="sourceLine" id="cb56-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/class">class</a></span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] "matrix"</code></pre>
-<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/typeof">typeof</a></span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] "integer"</code></pre>
-<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
-<a class="sourceLine" id="cb59-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
+<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"># Check the dimensions, each row is a gene, each column is a cell</span></a>
+<a class="sourceLine" id="cb60-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(sc_example_counts)</a></code></pre></div>
<pre><code>## [1] 2000 40</code></pre>
-<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
-<a class="sourceLine" id="cb61-2" data-line-number="2">sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
+<a class="sourceLine" id="cb62-2" data-line-number="2">sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell_001 Cell_002 Cell_003 Cell_004 Cell_005
## Gene_0001 0 123 2 0 0
## Gene_0002 575 65 3 1561 2311
## Gene_0003 0 0 0 0 1213
## Gene_0004 0 1 0 0 0
## Gene_0005 0 0 11 0 0</code></pre>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
+<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1">params <-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take a <code>SingleCellExperiment</code> object. The estimation process has the following steps:</p>
<ol style="list-style-type: decimal">
<li>Mean parameters are estimated by fitting a gamma distribution to the mean expression levels.</li>
@@ -489,16 +386,16 @@
<h1 class="hasAnchor">
<a href="#simulating-counts" class="anchor"></a>Simulating counts</h1>
<p>Once we have a set of parameters we are happy with we can use <code>splatSimulate</code> to simulate counts. If we want to make small adjustments to the parameters we can provide them as additional arguments, alternatively if we don’t supply any parameters the defaults will be used:</p>
-<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>)</a></code></pre></div>
<pre><code>## Getting parameters...</code></pre>
<pre><code>## Creating simulation object...</code></pre>
<pre><code>## Simulating library sizes...</code></pre>
<pre><code>## Simulating gene means...</code></pre>
<pre><code>## Simulating BCV...</code></pre>
-<pre><code>## Simulating counts..</code></pre>
+<pre><code>## Simulating counts...</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
-<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">sim</a></code></pre></div>
+<div class="sourceCode" id="cb74"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb74-1" data-line-number="1">sim</a></code></pre></div>
<pre><code>## class: SingleCellExperiment
## dim: 1000 40
## metadata(1): Params
@@ -509,62 +406,62 @@
## colData names(3): Cell Batch ExpLibSize
## reducedDimNames(0):
## spikeNames(0):</code></pre>
-<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
-<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" data-line-number="1"><span class="co"># Access the counts</span></a>
-<a class="sourceLine" id="cb75-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. 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="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" data-line-number="1"><span class="co"># Access the counts</span></a>
+<a class="sourceLine" id="cb76-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 55 2 0 11 0
-## Gene2 1 2 0 0 0
-## Gene3 7 2 2 74 8
-## Gene4 0 69 6 0 114
-## Gene5 1 70 40 0 0</code></pre>
-<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="co"># Information about genes</span></a>
-<a class="sourceLine" id="cb77-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+## Gene1 0 0 760 0 404
+## Gene2 0 0 0 0 0
+## Gene3 0 0 25 0 0
+## Gene4 0 0 4478 240 0
+## Gene5 181 14 414 0 2</code></pre>
+<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" data-line-number="1"><span class="co"># Information about genes</span></a>
+<a class="sourceLine" id="cb78-2" 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>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## 1 Gene1 76.9025430673341 1 76.9025430673341
-## 2 Gene2 11.5038956210654 1 11.5038956210654
-## 3 Gene3 9.5216589952532 1 9.5216589952532
-## 4 Gene4 740.124978536434 1 740.124978536434
-## 5 Gene5 71.5386607136642 1 71.5386607136642
-## 6 Gene6 1.06151313409539 1 1.06151313409539</code></pre>
-<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1"><span class="co"># Information about cells</span></a>
-<a class="sourceLine" id="cb79-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## Gene1 Gene1 99.8479163673404 1 99.8479163673404
+## Gene2 Gene2 49.5448552540982 1 49.5448552540982
+## Gene3 Gene3 58.3919742141577 1 58.3919742141577
+## Gene4 Gene4 242.585544471445 1 242.585544471445
+## Gene5 Gene5 162.483321514296 1 162.483321514296
+## Gene6 Gene6 0.0778059481609708 1 0.0778059481609708</code></pre>
+<div class="sourceCode" id="cb80"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb80-1" data-line-number="1"><span class="co"># Information about cells</span></a>
+<a class="sourceLine" id="cb80-2" 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>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 510286.263476612
-## Cell2 Cell2 Batch1 1202024.11389745
-## Cell3 Cell3 Batch1 183908.161529651
-## Cell4 Cell4 Batch1 154585.938029774
-## Cell5 Cell5 Batch1 619536.71187027
-## Cell6 Cell6 Batch1 266676.834832325</code></pre>
-<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
-<a class="sourceLine" id="cb81-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
+## Cell1 Cell1 Batch1 269067.826597298
+## Cell2 Cell2 Batch1 80882.792869467
+## Cell3 Cell3 Batch1 1203611.94280314
+## Cell4 Cell4 Batch1 120843.011071197
+## Cell5 Cell5 Batch1 498147.091634901
+## Cell6 Cell6 Batch1 204091.969439536</code></pre>
+<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
+<a class="sourceLine" id="cb82-2" 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>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
-<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
-<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 5.333124e+01 2.598563 1.529988e-01 11.676286605 3.982157e-03
-## Gene2 7.665400e-01 7.586450 1.614969e-25 0.372529598 6.068763e-03
-## Gene3 6.121509e+00 1.784225 6.033250e+00 74.377980371 6.435478e+00
-## Gene4 8.789318e-06 69.991629 7.918106e+00 0.026909108 1.193434e+02
-## Gene5 8.940025e-02 94.814168 3.921096e+01 0.008752188 1.123261e-01</code></pre>
+<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
+<a class="sourceLine" id="cb84-2" 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 1.007777e-03 8.018866e-04 7.568531e+02 1.718418e-04 4.114844e+02
+## Gene2 2.209976e-27 5.450164e-05 4.434856e-04 4.572322e-06 2.711027e-02
+## Gene3 2.026716e-02 4.165165e-02 2.670657e+01 9.643304e-03 4.586952e-15
+## Gene4 2.094954e-01 1.226730e-11 4.541537e+03 2.616588e+02 7.606362e-07
+## Gene5 1.923829e+02 1.534920e+01 3.976655e+02 5.842856e-12 4.705234e+00</code></pre>
<p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
-<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
-<a class="sourceLine" id="cb85-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
+<a class="sourceLine" id="cb86-2" 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>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
-<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
+<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"># Plot PCA</span></a>
+<a class="sourceLine" id="cb88-2" 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>
<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
<p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
<p>For more details about the <code>SingleCellExperiment</code> object refer to the [vignette] <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SCE-vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
<p>The <code>splatSimulate</code> function outputs the following additional information about the simulation:</p>
<ul>
<li>
-<strong>Cell information (<code>pData</code>)</strong>
+<strong>Cell information (<code>colData</code>)</strong>
<ul>
<li>
<code>Cell</code> - Unique cell identifier.</li>
@@ -577,7 +474,7 @@
</ul>
</li>
<li>
-<strong>Gene information (<code>fData</code>)</strong>
+<strong>Gene information (<code>rowData</code>)</strong>
<ul>
<li>
<code>Gene</code> - Unique gene identifier.</li>
@@ -594,7 +491,7 @@
</ul>
</li>
<li>
-<strong>Gene by cell information (<code>assayData</code>)</strong>
+<strong>Gene by cell information (<code>assays</code>)</strong>
<ul>
<li>
<code>BaseCellMeans</code> - The expression of genes in each cell adjusted for expected library size.</li>
@@ -615,22 +512,22 @@
<a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
<p>So far we have only simulated a single population of cells but often we are interested in investigating a mixed population of cells and looking to see what cell types are present or what differences there are between them. Splatter is able to simulate these situations by changing the <code>method</code> argument Here we are going to simulate two groups, by specifying the <code>group.prob</code> parameter and setting the <code>method</code> parameter to <code>"groups"</code>:</p>
<p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
-<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
-<a class="sourceLine" id="cb88-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb88-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" 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="cb89-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb89-3" 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>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<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="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>
<p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
-<p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
+<p>As we have set both the group probabilities to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilities that sum to 1.</p>
</div>
<div id="simulating-paths" class="section level2">
<h2 class="hasAnchor">
<a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
<p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
-<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb91-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
+<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" 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="cb92-2" 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>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
+<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="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>
<p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here the colours represent the “step†of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
</div>
@@ -638,31 +535,31 @@
<h2 class="hasAnchor">
<a href="#batch-effects" class="anchor"></a>Batch effects</h2>
<p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
-<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb94-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
+<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" 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="cb95-2" 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>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" 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>
<p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
<p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
-<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
-<a class="sourceLine" id="cb97-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb97-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<div class="sourceCode" id="cb98"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb98-1" 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="cb98-2" 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="cb98-3" 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>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="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>
<p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
</div>
<div id="convenience-functions" class="section level2">
<h2 class="hasAnchor">
<a href="#convenience-functions" class="anchor"></a>Convenience functions</h2>
-<p>Each of the Splatter simulation methods has it’s own convenience function. To simulate a single population use <code><a href="../reference/splatSimulate.html">splatSimulateSingle()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "single")</a></code>), to simulate grops use <code><a href="../reference/splatSimulate.html">splatSimulateGroups()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "groups")</a></code>) or to simulate paths use <code><a href="../reference/splatSimulate.html">splatSimulatePaths()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "paths")</a></code>).</p>
+<p>Each of the Splatter simulation methods has it’s own convenience function. To simulate a single population use <code><a href="../reference/splatSimulate.html">splatSimulateSingle()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "single")</a></code>), to simulate groups use <code><a href="../reference/splatSimulate.html">splatSimulateGroups()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "groups")</a></code>) or to simulate paths use <code><a href="../reference/splatSimulate.html">splatSimulatePaths()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "paths")</a></code>).</p>
</div>
</div>
<div id="other-simulations" class="section level1">
<h1 class="hasAnchor">
<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
<p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
-<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb101"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb101-1" 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
##
## Splat (splat)
@@ -716,110 +613,6 @@
## SparseDC (sparseDC)
## DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC
## The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</code></pre>
-<p>(or more conveniently for the vignette as a table)</p>
-<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
-<table class="table">
-<thead><tr class="header">
-<th align="left">Name</th>
-<th align="left">Prefix</th>
-<th align="left">DOI</th>
-<th align="left">GitHub</th>
-<th align="left">Description</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td align="left">Splat</td>
-<td align="left">splat</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.</td>
-</tr>
-<tr class="even">
-<td align="left">Splat Single</td>
-<td align="left">splatSingle</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation with a single population.</td>
-</tr>
-<tr class="odd">
-<td align="left">Splat Groups</td>
-<td align="left">splatGroups</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation with multiple groups. Each group can have it’s own differential expression probability and fold change distribution.</td>
-</tr>
-<tr class="even">
-<td align="left">Splat Paths</td>
-<td align="left">splatPaths</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">The Splat simulation with differentiation paths. Each path can have it’s own length, skew and probability. Genes can change in non-linear ways.</td>
-</tr>
-<tr class="odd">
-<td align="left">Simple</td>
-<td align="left">simple</td>
-<td align="left">10.1186/s13059-017-1305-0</td>
-<td align="left">Oshlack/splatter</td>
-<td align="left">A simple simulation with gamma means and negative binomial counts.</td>
-</tr>
-<tr class="even">
-<td align="left">Lun</td>
-<td align="left">lun</td>
-<td align="left">10.1186/s13059-016-0947-7</td>
-<td align="left">MarioniLab/Deconvolution2016</td>
-<td align="left">Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.</td>
-</tr>
-<tr class="odd">
-<td align="left">Lun 2</td>
-<td align="left">lun2</td>
-<td align="left">10.1093/biostatistics/kxw055</td>
-<td align="left">MarioniLab/PlateEffects2016</td>
-<td align="left">Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.</td>
-</tr>
-<tr class="even">
-<td align="left">scDD</td>
-<td align="left">scDD</td>
-<td align="left">10.1186/s13059-016-1077-y</td>
-<td align="left">kdkorthauer/scDD</td>
-<td align="left">The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</td>
-</tr>
-<tr class="odd">
-<td align="left">BASiCS</td>
-<td align="left">BASiCS</td>
-<td align="left">10.1371/journal.pcbi.1004333</td>
-<td align="left">catavallejos/BASiCS</td>
-<td align="left">The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects.</td>
-</tr>
-<tr class="even">
-<td align="left">mfa</td>
-<td align="left">mfa</td>
-<td align="left">10.12688/wellcomeopenres.11087.1</td>
-<td align="left">kieranrcampbell/mfa</td>
-<td align="left">The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</td>
-</tr>
-<tr class="odd">
-<td align="left">PhenoPath</td>
-<td align="left">pheno</td>
-<td align="left">10.1101/159913</td>
-<td align="left">kieranrcampbell/phenopath</td>
-<td align="left">The PhenoPath simulation produces a pseudotime trajectory with different types of genes.</td>
-</tr>
-<tr class="even">
-<td align="left">ZINB-WaVE</td>
-<td align="left">zinb</td>
-<td align="left">10.1101/125112</td>
-<td align="left">drisso/zinbwave</td>
-<td align="left">The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</td>
-</tr>
-<tr class="odd">
-<td align="left">SparseDC</td>
-<td align="left">sparseDC</td>
-<td align="left">10.1093/nar/gkx1113</td>
-<td align="left">cran/SparseDC</td>
-<td align="left">The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</td>
-</tr>
-</tbody>
-</table>
<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns a <code>SingleCellExperiment</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">? lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
</div>
<div id="other-expression-values" class="section level1">
@@ -828,25 +621,25 @@
<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb103-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
-<a class="sourceLine" id="cb103-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+<a class="sourceLine" id="cb103-3" 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>
<pre><code>## DataFrame with 6 rows and 3 columns
-## Gene GeneMean Length
-## <factor> <numeric> <numeric>
-## 1 Gene1 0.0489642776646331 1937
-## 2 Gene2 3.20462567086451 2196
-## 3 Gene3 0.364784855489904 9883
-## 4 Gene4 0.110583350422224 1810
-## 5 Gene5 0.661617770742839 1177
-## 6 Gene6 0.101683292027918 2012</code></pre>
+## Gene GeneMean Length
+## <factor> <numeric> <numeric>
+## Gene1 Gene1 0.37935966627652 1477
+## Gene2 Gene2 3.18357154159759e-05 5118
+## Gene3 Gene3 10.7328431924421 1854
+## Gene4 Gene4 0.00194229447546391 1812
+## Gene5 Gene5 2.35446446969376 7513
+## Gene6 Gene6 0.0928062223462787 5152</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
+<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="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="cb105-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 0.0000000 0.000000000 0.00000000 0.000000000 0.000000000
-## Gene2 0.2338332 0.033654084 0.09984799 0.000000000 0.066541011
-## Gene3 0.0000000 0.007477929 0.00000000 0.007379757 0.007392698
-## Gene4 0.0000000 0.000000000 0.04038051 0.000000000 0.000000000
-## Gene5 0.0000000 0.062790457 0.06209748 0.247864539 0.000000000</code></pre>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 105.2947 0.00000 0.00000 106.59129 104.66580
+## Gene2 0.0000 0.00000 0.00000 0.00000 0.00000
+## Gene3 1426.0217 324.18195 502.64066 339.66630 1834.41774
+## Gene4 0.0000 0.00000 0.00000 0.00000 0.00000
+## Gene5 0.0000 19.99978 41.34592 20.95506 41.15304</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">
@@ -855,38 +648,31 @@
<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb107-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb107-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
-<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.
-## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
-<pre><code>## [1] "FeatureData" "PhenoData" "Plots"</code></pre>
-<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
+<a class="sourceLine" id="cb107-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw"><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="cb107-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb107-5" 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>
+<pre><code>## [1] "RowData" "ColData" "Plots"</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/base/topics/names">names</a></span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
## [5] "ZerosGene" "ZerosCell" "MeanZeros"</code></pre>
-<p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<p>The returned list has three items. The first two are the combined datasets by gene (<code>RowData</code>) and by cell (<code>ColData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
+<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
-<a class="sourceLine" id="cb114-2" data-line-number="2"><span class="kw"><a href="ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
-<a class="sourceLine" id="cb114-3" data-line-number="3"> <span class="kw"><a href="ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
-<a class="sourceLine" id="cb114-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="ggplot2.tidyverse.org/reference/geom_point.html">geom_point</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" 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="cb112-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>ColData,</a>
+<a class="sourceLine" id="cb112-3" data-line-number="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb112-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
<div id="comparing-differences" class="section level2">
<h2 class="hasAnchor">
<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a></code></pre></div>
-<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.
-## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
-## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
-<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a>
+<a class="sourceLine" id="cb113-2" data-line-number="2">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-qq-1.png" width="576" style="display: block; margin: auto;"></p>
</div>
<div id="making-panels" class="section level2">
@@ -894,22 +680,22 @@
<a href="#making-panels" class="anchor"></a>Making panels</h2>
<p>Each of these comparisons makes several plots which can be a lot to look at. To make this easier, or to produce figures for publications, you can make use of the functions <code>makeCompPanel</code>, <code>makeDiffPanel</code> and <code>makeOverallPanel</code>.</p>
<p>These functions combine the plots into a single panel using the <code>cowplot</code> package. The panels can be quite large and hard to view (for example in RStudio’s plot viewer) so it can be better to output the panels and view them separately. Luckily <code>cowplot</code> provides a convenient function for saving the images. Here are some suggested parameters for outputting each of the panels:</p>
-<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
-<a class="sourceLine" id="cb119-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
-<a class="sourceLine" id="cb119-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb119-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb119-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
-<a class="sourceLine" id="cb119-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
-<a class="sourceLine" id="cb119-7" data-line-number="7"></a>
-<a class="sourceLine" id="cb119-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
-<a class="sourceLine" id="cb119-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
+<a class="sourceLine" id="cb115-2" 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="cb115-3" 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="cb115-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb115-5" 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="cb115-6" 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="cb115-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb115-8" 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="cb115-9" 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>
</div>
<div id="citing-splatter" class="section level1">
<h1 class="hasAnchor">
<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h1>
<p>If you use Splatter in your work please cite our paper:</p>
-<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" 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>
<pre><code>##
## Zappia L, Phipson B, Oshlack A. Splatter: Simulation of
## single-cell RNA sequencing data. Genome Biology. 2017;
@@ -929,14 +715,14 @@
<div id="session-information" class="section level1 unnumbered">
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
-<pre><code>## R version 3.5.1 (2018-07-02)
-## Platform: x86_64-apple-darwin15.6.0 (64-bit)
+<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/sessionInfo">sessionInfo</a></span>()</a></code></pre></div>
+<pre><code>## R Under development (unstable) (2019-04-13 r76389)
+## Platform: x86_64-apple-darwin16.7.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
-## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
-## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
+## BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
+## LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
@@ -946,58 +732,54 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.8.4 ggplot2_3.0.0
-## [3] splatter_1.4.3 SingleCellExperiment_1.2.0
-## [5] SummarizedExperiment_1.10.1 DelayedArray_0.6.5
-## [7] BiocParallel_1.14.2 matrixStats_0.54.0
-## [9] Biobase_2.40.0 GenomicRanges_1.32.6
-## [11] GenomeInfoDb_1.16.0 IRanges_2.14.11
-## [13] S4Vectors_0.18.3 BiocGenerics_0.26.0
-## [15] BiocStyle_2.8.2
+## [1] scater_1.11.16 ggplot2_3.1.1
+## [3] splatter_1.7.4 SingleCellExperiment_1.5.2
+## [5] SummarizedExperiment_1.13.0 DelayedArray_0.9.9
+## [7] BiocParallel_1.17.18 matrixStats_0.54.0
+## [9] Biobase_2.43.1 GenomicRanges_1.35.1
+## [11] GenomeInfoDb_1.19.3 IRanges_2.17.5
+## [13] S4Vectors_0.21.23 BiocGenerics_0.29.2
+## [15] BiocStyle_2.11.0
##
## loaded via a namespace (and not attached):
-## [1] bitops_1.0-6 fs_1.2.6
-## [3] rprojroot_1.3-2 tools_3.5.1
-## [5] backports_1.1.2 R6_2.2.2
-## [7] vipor_0.4.5 lazyeval_0.2.1
-## [9] colorspace_1.3-2 sp_1.3-1
-## [11] withr_2.1.2 tidyselect_0.2.4
-## [13] gridExtra_2.3 compiler_3.5.1
-## [15] xml2_1.2.0 desc_1.2.0
-## [17] labeling_0.3 bookdown_0.7
-## [19] scales_1.0.0 checkmate_1.8.6
-## [21] pkgdown_1.1.0 commonmark_1.5
-## [23] stringr_1.3.1 digest_0.6.16
-## [25] rmarkdown_1.10 XVector_0.20.0
-## [27] pkgconfig_2.0.2 htmltools_0.3.6
-## [29] akima_0.6-2 highr_0.7
-## [31] limma_3.36.3 rlang_0.2.2
-## [33] shiny_1.1.0 DelayedMatrixStats_1.2.0
-## [35] bindr_0.1.1 dplyr_0.7.6
-## [37] RCurl_1.95-4.11 magrittr_1.5
-## [39] GenomeInfoDbData_1.1.0 Matrix_1.2-14
-## [41] Rcpp_0.12.18 ggbeeswarm_0.6.0
-## [43] munsell_0.5.0 Rhdf5lib_1.2.1
-## [45] viridis_0.5.1 stringi_1.2.4
-## [47] yaml_2.2.0 edgeR_3.22.3
-## [49] MASS_7.3-51 zlibbioc_1.26.0
-## [51] rhdf5_2.24.0 plyr_1.8.4
-## [53] grid_3.5.1 promises_1.0.1
-## [55] shinydashboard_0.7.0 crayon_1.3.4
-## [57] lattice_0.20-35 cowplot_0.9.3
-## [59] splines_3.5.1 locfit_1.5-9.1
-## [61] knitr_1.20 pillar_1.3.0
-## [63] rjson_0.2.20 reshape2_1.4.3
-## [65] glue_1.3.0 evaluate_0.11
-## [67] data.table_1.11.4 httpuv_1.4.5
-## [69] gtable_0.2.0 purrr_0.2.5
-## [71] assertthat_0.2.0 xfun_0.3
-## [73] mime_0.5 xtable_1.8-3
-## [75] roxygen2_6.1.0 later_0.7.4
-## [77] survival_2.42-6 viridisLite_0.3.0
-## [79] tibble_1.4.2 beeswarm_0.2.3
-## [81] memoise_1.1.0 tximport_1.8.0
-## [83] bindrcpp_0.2.2 fitdistrplus_1.0-9</code></pre>
+## [1] viridis_0.5.1 edgeR_3.25.4
+## [3] BiocSingular_0.99.16 splines_3.7.0
+## [5] viridisLite_0.3.0 lsei_1.2-0
+## [7] DelayedMatrixStats_1.5.2 assertthat_0.2.1
+## [9] sp_1.3-1 BiocManager_1.30.4
+## [11] GenomeInfoDbData_1.2.1 vipor_0.4.5
+## [13] yaml_2.2.0 pillar_1.3.1
+## [15] backports_1.1.4 lattice_0.20-38
+## [17] limma_3.39.15 glue_1.3.1
+## [19] digest_0.6.18 XVector_0.23.2
+## [21] checkmate_1.9.1 colorspace_1.4-1
+## [23] cowplot_0.9.4 htmltools_0.3.6
+## [25] Matrix_1.2-17 plyr_1.8.4
+## [27] pkgconfig_2.0.2 bookdown_0.9
+## [29] zlibbioc_1.29.0 purrr_0.3.2
+## [31] scales_1.0.0 tibble_2.1.1
+## [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_0.13 fs_1.2.7
+## [41] MASS_7.3-51.4 xml2_1.2.0
+## [43] beeswarm_0.2.3 fitdistrplus_1.0-14
+## [45] tools_3.7.0 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_3.7.0 pkgdown_1.3.0
+## [53] rsvd_1.0.0 rlang_0.3.4
+## [55] grid_3.7.0 RCurl_1.95-4.12
+## [57] BiocNeighbors_1.1.13 rstudioapi_0.10
+## [59] labeling_0.3 bitops_1.0-6
+## [61] rmarkdown_1.12 npsurv_0.4-0
+## [63] gtable_0.3.0 roxygen2_6.1.1
+## [65] R6_2.4.0 gridExtra_2.3
+## [67] knitr_1.22 dplyr_0.8.0.1
+## [69] commonmark_1.7 rprojroot_1.3-2
+## [71] desc_1.2.0 stringi_1.4.3
+## [73] ggbeeswarm_0.6.0 Rcpp_1.0.1
+## [75] tidyselect_0.2.5 xfun_0.6</code></pre>
</div>
</div>
@@ -1008,11 +790,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#installation">Installation</a></li>
<li><a href="#quickstart">Quickstart</a></li>
- <li>
-<a href="#the-splat-simulation">The Splat simulation</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#parameters">Parameters</a></li>
- </ul>
-</li>
+ <li><a href="#the-splat-simulation">The Splat simulation</a></li>
<li>
<a href="#the-splatparams-object">The <code>SplatParams</code> object</a><ul class="nav nav-pills nav-stacked">
<li><a href="#getting-and-setting">Getting and setting</a></li>
@@ -1049,9 +827,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
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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
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diff --git a/docs/authors.html b/docs/authors.html
index a68dcbd91dcb470f657823f1bab9c8f3a062ceae..b0dcfc78bf4e6665fa5c58494fccdb4c12baeead 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Citation and Authors • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -37,7 +37,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -63,14 +64,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -88,6 +90,18 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
@@ -113,12 +127,13 @@
<div class="contents col-md-9">
<div class="page-header">
<h1>Citation</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
</div>
<p>Zappia L, Phipson B, Oshlack A (2017).
“Splatter: simulation of single-cell RNA sequencing data.”
<em>Genome Biology</em>.
-doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-0</a>, <a href="http://dx.doi.org/10.1186/s13059-017-1305-0">http://dx.doi.org/10.1186/s13059-017-1305-0</a>.
+doi: <a href="https://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-0</a>, <a href="http://dx.doi.org/10.1186/s13059-017-1305-0">http://dx.doi.org/10.1186/s13059-017-1305-0</a>.
</p>
<pre>@Article{,
author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
@@ -134,15 +149,15 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
<ul class="list-unstyled">
<li>
- <p><strong>Luke Zappia</strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7744-8565' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Luke Zappia</strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7744-8565' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li>
- <p><strong>Belinda Phipson</strong>. Author. <a href='https://orcid.org/0000-0002-1711-7454' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Belinda Phipson</strong>. Author. <a href='https://orcid.org/0000-0002-1711-7454' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li>
- <p><strong>Alicia Oshlack</strong>. Author. <a href='https://orcid.org/0000-0001-9788-5690' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Alicia Oshlack</strong>. Author. <a href='https://orcid.org/0000-0001-9788-5690' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
</ul>
@@ -158,9 +173,8 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/index.html b/docs/index.html
index d9fecf4a9ef3948c843b7f170aac62de6255b4cf..e7321353e3e27bdccf77e2a614621cee24ea32d6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,14 +1,14 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
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<title>Simple Simulation of Single-cell RNA Sequencing Data • Splatter</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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<meta property="og:title" content="Simple Simulation of Single-cell RNA Sequencing Data">
<meta property="og:description" content="Splatter is a package for the simulation of single-cell RNA
@@ -17,7 +17,7 @@
estimated from real data and functions are provided for comparing real and
simulated datasets.">
<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-52309538-4"></script><script>
@@ -33,14 +33,15 @@
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -58,6 +59,18 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+<li>
+ <a href="articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
@@ -80,7 +93,7 @@
</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>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>
@@ -104,26 +117,26 @@
install.packages("BiocManager")
BiocManager::install("splatter")</code></pre>
<p>If you wish to build a local version of the vignette use:</p>
-<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/BiocManager/topics/install">BiocManager::install("splatter", build_vignettes=TRUE)</a></code></pre>
+<pre class="{r}"><code><a href="https://www.rdocumentation.org/packages/BiocManager/topics/install">BiocManager::install("splatter", build_vignettes=TRUE)</a></code></pre>
<p>This will also build the vignette and install all suggested dependencies (which aren’t required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.</p>
</div>
<div id="development-version" class="section level3">
<h3 class="hasAnchor">
<a href="#development-version" class="anchor"></a>Development version</h3>
<p>If you want to try the <a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html">development version</a> this can also be installed from Bioconductor:</p>
-<pre class="{r}"><code>library(BiocManager)
+<pre class="{r}"><code><a href="https://www.rdocumentation.org/packages/base/topics/library">library(BiocManager)
valid() # checks for out of date packages
BiocManager::install() # (optional) updates out of date packages
-BiocManager::install("splatter")</code></pre>
+BiocManager::install("splatter")</a></code></pre>
<p>Depending on the current release cycle you may also need to install the development version of R. See <a href="https://www.bioconductor.org/developers/how-to/useDevel/">here</a> for more details.</p>
<p>Alternatively the development version can be installed directly from <a href="https://github.com/Oshlack/splatter">Github</a>:</p>
-<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/devtools/topics/install">devtools::install("Oshlack/splatter")</a></code></pre>
+<pre class="{r}"><code><a href="https://www.rdocumentation.org/packages/devtools/topics/install">devtools::install("Oshlack/splatter")</a></code></pre>
</div>
</div>
</div>
- <div class="col-md-3" id="sidebar">
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<div class="links">
<h2>Links</h2>
<ul class="list-unstyled">
@@ -152,9 +165,9 @@ BiocManager::install("splatter")</code></pre>
<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
-<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7744-8565" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
-<li>Belinda Phipson <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-1711-7454" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
-<li>Alicia Oshlack <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-9788-5690" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li>
+<li>Luke Zappia <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7744-8565" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" 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>
</ul>
</div>
@@ -172,15 +185,13 @@ BiocManager::install("splatter")</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="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 711ca5fe7e5f3513da3b67bb68bb4bafcee3af9e..65efca3d29df98bb2c620c8270ae374e1b588853 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Changelog • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
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+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
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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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@@ -37,7 +37,8 @@
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+<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>
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@@ -63,14 +64,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -88,6 +90,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -116,15 +130,56 @@
<small>Source: <a href='https://github.com/Oshlack/splatter/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
+ <div id="version-1-7-4-2018-04-17" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-4-2018-04-17" class="anchor"></a>Version 1.7.4 (2018-04-17)</h2>
+<ul>
+<li>Allow SplatParams parameters to be set in any order</li>
+</ul>
+</div>
+ <div id="version-1-7-3-2018-04-15" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-3-2018-04-15" class="anchor"></a>Version 1.7.3 (2018-04-15)</h2>
+<ul>
+<li>Minor changes to documentation</li>
+<li>Protect against integer overflow in simulation functions</li>
+<li>Fix order of groups in splatSimulate</li>
+</ul>
+</div>
+ <div id="version-1-7-2-2018-12-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-2-2018-12-06" class="anchor"></a>Version 1.7.2 (2018-12-06)</h2>
+<ul>
+<li>Add ImmunoOncology biocViews tag at request of Bioconductor team</li>
+</ul>
+</div>
+ <div id="version-1-7-1-2018-11-17" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-7-1-2018-11-17" class="anchor"></a>Version 1.7.1 (2018-11-17)</h2>
+<ul>
+<li>Fix bugs in vignette</li>
+</ul>
+</div>
<div id="version-1-7-0-2018-11-01" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-7-0-2018-11-01" class="anchor"></a>Version 1.7.0 (2018-11-01)</h2>
-<p>Bioconductor 3.9 devel</p>
+<ul>
+<li>Bioconductor 3.9 devel</li>
+</ul>
+</div>
+ <div id="version-1-6-1-2018-12-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#version-1-6-1-2018-12-06" class="anchor"></a>Version 1.6.1 (2018-12-06)</h2>
+<ul>
+<li>Add ImmunoOncology biocViews tag at request of Bioconductor team</li>
+</ul>
</div>
<div id="version-1-6-0-2018-11-01" class="section level1">
<h1 class="page-header">
<a href="#version-1-6-0-2018-11-01" class="anchor"></a>Version 1.6.0 (2018-11-01)</h1>
-<p>Bioconductor 3.8 release</p>
+<ul>
+<li>Bioconductor 3.8 release</li>
+</ul>
<div id="version-1-5-8-2018-10-22" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-8-2018-10-22" class="anchor"></a>Version 1.5.8 (2018-10-22)</h2>
@@ -167,7 +222,7 @@
<ul>
<li>Fix bug in getLNormFactors when reversing factors less than one</li>
<li>Update documentation to new Roxygen version (6.1.0)</li>
-<li>Change varible name in vignette for compatibility with scater</li>
+<li>Change variable name in vignette for compatibility with scater</li>
<li>Add suggested package checks to tests</li>
</ul>
</div>
@@ -448,7 +503,7 @@
<h2 class="hasAnchor">
<a href="#version-0-99-13-2017-03-25" class="anchor"></a>Version 0.99.13 (2017-03-25)</h2>
<ul>
-<li>Modify how Lun2Params stores gene paramters to use data.frame</li>
+<li>Modify how Lun2Params stores gene parameters to use data.frame</li>
<li>Move sampling of genes/cells to lun2Simulate</li>
<li>Return to old Lun2 nGenes estimate</li>
</ul>
@@ -461,7 +516,7 @@
<li>Update compareSCESets plots</li>
<li>Modify Lun2 nGenes estimate</li>
<li>Modify how addFeatureStats names columns</li>
-<li>Add infinte bcv.df warning to splatSimulate</li>
+<li>Add infinite bcv.df warning to splatSimulate</li>
</ul>
</div>
<div id="version-0-99-11-2017-03-20" class="section level2">
@@ -626,7 +681,7 @@
<ul>
<li>Redesign how parameters are stored</li>
<li>Each simulation now has it’s own S4 Params class</li>
-<li>Modify exisiting simulations to use new parameter objects</li>
+<li>Modify existing simulations to use new parameter objects</li>
</ul>
</div>
<div id="version-0-6-0-2016-10-12" class="section level2">
@@ -674,7 +729,12 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#version-1-7-4-2018-04-17">1.7.4</a></li>
+ <li><a href="#version-1-7-3-2018-04-15">1.7.3</a></li>
+ <li><a href="#version-1-7-2-2018-12-06">1.7.2</a></li>
+ <li><a href="#version-1-7-1-2018-11-17">1.7.1</a></li>
<li><a href="#version-1-7-0-2018-11-01">1.7.0</a></li>
+ <li><a href="#version-1-6-1-2018-12-06">1.6.1</a></li>
<li><a href="#version-1-6-0-2018-11-01">1.6.0</a></li>
<li><a href="#version-1-4-0-2018-05-02">1.4.0</a></li>
<li><a href="#version-1-2-0-2017-10-30">1.2.0</a></li>
@@ -692,9 +752,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 6ca2f37ab4f657e9f79e79032b2e34e0e13397d5..c03fb08d7092ce6ad54910f27996b28e0ef6df3c 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -58,9 +58,14 @@ img {
max-width: 100%;
}
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
/* Typographic tweaking ---------------------------------*/
-.contents h1.page-header {
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margin-top: calc(-60px + 1em);
}
@@ -136,10 +141,9 @@ a.anchor {
.ref-index th {font-weight: normal;}
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+.ref-index .icon {width: 40px;}
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.ref-index .title {width: 60%;}
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diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index de9bd7247cf858fdc66d64631f9b67f06b170f5a..eb7e83d2fecc7e7311197cc294f4a7131cc263e0 100644
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for (var i = 0; i < links.length; i++) {
if (links[i].getAttribute("href") === "#")
continue;
- var path = paths(links[i].pathname);
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
- var length = prefix_length(cur_path, path);
+ var length = prefix_length(nav_path, cur_path);
if (length > max_length) {
max_length = length;
pos = i;
@@ -52,13 +56,14 @@
return(pieces);
}
+ // Returns -1 if not found
function prefix_length(needle, haystack) {
if (needle.length > haystack.length)
- return(0);
+ return(-1);
// Special case for length-0 haystack, since for loop won't run
if (haystack.length === 0) {
- return(needle.length === 0 ? 1 : 0);
+ return(needle.length === 0 ? 0 : -1);
}
for (var i = 0; i < haystack.length; i++) {
@@ -78,9 +83,9 @@
element.setAttribute('data-original-title', tooltipOriginalTitle);
}
- if(Clipboard.isSupported()) {
+ if(ClipboardJS.isSupported()) {
$(document).ready(function() {
- var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+ var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
$(".examples, div.sourceCode").addClass("hasCopyButton");
@@ -91,7 +96,7 @@
$('.btn-copy-ex').tooltip({container: 'body'});
// Initialize clipboard:
- var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+ var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
text: function(trigger) {
return trigger.parentNode.textContent;
}
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 62c46f74eabe7b994e85a9559cb62cb7af13968e..e87c522f6ac1024a47263580a9a50c6db81f451e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,7 +1,8 @@
pandoc: 2.1.1
-pkgdown: 1.1.0
+pkgdown: 1.3.0
pkgdown_sha: ~
articles:
+ splat_params: splat_params.html
splatter: splatter.html
urls:
reference: http://oshlack.github.io/splatter/reference
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index 51890b3232712fd57200b120e9e76ff119dca730..d5a9fa7779f82472cac2896868c3f62f538926f2 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate BASiCS simulation parameters — BASiCSEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -154,7 +168,7 @@ containing count data to estimate parameters from.</p></td>
<th>spike.info</th>
<td><p>data.frame describing spike-ins with two columns: "Name"
giving the names of the spike-in features (must match
-<code>rownames(counts)</code>) and "Input" giving the number of input
+<code><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames(counts)</a></code>) and "Input" giving the number of input
molecules.</p></td>
</tr>
<tr>
@@ -178,7 +192,7 @@ a multiple of <code>thin</code>.</p></td>
<tr>
<th>regression</th>
<td><p>logical. Whether to use regression to identify
-over-dispersion. See <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p></td>
+over-dispersion. See <code><a href='https://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p></td>
</tr>
<tr>
<th>params</th>
@@ -195,7 +209,7 @@ messages.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Optional parameters passed to <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code>.</p></td>
+ <td><p>Optional parameters passed to <code><a href='https://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code>.</p></td>
</tr>
</table>
@@ -205,21 +219,21 @@ messages.</p></td>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> that
takes the output and converts it to a BASiCSParams object. Either a set of
spike-ins or batch information (or both) must be supplied. If only batch
information is provided there must be at least two batches. See
-<code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>BASiCS_MCMC</a></code> for details.</p>
+<code><a href='https://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_MCMC'>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>
<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
-<span class='no'>spike.info</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'>rownames</span>(<span class='no'>sc_example_counts</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
- <span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'>rnorm</span>(<span class='fl'>10</span>, <span class='fl'>500</span>, <span class='fl'>200</span>),
+<span class='no'>spike.info</span> <span class='kw'><-</span> <span class='fu'><a href='https://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'>sc_example_counts</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
+ <span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'><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='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>BASiCSEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>100</span>, <span class='fl'>1</span>:<span class='fl'>30</span>],
<span class='no'>spike.info</span>)
@@ -247,9 +261,8 @@ information is provided there must be at least two batches. See
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
index 9c2a7b92ce80c4a7964edc3940bc085270f5ace1..bdb9b36cb319947d28ffc63c967776bf1c448b08 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The BASiCSParams class — BASiCSParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -140,7 +154,7 @@
</dl></p></dd>
<dt><em>Gene parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>gene.params</code></dt><dd><p>A <code>data.frame</code> containing gene
- parameters with two coloumns: <code>Mean</code> (mean expression for
+ parameters with two columns: <code>Mean</code> (mean expression for
each biological gene) and <code>Delta</code> (cell-to-cell
heterogeneity for each biological gene).</p></dd>
</dl></p></dd>
@@ -150,7 +164,7 @@
</dl></p></dd>
<dt><em>Cell parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>cell.params</code></dt><dd><p>A <code>data.frame</code> containing gene
- parameters with two coloumns: <code>Phi</code> (mRNA content factor for
+ parameters with two columns: <code>Phi</code> (mRNA content factor for
each cell, scaled to sum to the number of cells in each batch)
and <code>S</code> (capture efficient for each cell).</p></dd>
</dl></p></dd>
@@ -181,9 +195,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index c0992a6a4d5524a6cbbc47d6ae0c2457c3ff3cff..061b9b3d155257642a984f2ed136d7e660fe3e9c 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>BASiCS simulation — BASiCSSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -152,16 +166,16 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> that
takes a <code><a href='BASiCSParams.html'>BASiCSParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> for more details of how the simulation
+output to a <code><a href='https://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
works.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
-Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
+Single-Cell Sequencing data. PLoS Computational Biology (2015).</p>
<p>Paper: <a href='10.1371/journal.pcbi.1004333'>10.1371/journal.pcbi.1004333</a></p>
<p>Code: <a href='https://github.com/catavallejos/BASiCS'>https://github.com/catavallejos/BASiCS</a></p>
@@ -192,9 +206,8 @@ Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index 92ffb513141ff6c55356fa1d50dd67e06d1dc2f0..7a67bd6cd5332e4f82309160b8ea1f7edccac621 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The Lun2Params class — Lun2Params • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -137,16 +151,16 @@
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
<dt><em>Gene parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>gene.params</code></dt><dd><p>A <code>data.frame</code> containing gene
- parameters with two coloumns: <code>Mean</code> (mean expression for
+ parameters with two columns: <code>Mean</code> (mean expression for
each gene) and <code>Disp</code> (dispersion for each gene).</p></dd>
<dt><code>zi.params</code></dt><dd><p>A <code>data.frame</code> containing
- zero-inflated gene parameters with three coloumns: <code>Mean</code>
+ zero-inflated gene parameters with three columns: <code>Mean</code>
(mean expression for each gene), <code>Disp</code> (dispersion for
each, gene), and <code>Prop</code> (zero proportion for each gene).</p></dd>
</dl></p></dd>
<dt><code>[nPlates]</code></dt><dd><p>The number of plates to simulate.</p></dd>
<dt><em>Plate parameters</em></dt><dd><p><dl class='dl-horizontal'>
- <dt><code>plate.ingroup</code></dt><dd><p>Character vecotor giving the plates
+ <dt><code>plate.ingroup</code></dt><dd><p>Character vector giving the plates
considered to be part of the "ingroup".</p></dd>
<dt><code>plate.mod</code></dt><dd><p>Plate effect modifier factor. The plate
effect variance is divided by this value.</p></dd>
@@ -188,9 +202,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
index 67a076289bf4b4877c782ff37df868fe23e2dfa6..8aab85d808c77c07492666bed76cf17feccc96ef 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The LunParams class — LunParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -180,9 +194,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/MFAParams.html b/docs/reference/MFAParams.html
index 2e5f571d4f40137f799f78a92fb688e9cd338bd4..5b4e995a26a9a4f72f56a2f03f633f28a66e8ad8 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The MFAParams class — MFAParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -144,7 +158,7 @@
dropout function.</p></dd>
</dl>
<p>The parameters not shown in brackets can be estimated from real data using
-<code><a href='mfaEstimate.html'>mfaEstimate</a></code>. See <code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code> for more
+<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
details about the parameters. For details of the Splatter implementation of
the mfa simulation see <code><a href='mfaSimulate.html'>mfaSimulate</a></code>.</p>
@@ -166,9 +180,8 @@ the mfa simulation see <code><a href='mfaSimulate.html'>mfaSimulate</a></code>.<
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
index 25b222320b6d26f969b59a15a863e3a25bbe29a6..023afc0a3e812c158800cb1493748f9d8e333805 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The Params virtual class — Params • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -156,9 +170,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
index 449a50746511957f332d6d30dee340fd13e56690..4913692b5488537bb312e4a58286d3f694af3d41 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The PhenoParams class — PhenoParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -166,9 +180,8 @@ see <code><a href='phenoSimulate.html'>phenoSimulate</a></code>.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
index de57312ca7a08092ec5f74a3ade2b170ae1f06e9..cd216d0e8463492138b0f1a191845e8d7a9d3848 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The SCDDParams class — SCDDParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -135,7 +149,7 @@
<dt><code>nGenes</code></dt><dd><p>The number of genes to simulate (not used).</p></dd>
<dt><code>nCells</code></dt><dd><p>The number of cells to simulate in each condition.</p></dd>
<dt><code>[seed]</code></dt><dd><p>Seed to use for generating random numbers.</p></dd>
- <dt><code>SCdat</code></dt><dd><p><code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> containing real
+ <dt><code>SCdat</code></dt><dd><p><code><a href='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>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>
@@ -151,7 +165,7 @@
biological group of interest.</p></dd>
</dl>
<p>The parameters not shown in brackets can be estimated from real data using
-<code><a href='scDDEstimate.html'>scDDEstimate</a></code>. See <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more
+<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
details about the parameters. For details of the Splatter implementation of
the scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code>.</p>
@@ -173,9 +187,8 @@ the scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
index 9d678e46cce9d10f580c68a3b9d8617251f37455..1a26f8f04b783934bc3f345971f70980c8f4d69f 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The SimpleParams class — SimpleParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -164,9 +178,8 @@ see <code><a href='simpleSimulate.html'>simpleSimulate</a></code>.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/SparseDCParams.html b/docs/reference/SparseDCParams.html
index 819e4e341723e17612cf0d85b20a6087d040dae0..afd840c046f3c627dc65bff1d950381335e9d985 100644
--- a/docs/reference/SparseDCParams.html
+++ b/docs/reference/SparseDCParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The SparseDCParams class — SparseDCParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -173,9 +187,8 @@ see <code><a href='sparseDCSimulate.html'>sparseDCSimulate</a></code>.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
index 687e6b5670a5b2088d78c88ab1facd06accd63b8..4bab5e8f4df00158be6a4fb5b5dfdbb283095436 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The SplatParams class — SplatParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -177,7 +191,7 @@
<dt><em>Differential expression parameters</em></dt><dd><p><dl class='dl-horizontal'>
<dt><code>[de.prob]</code></dt><dd><p>Probability that a gene is differentially
expressed in a group. Can be a vector.</p></dd>
- <dt><code>[de.loProb]</code></dt><dd><p>Probability that a differentially
+ <dt><code>[de.downProb]</code></dt><dd><p>Probability that a differentially
expressed gene is down-regulated. Can be a vector.</p></dd>
<dt><code>[de.facLoc]</code></dt><dd><p>Location (meanlog) parameter for the
differential expression factor log-normal distribution. Can be a
@@ -212,9 +226,10 @@
this form would have a "from" parameter of c(0, 1, 1) (where 0 is
the origin). If no vector is given all paths will start at the
origin.</p></dd>
- <dt><code>[path.length]</code></dt><dd><p>Vector giving the number of steps to
+ <dt><code>[path.nSteps]</code></dt><dd><p>Vector giving the number of steps to
simulate along each path. If a single value is given it will be
- applied to all paths.</p></dd>
+ applied to all paths. This parameter was previously called
+ <code>path.length</code>.</p></dd>
<dt><code>[path.skew]</code></dt><dd><p>Vector giving the skew of each path.
Values closer to 1 will give more cells towards the starting
population, values closer to 0 will give more cells towards the
@@ -252,9 +267,8 @@ see <code><a href='splatSimulate.html'>splatSimulate</a></code>.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
index 9783ea87d183a03d0fa81e523017e87c3d9b1e19..862945aeaf2818c89169cc53afc52f9ed76ca5f0 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The ZINBParams class — ZINBParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -138,8 +152,8 @@
<dt><code>model</code></dt><dd><p>Object describing a ZINB model.</p></dd>
</dl>
<p>The majority of the parameters for this simulation are stored in a
-<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/ZinbModel-class'>ZinbModel</a></code> object. Please refer to the documentation
-for this class and its constructor(<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbModel'>zinbModel</a></code>) for
+<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
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
@@ -163,9 +177,8 @@ see <code><a href='zinbSimulate.html'>zinbSimulate</a></code>.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index d60618c426830800a40af5beeee3375fc350e462..1d57ab94a816c9148e546a53b65e94ce477e093e 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Add feature statistics — addFeatureStats • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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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>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -126,7 +140,7 @@
</div>
- <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>),
+ <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://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>),
<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>
@@ -191,9 +205,8 @@ analysis packages.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 8e234151c5347cabc79e4a5bb966c1fae7006836..3c01e4c2e6589388d3b42004b88a5d9422f4b2f0 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Add gene lengths — addGeneLengths • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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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>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -126,7 +140,7 @@
</div>
- <pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"generate"</span>, <span class='st'>"sample"</span>), <span class='kw'>loc</span> <span class='kw'>=</span> <span class='fl'>7.9</span>,
+ <pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://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>,
<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>
@@ -162,7 +176,7 @@
<p>This function adds simulated gene lengths to the
<code>rowData</code> slot of a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that can be
+<code><a href='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>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
@@ -174,22 +188,22 @@ vector.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Default generate method</span>
<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
-<span class='fu'>head</span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> DataFrame with 6 rows and 3 columns
-#> Gene GeneMean Length
-#> <factor> <numeric> <numeric>
-#> 1 Gene1 0.197443857880758 1235
-#> 2 Gene2 5.46465220002874 2081
-#> 3 Gene3 0.707714763953083 2387
-#> 4 Gene4 0.15575800464631 995
-#> 5 Gene5 0.0181238728394951 2635
-#> 6 Gene6 1.30100599611438 2357</div><div class='input'># Sample method (human coding genes)
+<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 1.8758247946425 1106
+#> Gene2 Gene2 0.0233473092596537 9585
+#> Gene3 Gene3 7.2118635203533 1511
+#> Gene4 Gene4 0.157075337775195 10184
+#> Gene5 Gene5 2.68786806249153 998
+#> Gene6 Gene6 0.267592057034904 1334</div><div class='input'># Sample method (human coding genes)
</div><span class='co'># NOT RUN {</span>
-<span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
-<span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
+<span class='fu'><a href='https://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='no'>txdb</span> <span class='kw'><-</span> <span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>
<span class='no'>tx.lens</span> <span class='kw'><-</span> <span class='fu'>transcriptLengths</span>(<span class='no'>txdb</span>, <span class='kw'>with.cds_len</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>tx.lens</span> <span class='kw'><-</span> <span class='no'>tx.lens</span>[<span class='no'>tx.lens</span>$<span class='no'>cds_len</span> <span class='kw'>></span> <span class='fl'>0</span>, ]
-<span class='no'>gene.lens</span> <span class='kw'><-</span> <span class='fu'>max</span>(<span class='fu'>splitAsList</span>(<span class='no'>tx.lens</span>$<span class='no'>tx_len</span>, <span class='no'>tx.lens</span>$<span class='no'>gene_id</span>))
+<span class='no'>gene.lens</span> <span class='kw'><-</span> <span class='fu'><a href='https://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'>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>
@@ -214,9 +228,8 @@ vector.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
index 4c3f93eb85573c80f6fa980b4d0316f0f4ad84b5..28f4960c23fc8cd94628ba9ac808ed5a13483e9a 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Brownian bridge — bridge • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ a random walk with fixed end points." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ a random walk with fixed end points." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ a random walk with fixed end points." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -178,9 +192,8 @@ a random walk with fixed end points.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/bringItemsForward.html b/docs/reference/bringItemsForward.html
new file mode 100644
index 0000000000000000000000000000000000000000..57083378af5f47886932ff61f7007b6d7ad081e0
--- /dev/null
+++ b/docs/reference/bringItemsForward.html
@@ -0,0 +1,191 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Bring items forward — bringItemsForward • Splatter</title>
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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="../pkgdown.js"></script>
+
+
+
+ <link href="../extra.css" rel="stylesheet">
+
+<meta property="og:title" content="Bring items forward — bringItemsForward" />
+
+<meta property="og:description" content="Move selected items to the start of a list." />
+<meta name="twitter:card" content="summary" />
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+<!-- Global site tag (gtag.js) - Google Analytics -->
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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">1.7.4</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../index.html">
+ <span class="fa fa-home fa-lg"></span>
+
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+<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="fa fa-github fa-lg"></span>
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+</li>
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Bring items forward</h1>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/utils.R'><code>R/utils.R</code></a></small>
+ <div class="hidden name"><code>bringItemsForward.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Move selected items to the start of a list.</p>
+
+ </div>
+
+ <pre class="usage"><span class='fu'>bringItemsForward</span>(<span class='no'>ll</span>, <span class='no'>items</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>ll</th>
+ <td><p>list to adjust item order.</p></td>
+ </tr>
+ <tr>
+ <th>items</th>
+ <td><p>vector of items to bring to the front. Any not in the list will
+be ignored.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>list with selected items first</p>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+</div>
+ </footer>
+ </div>
+
+
+
+ </body>
+</html>
+
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
index 663faca6b09e5a0dd9137d91902566b92386fce1..41f9b5e997b555a813a285594be11a38b4bee4d5 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Compare SingleCellExperiment objects — compareSCEs • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ basic plots comparing them." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ basic plots comparing them." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ basic plots comparing them." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -165,9 +179,9 @@ compare.</p></td>
<p>The returned list has three items:</p>
<dl class='dl-horizontal'>
- <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+ <dt><code>RowData</code></dt><dd><p>Combined row data from the provided
SingleCellExperiments.</p></dd>
- <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
+ <dt><code>ColData</code></dt><dd><p>Combined column data from the provided
SingleCellExperiments.</p></dd>
<dt><code>Plots</code></dt><dd><p>Comparison plots
<dl class='dl-horizontal'>
@@ -175,7 +189,7 @@ compare.</p></td>
<dt><code>Variances</code></dt><dd><p>Boxplot of variance distribution.</p></dd>
<dt><code>MeanVar</code></dt><dd><p>Scatter plot with fitted lines showing the
mean-variance relationship.</p></dd>
- <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+ <dt><code>LibrarySizes</code></dt><dd><p>Boxplot of the library size
distribution.</p></dd>
<dt><code>ZerosGene</code></dt><dd><p>Boxplot of the percentage of each gene
that is zero.</p></dd>
@@ -186,16 +200,15 @@ compare.</p></td>
</dl></p></dd>
</dl>
<p>The plots returned by this function are created using
-<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
+<code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
+using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "FeatureData" "PhenoData" "Plots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+ <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"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -219,9 +232,8 @@ using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></co
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
index 30744dc31501007f995b9ff7e1e51735426a61ae..6e98eea9a0e01def8e9801155bcbc3121e01fbdf 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Diff SingleCellExperiment objects — diffSCEs • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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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>
@@ -41,7 +41,8 @@ basic plots comparing them to a reference." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ basic plots comparing them to a reference." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ basic plots comparing them to a reference." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -177,9 +191,9 @@ Q-Q plots are also returned.</p>
<p>The returned list has five items:</p>
<dl class='dl-horizontal'>
<dt><code>Reference</code></dt><dd><p>The SingleCellExperiment used as the reference.</p></dd>
- <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+ <dt><code>RowData</code></dt><dd><p>Combined feature data from the provided
SingleCellExperiments.</p></dd>
- <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
+ <dt><code>ColData</code></dt><dd><p>Combined column data from the provided
SingleCellExperiments.</p></dd>
<dt><code>Plots</code></dt><dd><p>Difference plots
<dl class='dl-horizontal'>
@@ -187,7 +201,7 @@ Q-Q plots are also returned.</p>
<dt><code>Variances</code></dt><dd><p>Boxplot of variance differences.</p></dd>
<dt><code>MeanVar</code></dt><dd><p>Scatter plot showing the difference from
the reference variance across expression ranks.</p></dd>
- <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+ <dt><code>LibraeySizes</code></dt><dd><p>Boxplot of the library size
differences.</p></dd>
<dt><code>ZerosGene</code></dt><dd><p>Boxplot of the differences in the
percentage of each gene that is zero.</p></dd>
@@ -208,16 +222,15 @@ Q-Q plots are also returned.</p>
</dl></p></dd>
</dl>
<p>The plots returned by this function are created using
-<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
+<code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
+using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "FeatureData" "PhenoData" "Plots" "QQPlots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'><a href='https://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"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -241,9 +254,8 @@ using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></co
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index 960dcab37dd7426ec29f1ad517edfdef1e80d9f6..d2dc2af8cc1ffd72e8721ff5048155e6b605d138 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Expand parameters — expandParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ the number of groups." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ the number of groups." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ the number of groups." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -175,9 +189,8 @@ the number of groups.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
index 0eae1399a1620b3bf8dc864e242701b0efa77161..175a6a9f50a3b10ed27e30bf13f03c320413cce2 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Get log-normal factors — getLNormFactors • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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 -->
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@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
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</li>
@@ -177,9 +191,8 @@ from 1.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
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diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
index c2c7a3877a4c677283f4b9a1dcfb5ebd9973db57..1dee108e3f92e929db0e96bf8c92ab8e4ce7676c 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Get a parameter — getParam • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -173,9 +187,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
index 8c2f7bc0769398cf372ecb1fb7b076693eed859a..aa24734d8c20639097b6691a1919415be3387579 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Get parameters — getParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -148,7 +162,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
-<span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='fu'>c</span>(<span class='st'>"nGenes"</span>, <span class='st'>"nCells"</span>, <span class='st'>"mean.rate"</span>))</div><div class='output co'>#> $nGenes
+<span class='fu'>getParams</span>(<span class='no'>params</span>, <span class='fu'><a href='https://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
#> [1] 10000
#>
#> $nCells
@@ -177,9 +191,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
index 3b14391f0f30718d863e20e8a01e2d50bc76d74e..7581d72a50021f5167a7807943da28f60715c93b 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Get path order — getPathOrder • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ already been simulated." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ already been simulated." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ already been simulated." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -135,7 +149,7 @@ already been simulated.</p>
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>path.from</th>
- <td><p>vector giving the path endpoints that each path orginates
+ <td><p>vector giving the path endpoints that each path originates
from.</p></td>
</tr>
</table>
@@ -163,9 +177,8 @@ from.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 494a3e562a804eff203df6fa980117ff0273678a..bfae825b85425fc31c91303069b0d0bc41782067 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Function reference • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -37,7 +37,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -63,14 +64,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -88,6 +90,18 @@
<li>
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+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
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+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
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</li>
@@ -620,9 +634,8 @@
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<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
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diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index 10d46c20e5a00beb47fbb18633a69a92fea548ed..a5bf4d2fc81a6f9f313a54489b2c4e2e077e13a0 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -1,6 +1,6 @@
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<title>List simulations — listSims • 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>
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" 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" />
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@@ -41,7 +41,8 @@ brief description." />
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<span class="navbar-brand">
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- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
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@@ -92,6 +94,18 @@ brief description." />
<li>
<a href="../reference/index.html">Reference</a>
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+<li class="dropdown">
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</li>
@@ -148,58 +162,58 @@ 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
#>
-#> Splat (splat)
-#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
+#> <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>
#> 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.
#>
-#> Splat Single (splatSingle)
-#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
+#> </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>
#> The Splat simulation with a single population.
#>
-#> Splat Groups (splatGroups)
-#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
+#> </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>
#> The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution.
#>
-#> Splat Paths (splatPaths)
-#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
+#> </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>
#> The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways.
#>
-#> Simple (simple)
-#> DOI: 10.1186/s13059-017-1305-0 GitHub: Oshlack/splatter
+#> </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>
#> A simple simulation with gamma means and negative binomial counts.
#>
-#> Lun (lun)
-#> DOI: 10.1186/s13059-016-0947-7 GitHub: MarioniLab/Deconvolution2016
+#> </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>
#> Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.
#>
-#> Lun 2 (lun2)
-#> DOI: 10.1093/biostatistics/kxw055 GitHub: MarioniLab/PlateEffects2016
+#> </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>
#> 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.
#>
-#> scDD (scDD)
-#> DOI: 10.1186/s13059-016-1077-y GitHub: kdkorthauer/scDD
+#> </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>
#> The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.
#>
-#> BASiCS (BASiCS)
-#> DOI: 10.1371/journal.pcbi.1004333 GitHub: catavallejos/BASiCS
+#> </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>
#> The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects.
#>
-#> mfa (mfa)
-#> DOI: 10.12688/wellcomeopenres.11087.1 GitHub: kieranrcampbell/mfa
+#> </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>
#> The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.
#>
-#> PhenoPath (pheno)
-#> DOI: 10.1101/159913 GitHub: kieranrcampbell/phenopath
+#> </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>
#> The PhenoPath simulation produces a pseudotime trajectory with different types of genes.
#>
-#> ZINB-WaVE (zinb)
-#> DOI: 10.1101/125112 GitHub: drisso/zinbwave
+#> </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>
#> The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.
#>
-#> SparseDC (sparseDC)
-#> DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC
+#> </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>
#> The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.
-#> </div></pre>
+#> </div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@@ -220,9 +234,8 @@ displayed.</p>
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<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
</footer>
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diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
index b940b0ad1d050f8aef52c509492d852018706767..5250a761623a5affaa0234a6aab28f1900609c9a 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -1,6 +1,6 @@
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+<html lang="en">
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@@ -9,17 +9,17 @@
<title>Logistic function — logistic • 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>
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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" />
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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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@@ -40,7 +40,8 @@
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@@ -66,14 +67,15 @@
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<div class="container">
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- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
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@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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+ <ul class="dropdown-menu" role="menu">
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</li>
@@ -147,7 +161,7 @@
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>Value of logistic funciton with given parameters</p>
+ <p>Value of logistic function with given parameters</p>
</div>
@@ -168,9 +182,8 @@
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- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 8ece3e84a66ec7851c2849975e614551a4a85ef9..32f3783adbddf2fc18f2e0d0ebbdad8f28c4f794 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -1,6 +1,6 @@
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+<html lang="en">
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@@ -9,17 +9,17 @@
<title>Estimate Lun2 simulation parameters — lun2Estimate • Splatter</title>
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+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -183,11 +197,11 @@ single core.</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_cell_info"</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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_cell_info"</span>)
-<span class='no'>plates</span> <span class='kw'><-</span> <span class='fu'>factor</span>(<span class='no'>sc_example_cell_info</span>$<span class='no'>Mutation_Status</span>)
+<span class='no'>plates</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/factor'>factor</a></span>(<span class='no'>sc_example_cell_info</span>$<span class='no'>Mutation_Status</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lun2Estimate</span>(<span class='no'>sc_example_counts</span>, <span class='no'>plates</span>, <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>params</span>
<span class='co'># }</span></pre>
@@ -213,9 +227,8 @@ single core.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index a2c680d0218402dffd85bf5cb983b21b64d83fab..5eeee1ae6f6c06b5c2c762df465e0d82210eac5a 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Lun2 simulation — lun2Simulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -42,7 +42,8 @@ analyses of single-cell RNA-seq data"." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ analyses of single-cell RNA-seq data"." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ analyses of single-cell RNA-seq data"." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,9 +182,9 @@ simulation is the addition of plate effects. Differential expression can be
added between two groups of plates (an "ingroup" and all other plates).
Library size factors are also applied and optionally a zero-inflated
negative-binomial can be used.</p>
-<p>If the number of genes to simulate differs from the number of provied gene
+<p>If the number of genes to simulate differs from the number of provided gene
parameters or the number of cells to simulate differs from the number of
-library sizes the relevant paramters will be sampled with a warning. This
+library sizes the relevant parameters will be sampled with a warning. This
allows any number of genes or cells to be simulated regardless of the
number in the dataset used in the estimation step but has the downside that
some genes or cells may be simulated multiple times.</p>
@@ -184,7 +198,7 @@ expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating plate means...</span></div><div class='output co'>#> <span class='message'>Simulating libray size factors...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
+ <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Simulating plate means...</span></div><div class='output co'>#> <span class='message'>Simulating library size factors...</span></div><div class='output co'>#> <span class='message'>Simulating cell means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='output co'>#> <span class='message'>Done!</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -209,9 +223,8 @@ expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 2844626c1c9c1211985343333010c284cf89a35e..2425439a53ca8d241cb4302689284ec4f174a685 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Lun simulation parameters — lunEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -162,39 +176,39 @@ for more details on the parameters.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)</div><div class='output co'>#> <span class='message'>Loading required package: ggplot2</span></div><div class='output co'>#> <span class='message'></span>
+<span class='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='message'>Loading required package: ggplot2</span></div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>Attaching package: ‘scater’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:S4Vectors’:</span>
#> <span class='message'></span>
#> <span class='message'> rename</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:stats’:</span>
#> <span class='message'></span>
-#> <span class='message'> filter</span></div><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+#> <span class='message'> filter</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>lunEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='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'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> </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;'> 40</span><span> 74391
#>
#> 9 additional parameters
#>
-#> Mean:
-#> [Rate] [Shape]
+#> </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>
#> 2 2
#>
-#> Counts:
-#> [Dispersion]
+#> </span><span style='font-weight: bold;'>Counts:</span><span>
+#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
#> 0.1
#>
-#> Groups:
-#> [GROUPS] [GROUP CELLS]
-#> 1 40
+#> </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;'> 40</span><span>
#>
-#> Diff expr:
-#> [Genes] [Up Prop] [Up FC] [Down FC]
+#> </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>
#> 1000 0.5 5 0
-#> </div></pre>
+#> </div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -217,9 +231,8 @@ for more details on the parameters.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index f23ba51fdad42d89815464e25612d5d867e9613b..9f132453038dea0bf01ec2c96250e7fa5f71d4d9 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Lun simulation — lunSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -42,7 +42,8 @@ sequencing data with many zero counts"." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ sequencing data with many zero counts"." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ sequencing data with many zero counts"." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -200,9 +214,8 @@ RNA sequencing data with many zero counts. Genome Biology (2016).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index 5955b69981b7927caba9fb1f2815e96a9dd1c43c..1537851d75118d5f09c98746de81a2fcb4992bcc 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Make comparison panel — makeCompPanel • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -126,7 +140,7 @@
</div>
- <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>,
+ <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://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='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>
@@ -156,7 +170,7 @@
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'><a href='https://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'>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>
@@ -180,9 +194,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index 8d139fa6ede801d3e682bd7ff9b9107f8dc7a9f5..b275be9b00edc7e2d3e4a8dafd728dc93a760d1c 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Make difference panel — makeDiffPanel • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -127,7 +141,7 @@
</div>
<pre class="usage"><span class='fu'>makeDiffPanel</span>(<span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Difference comparison"</span>,
- <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Library size"</span>, <span class='st'>"Zeros per cell"</span>,
+ <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://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='st'>"Zeros per gene"</span>, <span class='st'>"Mean-variance relationship"</span>,
<span class='st'>"Mean-zeros relationship"</span>))</pre>
@@ -157,7 +171,7 @@
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'><a href='https://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'>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>
@@ -181,9 +195,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index 62731232a3782c8214f6a476dc8d666467bc913b..74fa1918489a0c8549b9453a11646e5cd9756c9a 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Make overall panel — makeOverallPanel • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ single panel." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ single panel." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ single panel." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -129,7 +143,7 @@ single panel.</p>
</div>
<pre class="usage"><span class='fu'>makeOverallPanel</span>(<span class='no'>comp</span>, <span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Overall comparison"</span>,
- <span class='kw'>row.labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>, <span class='st'>"Mean-variance relationship"</span>,
+ <span class='kw'>row.labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://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='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>
@@ -163,8 +177,8 @@ single panel.</p>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
<span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
-<span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compSCEs</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'>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>
@@ -188,9 +202,8 @@ single panel.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 3384d70b7a62445b836b6153995157be88e81ffd..d310094ea0b99b4b7d36cc92068c238d4fe175f1 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate mfa simulation parameters — mfaEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -157,37 +171,37 @@ containing count data to estimate parameters from.</p></td>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The dropout lambda parameter is estimate using
-<code><a href='http://www.rdocumentation.org/packages/mfa/topics/empirical_lambda'>empirical_lambda</a></code>. See <code><a href='MFAParams.html'>MFAParams</a></code> for more
+<code><a href='https://www.rdocumentation.org/packages/mfa/topics/empirical_lambda'>empirical_lambda</a></code>. See <code><a href='MFAParams.html'>MFAParams</a></code> for more
details on the parameters.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>mfaEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class MFAParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> </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;'> 40</span><span> 74391
#>
#> 4 additional parameters
#>
-#> Transient:
-#> [Proportion]
+#> </span><span style='font-weight: bold;'>Transient:</span><span>
+#> </span><span style='color: #0000BB;'>[Proportion]</span><span>
#> 0
#>
-#> Negative:
-#> [Zero]
+#> </span><span style='font-weight: bold;'>Negative:</span><span>
+#> </span><span style='color: #0000BB;'>[Zero]</span><span>
#> TRUE
#>
-#> Dropout:
-#> [Present] (LAMBDA)
-#> FALSE 0.00352186231063193
-#> </div></pre>
+#> </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;'>0.00352186230722432</span><span>
+#> </div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -210,9 +224,8 @@ details on the parameters.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index 4da15e2a8e8706a37645b7f837c742f14ff37172..f4e5c54be7f8c78f4ab38ee2319499575e7787eb 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>MFA simulation — mfaSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -152,11 +166,11 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code>
+ <p>This function is just a wrapper around <code><a href='https://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code>
that takes a <code><a href='MFAParams.html'>MFAParams</a></code>, runs the simulation then converts the
output from log-expression to counts and returns a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. See
-<code><a href='http://www.rdocumentation.org/packages/mfa/topics/create_synthetic'>create_synthetic</a></code> and the mfa paper for more details about
+<code><a href='https://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
how the simulation works.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
@@ -194,9 +208,8 @@ Open Research (2017).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 1cdcfed260cac0419053e9d968b822fb992091a8..520126451e9d38c5181450589fa2fece4cb544ed 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>New Params — newParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ Params subtypes." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ Params subtypes." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ Params subtypes." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -185,9 +199,8 @@ Params subtypes.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 639dde8f40616f51eba9c1c16d55024213e6fb32..6887c89b6cf0c8773e3ead05c7c12cbabcc636ef 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate PhenoPath simulation parameters — phenoEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ dataset." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ dataset." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ dataset." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -164,23 +178,23 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>phenoEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class PhenoParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> </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;'> 40</span><span> 74391
#>
#> 4 additional parameters
#>
-#> Genes:
-#> [DE] [PST] [PST + BETA] [DE + PST + BETA]
-#> 500 500 500 500
-#> </div></pre>
+#> </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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -203,9 +217,8 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
index 5920e71a08341d65964d7db0ae062e7cde98da9e..56ad023b01b9a276e50a77f9b183d1a6be8913f1 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>PhenoPath simulation — phenoSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -153,12 +167,12 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is just a wrapper around
-<code><a href='http://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> that takes a
+<code><a href='https://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> that takes a
<code><a href='PhenoParams.html'>PhenoParams</a></code>, runs the simulation then converts the
output from log-expression to counts and returns a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
+<code><a href='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
simulated log-expression values are returned in the <code>LogExprs</code> assay.
-See <code><a href='http://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>simulate_phenopath</a></code> and the PhenoPath paper for
+See <code><a href='https://www.rdocumentation.org/packages/phenopath/topics/simulate_phenopath'>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>
@@ -197,9 +211,8 @@ and environmental backgrounds across single-cells and populations. bioRxiv
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
index 0545cb0bee3caa0878198f42c608b64956e9e641..136c7d3bb97dab4f0112ed5d35a34b0e2a884e32 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Bind rows (matched) — rbindMatched • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ to both." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ to both." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ to both." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -167,9 +181,8 @@ to both.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index 3bc5c0891dccbd2f5b7a0e0d801c625ce72bd26a..a29f13701c5168967c07a15450129f438e4086a8 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate scDD simulation parameters — scDDEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -186,19 +200,19 @@ interest.</p></td>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function applies <code><a href='http://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> to the counts then uses
-<code><a href='http://www.rdocumentation.org/packages/scDD/topics/scDD'>scDD</a></code> to estimate the numbers of each gene type to
+ <p>This function applies <code><a href='https://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
simulate. The output is then converted to a SCDDParams object. See
-<code><a href='http://www.rdocumentation.org/packages/scDD/topics/preprocess'>preprocess</a></code> and <code><a href='http://www.rdocumentation.org/packages/scDD/topics/scDD'>scDD</a></code> for details.</p>
+<code><a href='https://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>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
-<span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>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'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>scDDEstimate</span>(<span class='no'>sc_example_counts</span>, <span class='kw'>conditions</span> <span class='kw'>=</span> <span class='no'>conditions</span>)
<span class='no'>params</span>
<span class='co'># }</span></pre>
@@ -224,9 +238,8 @@ simulate. The output is then converted to a SCDDParams object. See
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index aa65f8fce98f98b5de6e568eb14995fccbfc4ae3..fd5be586bfbb741329d5e31ef00f7d009da417ba 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>scDD simulation — scDDSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,10 +182,10 @@ single core.</p></td>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> that
takes a <code><a href='SCDDParams.html'>SCDDParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more details about how the simulation
+output to a <code><a href='https://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
works.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
@@ -211,9 +225,8 @@ single-cell RNA-seq experiments. Genome Biology (2016).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index c238ca25c5b9b13e93b8854a375f932d1425844f..3c37c74d5fc2754c34e8bb89b5101ad4b57f02ba 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Set a parameter — setParam • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -165,7 +179,7 @@
</tr>
<tr>
<th>value</th>
- <td><p>value to set the paramter to.</p></td>
+ <td><p>value to set the parameter to.</p></td>
</tr>
</table>
@@ -176,24 +190,24 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
-<span class='fu'>setParam</span>(<span class='no'>params</span>, <span class='st'>"nGenes"</span>, <span class='fl'>100</span>)</div><div class='output co'>#> A Params object of class SimpleParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (Cells) [Seed]
-#> 100 100 667401
+#> </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 74391
#>
#> 3 additional parameters
#>
-#> Mean:
+#> </span><span style='font-weight: bold;'>Mean:</span><span>
#> (Rate) (Shape)
#> 0.3 0.4
#>
-#> Counts:
-#> [Dispersion]
+#> </span><span style='font-weight: bold;'>Counts:</span><span>
+#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
#> 0.1
#> </div><div class='input'>
-</div></pre>
+</div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -214,9 +228,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index 39253e00a8f26475b635a1774a98e2ef781034ba..068acbc01d44102f898c288bff5d3aba0903dc71 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Set a parameter UNCHECKED — setParamUnchecked • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ VALIDITY!" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ VALIDITY!" />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ VALIDITY!" />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -146,7 +160,7 @@ VALIDITY!</p>
</tr>
<tr>
<th>value</th>
- <td><p>value to set the paramter to.</p></td>
+ <td><p>value to set the parameter to.</p></td>
</tr>
</table>
@@ -173,9 +187,8 @@ VALIDITY!</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 55aec388f6e6732640c8a8e78b7e3280cba6d8d3..126a1b08ea097b44fc01dabe863bb9e6d1e224e1 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Set parameters — setParams • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -116,7 +130,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Set parameters</h1>
- <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/params-functions.R'><code>R/params-functions.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/Oshlack/splatter/blob/master/R/AllGenerics.R'><code>R/AllGenerics.R</code></a>, <a href='https://github.com/Oshlack/splatter/blob/master/R/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>
<div class="hidden name"><code>setParams.Rd</code></div>
</div>
@@ -126,18 +140,24 @@
</div>
- <pre class="usage"><span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+ <pre class="usage"><span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
+
+<span class='co'># S4 method for Params</span>
+<span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
+
+<span class='co'># S4 method for SplatParams</span>
+<span class='fu'>setParams</span>(<span class='no'>object</span>, <span class='kw'>update</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
- <th>params</th>
+ <th>object</th>
<td><p>Params object to set parameters in.</p></td>
</tr>
<tr>
<th>update</th>
- <td><p>list of parameters to set where <code>names(update)</code> are the
+ <td><p>list of parameters to set where <code><a href='https://www.rdocumentation.org/packages/base/topics/names'>names(update)</a></code> are the
names of the parameters to set and the items in the list are values.</p></td>
</tr>
<tr>
@@ -162,59 +182,60 @@ them manually), see examples.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>()
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (Genes) (Cells) [Seed]
-#> 10000 100 667401
+#> </span><span style='font-weight: bold;'>Global:</span><span>
+#> (Genes) (Cells) </span><span style='color: #0000BB;'> [Seed]</span><span>
+#> 10000 100 74391
#>
#> 3 additional parameters
#>
-#> Mean:
+#> </span><span style='font-weight: bold;'>Mean:</span><span>
#> (Rate) (Shape)
#> 0.3 0.4
#>
-#> Counts:
-#> [Dispersion]
+#> </span><span style='font-weight: bold;'>Counts:</span><span>
+#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
#> 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 Params object of class SimpleParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 1000 50 667401
+#> </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> 74391
#>
#> 3 additional parameters
#>
-#> Mean:
+#> </span><span style='font-weight: bold;'>Mean:</span><span>
#> (Rate) (Shape)
#> 0.3 0.4
#>
-#> Counts:
-#> [Dispersion]
+#> </span><span style='font-weight: bold;'>Counts:</span><span>
+#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
#> 0.1
#> </div><div class='input'><span class='co'># Set via update list</span>
-<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>setParams</span>(<span class='no'>params</span>, <span class='fu'>list</span>(<span class='kw'>mean.rate</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>mean.shape</span> <span class='kw'>=</span> <span class='fl'>0.8</span>))
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 1000 50 667401
+#> </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> 74391
#>
#> 3 additional parameters
#>
-#> Mean:
-#> (RATE) (SHAPE)
-#> 0.2 0.8
+#> </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>
#>
-#> Counts:
-#> [Dispersion]
+#> </span><span style='font-weight: bold;'>Counts:</span><span>
+#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
#> 0.1
-#> </div></pre>
+#> </div><div class='input'>
+</div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -237,9 +258,8 @@ them manually), see examples.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
index 44d12b82bc3c4950881445e1564881c713bba0c0..3e6603068dd8f1ee29a693bfdd28eccd68e5df90 100644
--- a/docs/reference/setParamsUnchecked.html
+++ b/docs/reference/setParamsUnchecked.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Set parameters UNCHECKED — setParamsUnchecked • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -137,7 +151,7 @@
</tr>
<tr>
<th>update</th>
- <td><p>list of parameters to set where <code>names(update)</code> are the
+ <td><p>list of parameters to set where <code><a href='https://www.rdocumentation.org/packages/base/topics/names'>names(update)</a></code> are the
names of the parameters to set and the items in the list are values.</p></td>
</tr>
<tr>
@@ -180,9 +194,8 @@ them manually), see examples. THE FINAL OBJECT IS NOT CHECKED FOR VALIDITY!</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/showDFs.html b/docs/reference/showDFs.html
index f847334ce6629f8b086378be0dee6cbeaefcaaaf..818d6de857ae30d8e56b6b31c5a0372f525e3416 100644
--- a/docs/reference/showDFs.html
+++ b/docs/reference/showDFs.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Show data.frame — showDFs • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -158,9 +172,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
index 33d88d60028bc6fbd0432a75979e2b2c826844fd..a2be97e4b59a4f4d47f4656efd0bfda5d95e03ca 100644
--- a/docs/reference/showPP.html
+++ b/docs/reference/showPP.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Show pretty print — showPP • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
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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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@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -164,9 +178,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/showValues.html b/docs/reference/showValues.html
index cac7b285b98fd7bc8b5a1584c178a8f58d3ef2f7..02d3d6f9048778e2da75b5bb92d78102591359df 100644
--- a/docs/reference/showValues.html
+++ b/docs/reference/showValues.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Show vales — showValues • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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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>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -158,9 +172,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 9ced2b7f06ba101a450481458917562441deae72..629175bb00a1b7357d64a6db352d20a1ad0d6454 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate simple simulation parameters — simpleEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -158,33 +172,33 @@ containing count data to estimate parameters from.</p></td>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The mean parameters are estimated by fitting a gamma distribution
to the library size normalised mean expression level using
-<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
+<code><a href='https://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. See <code><a href='SimpleParams.html'>SimpleParams</a></code> for more
details on the parameters.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>simpleEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SimpleParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> </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;'> 40</span><span> 74391
#>
#> 3 additional parameters
#>
-#> Mean:
-#> (RATE) (SHAPE)
-#> 0.0008052293183292 0.131835949613878
+#> </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;'>0.0008052293183292</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0.131835949613878</span><span>
#>
-#> Counts:
-#> [Dispersion]
+#> </span><span style='font-weight: bold;'>Counts:</span><span>
+#> </span><span style='color: #0000BB;'>[Dispersion]</span><span>
#> 0.1
-#> </div></pre>
+#> </div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -207,9 +221,8 @@ details on the parameters.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
index 366c133ea5dc92275d84bbb9708bb7e5880b69ab..e128ca4a16c0e4a66d88c653d8b8792dc9fd630e 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simple simulation — simpleSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -41,7 +41,8 @@ simulated library sizes, differential expression etc." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ simulated library sizes, differential expression etc." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ simulated library sizes, differential expression etc." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -186,9 +200,8 @@ details of the parameters.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
</footer>
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diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index fe37d83eb6e71054ec555e18a50d053c7c171681..0ae51688a02c5cb41411b4099ea587b98a22f89e 100644
--- a/docs/reference/sparseDCEstimate.html
+++ b/docs/reference/sparseDCEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate SparseDC simulation parameters — sparseDCEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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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" />
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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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@@ -41,7 +41,8 @@ dataset." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ dataset." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ dataset." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -157,7 +171,7 @@ containing count data to estimate parameters from.</p></td>
</tr>
<tr>
<th>norm</th>
- <td><p>logical, whether to libray size normalise counts before
+ <td><p>logical, whether to library size normalise counts before
estimation. Set this to FALSE if counts is already normalised.</p></td>
</tr>
<tr>
@@ -174,44 +188,44 @@ estimation. Set this to FALSE if counts is already normalised.</p></td>
<p>The <code>nGenes</code> and <code>nCells</code> parameters are taken from the size of the
input data. The counts are preprocessed using
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/pre_proc_data'>pre_proc_data</a></code> and then parameters are estimated using
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/sparsedc_cluster'>sparsedc_cluster</a></code> using lambda values calculated using
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/lambda1_calculator'>lambda1_calculator</a></code> and
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/lambda2_calculator'>lambda2_calculator</a></code>.</p>
+<code><a href='https://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>
<p>See <code><a href='SparseDCParams.html'>SparseDCParams</a></code> for more details on the parameters.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
-<span class='fu'>set.seed</span>(<span class='fl'>1</span>)
-<span class='no'>conditions</span> <span class='kw'><-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Random'>set.seed</a></span>(<span class='fl'>1</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'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>sparseDCEstimate</span>(<span class='no'>sc_example_counts</span>[<span class='fl'>1</span>:<span class='fl'>500</span>, ], <span class='no'>conditions</span>,
<span class='kw'>nclusters</span> <span class='kw'>=</span> <span class='fl'>3</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SparseDCParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 500 20 667401
+#> </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;'> 500</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 20</span><span> 74391
#>
#> 7 additional parameters
#>
-#> Markers:
-#> (NUMBER) (SHARED) [Same]
-#> 1 1 FALSE
+#> </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
#>
-#> Clusters:
-#> (CONDITION 1) (CONDITION 2)
-#> 1, 2, 3 1, 2, 3
+#> </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;'> 1, 2, 3</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 1, 2, 3</span><span>
#>
-#> Means:
-#> [Lower] [Upper]
+#> </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>
#> 1 2
-#> </div></pre>
+#> </div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -234,9 +248,8 @@ input data. The counts are preprocessed using
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/sparseDCSimulate.html b/docs/reference/sparseDCSimulate.html
index f71ca37c6e061ff6fefce7ea9a459a9c2f081f67..1fd72fb05eb9cdbdb0928ee24a059583c769a627 100644
--- a/docs/reference/sparseDCSimulate.html
+++ b/docs/reference/sparseDCSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>SparseDC simulation — sparseDCSimulate • Splatter</title>
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
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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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@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -153,12 +167,12 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is just a wrapper around
-<code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/sim_data'>sim_data</a></code> that takes a
+<code><a href='https://www.rdocumentation.org/packages/SparseDC/topics/sim_data'>sim_data</a></code> that takes a
<code><a href='SparseDCParams.html'>SparseDCParams</a></code>, runs the simulation then converts the
output from log-expression to counts and returns a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
+<code><a href='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object. The original
simulated log-expression values are returned in the <code>LogExprs</code> assay.
-See <code><a href='http://www.rdocumentation.org/packages/SparseDC/topics/sim_data'>sim_data</a></code> and the SparseDC paper for
+See <code><a href='https://www.rdocumentation.org/packages/SparseDC/topics/sim_data'>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>
@@ -199,9 +213,8 @@ Nucleic Acids Research (2017).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
</footer>
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diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
index 6b3ec33b6adf1e96e8ab5f3890dbb86d9213fe9d..066518b8ab3e087bb963499745ef1eb1c04284d7 100644
--- a/docs/reference/splatEstBCV.html
+++ b/docs/reference/splatEstBCV.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Splat Biological Coefficient of Variation parameters — splatEstBCV • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
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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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@@ -41,7 +41,8 @@ in the edgeR package." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ in the edgeR package." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ in the edgeR package." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -123,7 +137,7 @@ in the edgeR package." />
<div class="ref-description">
- <p>Parameters are estimated using the <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function
+ <p>Parameters are estimated using the <code><a href='https://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function
in the <code>edgeR</code> package.</p>
</div>
@@ -149,9 +163,9 @@ in the <code>edgeR</code> package.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>The <code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function is used to estimate the common
+ <p>The <code><a href='https://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> function is used to estimate the common
dispersion and prior degrees of freedom. See
-<code><a href='http://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>estimateDisp</a></code> for details. When estimating parameters on
+<code><a href='https://www.rdocumentation.org/packages/edgeR/topics/estimateDisp'>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>
@@ -177,9 +191,8 @@ apply a small correction, <code>disp = 0.1 + 0.25 * edgeR.disp</code>.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
index 772c473f74b6cb472ee65aadf6de28be637cabbb..bd907226de3bc55e35bed1abfab9c16990067347 100644
--- a/docs/reference/splatEstDropout.html
+++ b/docs/reference/splatEstDropout.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Splat dropout parameters — splatEstDropout • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ when simulating dropout." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ when simulating dropout." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ when simulating dropout." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -151,7 +165,7 @@ when simulating dropout.</p>
<p>Logistic function parameters are estimated by fitting a logistic function
to the relationship between log2 mean gene expression and the proportion of
-zeros in each gene. See <code><a href='http://www.rdocumentation.org/packages/stats/topics/nls'>nls</a></code> for details of fitting.
+zeros in each gene. See <code><a href='https://www.rdocumentation.org/packages/stats/topics/nls'>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>
@@ -176,9 +190,8 @@ level dropout is not estimated.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
index 7da2a211bfc7ba006f67c22b630a715ed6357dbf..aeb4328a6f7fc3090e6dc08c6c5201c6f6e9a26d 100644
--- a/docs/reference/splatEstLib.html
+++ b/docs/reference/splatEstLib.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Splat library size parameters — splatEstLib • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -44,7 +44,8 @@ fitdist for details on the fitting." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -70,14 +71,15 @@ fitdist for details on the fitting." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -95,6 +97,18 @@ fitdist for details on the fitting." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -130,7 +144,7 @@ fitdist for details on the fitting." />
normally distributed. If so a normal distribution is fitted to the library
sizes, if not (most cases) a log-normal distribution is fitted and the
estimated parameters are added to the params object. See
-<code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code> for details on the fitting.</p>
+<code><a href='https://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code> for details on the fitting.</p>
</div>
@@ -172,9 +186,8 @@ estimated parameters are added to the params object. See
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
index cad61299ea231e6dda6a281d4e8ce5478ee87c97..161895bfb9b77cbfb2a728fc78effe183d2863ab 100644
--- a/docs/reference/splatEstMean.html
+++ b/docs/reference/splatEstMean.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Splat mean parameters — splatEstMean • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ simulate gene expression means." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ simulate gene expression means." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ simulate gene expression means." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -150,7 +164,7 @@ simulate gene expression means.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Parameter for the gamma distribution are estimated by fitting the mean
-normalised counts using <code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>. The 'maximum
+normalised counts using <code><a href='https://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>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
@@ -178,9 +192,8 @@ and 90th percentiles.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
index feafe8971935af2b17818e237cbc35144de38e15..56f7cf18406be32666f77fe85829233e7dbbd935 100644
--- a/docs/reference/splatEstOutlier.html
+++ b/docs/reference/splatEstOutlier.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Splat expression outlier parameters — splatEstOutlier • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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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" />
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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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@@ -41,7 +41,8 @@ median mean expression level." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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@@ -67,14 +68,15 @@ median mean expression level." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
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- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ median mean expression level." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -156,7 +170,7 @@ outlier. The proportion of outlier genes is used to estimate the outlier
probability. Factors for each outlier gene are calculated by dividing mean
expression by the median mean expression. A log-normal distribution is then
fitted to these factors in order to estimate the outlier factor location and
-scale parameters using <code><a href='http://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>.</p>
+scale parameters using <code><a href='https://www.rdocumentation.org/packages/fitdistrplus/topics/fitdist'>fitdist</a></code>.</p>
</div>
@@ -179,9 +193,8 @@ scale parameters using <code><a href='http://www.rdocumentation.org/packages/fit
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index ab01b87b9c45c1a9ecb3f913b37449c12d48393f..d4c074f2e7938f4ecf68dac43128ea93e36d4824 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -1,6 +1,6 @@
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<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate Splat simulation parameters — splatEstimate • 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>
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" 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" />
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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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@@ -42,7 +42,8 @@ is done." />
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+<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>
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@@ -68,14 +69,15 @@ is done." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
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- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ is done." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -166,55 +180,55 @@ containing count data to estimate parameters from.</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='fu'><a href='https://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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sc_example_counts</span>)
-<span class='no'>params</span></div><div class='output co'>#> A Params object of class SplatParams
-#> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'
+<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>
#>
-#> Global:
-#> (GENES) (CELLS) [Seed]
-#> 2000 40 667401
+#> </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;'> 40</span><span> 74391
#>
#> 28 additional parameters
#>
-#> Batches:
-#> [BATCHES] [BATCH CELLS] [Location] [Scale]
-#> 1 40 0.1 0.1
+#> </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;'> 40</span><span> 0.1 0.1
#>
-#> Mean:
-#> (RATE) (SHAPE)
-#> 0.0032639148887191 0.419304527025529
+#> </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;'>0.0032639148887191</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0.419304527025529</span><span>
#>
-#> Library size:
-#> (LOCATION) (SCALE) (Norm)
-#> 12.7053037408488 0.58910919018286 FALSE
+#> </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> (Norm)
+#> </span><span style='color: #00BB00;font-weight: bold;'>12.7053037408488</span><span> </span><span style='color: #00BB00;font-weight: bold;'>0.58910919018286</span><span> FALSE
#>
-#> Exprs outliers:
-#> (PROBABILITY) (LOCATION) (SCALE)
-#> 0.00623376623376623 4.22280669039478 0.422108697251885
+#> </span><span style='font-weight: bold;'>Exprs outliers:</span><span>
+#> </span><span style='font-weight: bold;'> (PROBABILITY)</span><span> </span><span style='font-weight: bold;'> (LOCATION)</span><span> </span><span style='font-weight: bold;'> (SCALE)</span><span>
+#> </span><span style='color: #00BB00;font-weight: bold;'>0.00623376623376623</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 4.22280669039478</span><span> </span><span style='color: #00BB00;font-weight: bold;'> 0.422108697251885</span><span>
#>
-#> Groups:
-#> [Groups] [Group Probs]
+#> </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>
#> 1 1
#>
-#> Diff expr:
-#> [Probability] [Down Prob] [Location] [Scale]
+#> </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>
#> 0.1 0.5 0.1 0.4
#>
-#> BCV:
-#> (COMMON DISP) (DOF)
-#> 3.21969047393022 14.7262017878812
+#> </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;'>3.21969047393022</span><span> </span><span style='color: #00BB00;font-weight: bold;'>14.7262017878812</span><span>
#>
-#> Dropout:
-#> [Type] (MIDPOINT) (SHAPE)
-#> none 5.00420976858168 -0.652889139821156
+#> </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;'> 5.00420976886178</span><span> </span><span style='color: #00BB00;font-weight: bold;'>-0.652889139104032</span><span>
#>
-#> Paths:
-#> [From] [Length] [Skew] [Non-linear] [Sigma Factor]
+#> </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>
#> 0 100 0.5 0.1 0.8
-#> </div></pre>
+#> </div></span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -237,9 +251,8 @@ containing count data to estimate parameters from.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
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diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index 328e91bfef28ca7fb15b345d03c6ea8bf3a36602..740ecb4b88d0935cd76546fd9168ae961d081b7b 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -1,6 +1,6 @@
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-<html>
+<html lang="en">
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<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate BCV means — splatSimBCVMeans • Splatter</title>
<!-- jquery -->
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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>
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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" />
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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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@@ -42,7 +42,8 @@ and inverse gamma distribution." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ and inverse gamma distribution." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ and inverse gamma distribution." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,9 +182,8 @@ and inverse gamma distribution.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index 2dc5f20b39bb28d9bd76a8a19c0a43f62abf4d88..2d44938799a4f5a263c72059d5e5c0e6b2cd3a7b 100644
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+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -1,6 +1,6 @@
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<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate batch means — splatSimBatchCellMeans • 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://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
@@ -41,7 +41,8 @@ factors." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ factors." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ factors." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -166,9 +180,8 @@ factors.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 05ed4c5a81e3b4e31db4bf5c85f295d634fcac53..ae17990880d55d1442a7278ff4ac2befe5701b9e 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate batch effects — splatSimBatchEffects • Splatter</title>
<!-- jquery -->
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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://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
@@ -42,7 +42,8 @@ means for each batch." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ means for each batch." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ means for each batch." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,9 +182,8 @@ means for each batch.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index f66e44a91a32aa251955ff3f6f6dc2bb5c5c8b31..4e52f001a20fd26fbd1fcdc6fdde68bbc41551be 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate cell means — splatSimCellMeans • Splatter</title>
<!-- jquery -->
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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://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
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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" />
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@@ -44,7 +44,8 @@ means are adjusted for each cell's expected library size." />
<!-- mathjax -->
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+<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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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -70,14 +71,15 @@ means are adjusted for each cell's expected library size." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -95,6 +97,18 @@ means are adjusted for each cell's expected library size." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -176,9 +190,8 @@ means are adjusted for each cell's expected library size.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index e394fc9c213b0e743203a7ebc215537f750737a2..22c9060252abd02b9be97c9cfea7f06fe7f64627 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate group differential expression — splatSimDE • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
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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>
@@ -36,14 +36,15 @@
<meta property="og:description" content="Simulate differential expression. Differential expression factors for each
group are produced using getLNormFactors and these are added
-along with updated means for each group. For paths care is taked to make sure
+along with updated means for each group. For paths care is taken to make sure
they are simulated in the correct order." />
<meta name="twitter:card" content="summary" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -69,14 +70,15 @@ they are simulated in the correct order." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -94,6 +96,18 @@ they are simulated in the correct order." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -127,7 +141,7 @@ they are simulated in the correct order." />
<p>Simulate differential expression. Differential expression factors for each
group are produced using <code><a href='getLNormFactors.html'>getLNormFactors</a></code> and these are added
-along with updated means for each group. For paths care is taked to make sure
+along with updated means for each group. For paths care is taken to make sure
they are simulated in the correct order.</p>
</div>
@@ -172,9 +186,8 @@ they are simulated in the correct order.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index 81abab016da0b427f4ee9e9db63424783a078f95..0ec924ff160288cefd9e3c418509e4fccf83d8e1 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate dropout — splatSimDropout • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -34,7 +34,7 @@
<meta property="og:title" content="Simulate dropout — splatSimDropout" />
-<meta property="og:description" content="A logistic function is used to form a relationshop between the expression
+<meta property="og:description" content="A logistic function is used to form a relationship between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped." />
@@ -43,7 +43,8 @@ to decide which counts should be dropped." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -69,14 +70,15 @@ to decide which counts should be dropped." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -94,6 +96,18 @@ to decide which counts should be dropped." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -125,7 +139,7 @@ to decide which counts should be dropped." />
<div class="ref-description">
- <p>A logistic function is used to form a relationshop between the expression
+ <p>A logistic function is used to form a relationship between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped.</p>
@@ -170,9 +184,8 @@ to decide which counts should be dropped.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index 5375508f309a5af51ecff06d235d48875c8c01cc..e1f0129083c7a488672978be4b25ce24b78397b5 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate gene means — splatSimGeneMeans • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -42,7 +42,8 @@ with the median mean expression multiplied by the outlier factor." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ with the median mean expression multiplied by the outlier factor." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ with the median mean expression multiplied by the outlier factor." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,9 +182,8 @@ with the median mean expression multiplied by the outlier factor.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index 400123fa1865dec2baba6ec8c2268abfd306c566..04bc9376cd5e46a0d7c3b873be75072393a39400 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate library sizes — splatSimLibSizes • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -42,7 +42,8 @@ negative values are set to half the minimum non-zero value." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ negative values are set to half the minimum non-zero value." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ negative values are set to half the minimum non-zero value." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,9 +182,8 @@ negative values are set to half the minimum non-zero value.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 1c3b745daa4ee725f977ec948bece64289f320b2..b8337eac510ca8f2a490dba88a8c38a2c9f4544a 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Simulate true counts — splatSimTrueCounts • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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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>
@@ -42,7 +42,8 @@ group (or path position), expected library size and BCV." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,14 +69,15 @@ group (or path position), expected library size and BCV." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ group (or path position), expected library size and BCV." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -168,9 +182,8 @@ group (or path position), expected library size and BCV.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index ae36dcd087ef88a05f08d9cc75ec26dfde751956..461dcad4b955e6976a24214dd368d8309306c896 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Splat simulation — splatSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -41,7 +41,8 @@ the Splat method." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ the Splat method." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ the Splat method." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -128,7 +142,7 @@ the Splat method.</p>
</div>
- <pre class="usage"><span class='fu'>splatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"single"</span>, <span class='st'>"groups"</span>,
+ <pre class="usage"><span class='fu'>splatSimulate</span>(<span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>(), <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>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>)
@@ -188,19 +202,19 @@ can be used.</p>
<li><p>Create final dataset</p></li>
</ol>
<p>The final output is a
-<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that
+<code><a href='https://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that
contains the simulated counts but also the values for various intermediate
steps. These are stored in the <code>colData</code> (for cell specific
information), <code>rowData</code> (for gene specific information) or
<code>assays</code> (for gene by cell matrices) slots. This additional
information includes:</p><dl class='dl-horizontal'>
- <dt><code>phenoData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>colData</code></dt><dd><p><dl class='dl-horizontal'>
<dt>Cell</dt><dd><p>Unique cell identifier.</p></dd>
<dt>Group</dt><dd><p>The group or path the cell belongs to.</p></dd>
<dt>ExpLibSize</dt><dd><p>The expected library size for that cell.</p></dd>
<dt>Step (paths only)</dt><dd><p>how far along the path each cell is.</p></dd>
</dl></p></dd>
- <dt><code>featureData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>rowData</code></dt><dd><p><dl class='dl-horizontal'>
<dt>Gene</dt><dd><p>Unique gene identifier.</p></dd>
<dt>BaseGeneMean</dt><dd><p>The base expression level for that gene.</p></dd>
<dt>OutlierFactor</dt><dd><p>Expression outlier factor for that gene.
@@ -214,7 +228,7 @@ information includes:</p><dl class='dl-horizontal'>
<dt>SigmaFac[Path]</dt><dd><p>Factor applied to genes that have
non-linear changes in expression along a path.</p></dd>
</dl></p></dd>
- <dt><code>assayData</code></dt><dd><p><dl class='dl-horizontal'>
+ <dt><code>assays</code></dt><dd><p><dl class='dl-horizontal'>
<dt>BatchCellMeans</dt><dd><p>The mean expression of genes in each cell
after adding batch effects.</p></dd>
<dt>BaseCellMeans</dt><dd><p>The mean expression of genes in each cell
@@ -290,9 +304,8 @@ sequencing data. Genome Biology (2017).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
index 780d10b216c85c0511b5f8440fd598f93f8ff775..70efb1e7c8f3d7b3f45bff8ba38d8c593e740e9a 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>splatter. — splatter • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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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>
@@ -41,7 +41,8 @@ simulation of single-cell RNA-seq count data." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ simulation of single-cell RNA-seq count data." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ simulation of single-cell RNA-seq count data." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -159,9 +173,8 @@ Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p></div>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index eec87084e1f4c9a97037ba59bc03b27499e153f1..d0fb58a39cf9968d36050461c2bc5d6412391384 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Summarise diffSCESs — summariseDiff • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
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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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@@ -42,7 +42,8 @@ Error (RMSE) for the various properties and ranks them." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -68,14 +69,15 @@ Error (RMSE) for the various properties and ranks them." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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+ <span class="sr-only">Toggle navigation</span>
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<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -93,6 +95,18 @@ Error (RMSE) for the various properties and ranks them." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
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+ </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>
@@ -147,23 +161,22 @@ Error (RMSE) for the various properties and ranks them.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
-#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
-<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
-#> 1 Splat Mean 2.623408 NaN 1 2.659195 NaN
-#> 2 Splat Variance 11.848783 NaN 1 10.505147 NaN
-#> 3 Splat ZerosGene 40.000000 NaN 1 44.110000 NaN
-#> 4 Splat MeanVar 11.400920 NaN 1 12.415584 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 43.945000 NaN
-#> 6 Splat LibSize 55997.500000 NaN 1 56484.550000 NaN
-#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.21666 NaN 1
-#> 2 1 13.21816 NaN 1
-#> 3 1 47.71111 NaN 1
-#> 4 1 15.39405 NaN 1
-#> 5 1 53.33878 NaN 1
-#> 6 1 57530.14610 NaN 1</div></pre>
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'><a href='https://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'>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 2.526815 NaN 1 2.445861 NaN
+#> 2 Splat Variance 11.390815 NaN 1 10.045729 NaN
+#> 3 Splat ZerosGene 35.000000 NaN 1 41.305000 NaN
+#> 4 Splat MeanVar 10.687854 NaN 1 11.962774 NaN
+#> 5 Splat MeanZeros 40.000000 NaN 1 41.495000 NaN
+#> 6 Splat LibSize 55882.500000 NaN 1 58030.650000 NaN
+#> MAERank RMSE RMSEScaled RMSERank
+#> 1 1 2.986489 NaN 1
+#> 2 1 12.686655 NaN 1
+#> 3 1 45.644003 NaN 1
+#> 4 1 14.905983 NaN 1
+#> 5 1 51.031118 NaN 1
+#> 6 1 59276.438841 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -184,9 +197,8 @@ Error (RMSE) for the various properties and ranks them.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
</footer>
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diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index ad3548cb5e3d7f4613be0539de95c4acf7846208..5dadeba641edb9c5e2f31c32b3f765c7f3d37356 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -1,6 +1,6 @@
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<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Winsorize vector — winsorize • Splatter</title>
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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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" />
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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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@@ -40,7 +40,8 @@
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -164,9 +178,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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-
</footer>
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diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 47f4a54d1e446d936938e8183452bc370d07e286..c13622f5147df0e01366ecd747176e428fd0ff37 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Estimate ZINB-WaVE simulation parameters — zinbEstimate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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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" />
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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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@@ -41,7 +41,8 @@ dataset." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -67,14 +68,15 @@ dataset." />
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -92,6 +94,18 @@ dataset." />
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -169,7 +183,7 @@ features is estimated.</p></td>
</tr>
<tr>
<th>iter.init</th>
- <td><p>number of iterations to use for initalization.</p></td>
+ <td><p>number of iterations to use for initialization.</p></td>
</tr>
<tr>
<th>iter.opt</th>
@@ -195,7 +209,7 @@ single core.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>additional arguments passes to <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code>.</p></td>
+ <td><p>additional arguments passes to <code><a href='https://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code>.</p></td>
</tr>
</table>
@@ -205,17 +219,17 @@ single core.</p></td>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>The function is a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> that takes
+ <p>The function is a wrapper around <code><a href='https://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> that takes
the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParams</a></code> object. See
<code><a href='ZINBParams.html'>ZINBParams</a></code> for more details on the parameters and
-<code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> for details of the estimation procedure.</p>
+<code><a href='https://www.rdocumentation.org/packages/zinbwave/topics/zinbFit'>zinbFit</a></code> for details of the estimation procedure.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># Load example data</span>
-<span class='fu'>library</span>(<span class='no'>scater</span>)
-<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+<span class='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/utils/topics/data'>data</a></span>(<span class='st'>"sc_example_counts"</span>)
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'>zinbEstimate</span>(<span class='no'>sc_example_counts</span>)
<span class='no'>params</span>
@@ -242,9 +256,8 @@ the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParam
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
index f75ed36cbf8daef9071b29d9580ac2c0dddddb62..11a3a90b62fdd9d88e639d2cfed212aca005cfdc 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>ZINB-WaVE simulation — zinbSimulate • Splatter</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
-<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
+<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/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/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -66,14 +67,15 @@
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
- <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.7.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.4</span>
</span>
</div>
@@ -91,6 +93,18 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/splat_params.html">Splat simulation parameters</a>
+ </li>
+ </ul>
+</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
@@ -152,10 +166,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> that
+ <p>This function is just a wrapper around <code><a href='https://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> that
takes a <code><a href='ZINBParams.html'>ZINBParams</a></code>, runs the simulation then converts the
-output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
-See <code><a href='http://www.rdocumentation.org/packages/zinbwave/topics/zinbSim'>zinbSim</a></code> and the ZINB-WaVE paper for
+output to a <code><a href='https://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
more details about how the simulation works.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
@@ -197,9 +211,8 @@ bioRxiv (2017).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index aa9d8d203d73e2543e4af1799371052490904b10..db3a14813d5f98d9b71472cc34827f2ab57980ab 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -51,6 +51,9 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/bridge.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/reference/bringItemsForward.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/reference/compareSCEs.html</loc>
</url>
@@ -219,6 +222,9 @@
<url>
<loc>http://oshlack.github.io/splatter/reference/zinbSimulate.html</loc>
</url>
+ <url>
+ <loc>http://oshlack.github.io/splatter/articles/splat_params.html</loc>
+ </url>
<url>
<loc>http://oshlack.github.io/splatter/articles/splatter.html</loc>
</url>
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index b43862c6092f087996a77f7134806fe2df05ec25..39facd952f2bf5a52bdfc88bf61310d5e146b6fd 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,6 +1,17 @@
\name{NEWS}
\title{News for Package \pkg{splatter}}
+\section{Version 1.8.0, Bioconductor 3.9 Release (2018-04-18)}{
+ \itemize{
+ \item{Add a Splat parameters vignette}
+ \item{Rename the Splat path.length parameter to path.nSteps}
+ \item{Fix a bug with parameter order in setParams}
+ \item{Fix a bug where Splat groups were being simulated in alphanumeric
+ order}
+ \item{Protect against integer overflow in simulation functions}
+ }
+}
+
\section{Version 1.6.0, Bioconductor 3.8 Release (2018-10-29)}{
\itemize{
\item{Fix bug and improve normality testing in splatEstLib}
diff --git a/inst/WORDLIST b/inst/WORDLIST
new file mode 100644
index 0000000000000000000000000000000000000000..c90a07c1acb75ab19822628bbea9cae3d6674a17
--- /dev/null
+++ b/inst/WORDLIST
@@ -0,0 +1,122 @@
+addFeatureStats
+addGeneLengths
+analyzers
+AppVeyor
+BASiCS
+BASiCSEstimate
+BASiCSParams
+bcv
+BCV
+Bioc
+Biocondutor
+biocViews
+bioRxiv
+BPPARAM
+Chu
+compareSCESets
+cpm
+cutoff
+df
+diffSCESets
+diffSCESs
+DM
+doi
+DP
+Dudoit
+EE
+eg
+etc
+fpkm
+FPKM
+getLNormFactors
+Github
+Gribkova
+ImmunoOncology
+ingroup
+JC
+KD
+Korthauer
+KR
+len
+Lifecycle
+listSims
+loProb
+lun
+Lun
+LunParams
+lunSimulate
+MADs
+MAEs
+Marioni
+meanlog
+MeanZeros
+mfa
+MFA
+MFAParams
+mfaSimulate
+modeling
+nGenes
+nGroups
+NOTEs
+params
+Params
+Perraudeau
+PhenoParams
+PhenoPath
+PLoS
+poisson
+Poisson
+pseudotime
+Quickstart
+Risso
+RMSEs
+Roxygen
+RStudio
+RStudio's
+scater
+scDD
+SCDD
+scDDEstimate
+SCDDParams
+scDDSimulate
+SCE
+SCESets
+sd
+sdlog
+seq
+SimpleParams
+SingleCellExperiment
+SingleCellExperiments
+SNE
+SparseDC
+sparseDCEstimate
+SparseDCParams
+SparseParams
+splatEstimate
+splatEstLib
+splatParams
+SplatParams
+splatSimulate
+splatSimulatePaths
+Splatter's
+summariseDiff
+SummarizedExperiment
+th
+thining
+tpm
+TPM
+UMAP
+UpperCamelCase
+Vallejos
+WaVE
+Wellcome
+Wilks
+winsorize
+Winsorize
+winsorized
+Winsorized
+WithSpikes
+Yau
+ZINB
+ZINBParams
+zinbwave
diff --git a/man/BASiCSParams.Rd b/man/BASiCSParams.Rd
index 0bfb09a000d4d203dedf0eb6e7f73e5161080802..852e5d15b03d2a83f0583f17abdce4d1809145f3 100644
--- a/man/BASiCSParams.Rd
+++ b/man/BASiCSParams.Rd
@@ -25,7 +25,7 @@ The BASiCS simulation uses the following parameters:
\item{\emph{Gene parameters}}{
\describe{
\item{\code{gene.params}}{A \code{data.frame} containing gene
- parameters with two coloumns: \code{Mean} (mean expression for
+ parameters with two columns: \code{Mean} (mean expression for
each biological gene) and \code{Delta} (cell-to-cell
heterogeneity for each biological gene).}
}
@@ -39,7 +39,7 @@ The BASiCS simulation uses the following parameters:
\item{\emph{Cell parameters}}{
\describe{
\item{\code{cell.params}}{A \code{data.frame} containing gene
- parameters with two coloumns: \code{Phi} (mRNA content factor for
+ parameters with two columns: \code{Phi} (mRNA content factor for
each cell, scaled to sum to the number of cells in each batch)
and \code{S} (capture efficient for each cell).}
}
diff --git a/man/BASiCSSimulate.Rd b/man/BASiCSSimulate.Rd
index 9a26e0d14e88a7cd42945651af0a26f882999ea4..635d549ee3c908deb937bbb4e145d0714c04e4bc 100644
--- a/man/BASiCSSimulate.Rd
+++ b/man/BASiCSSimulate.Rd
@@ -32,7 +32,7 @@ sim <- BASiCSSimulate()
}
\references{
Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of
-Single-Cell Sequencing data. PLoS Comput. Biol. (2015).
+Single-Cell Sequencing data. PLoS Computational Biology (2015).
Paper: \url{10.1371/journal.pcbi.1004333}
diff --git a/man/Lun2Params.Rd b/man/Lun2Params.Rd
index db97ba60ce719bf195a30172f9ae3b870fa2cb68..260bb5fbd1496c992a7d7575f0e99cd6eb389166 100644
--- a/man/Lun2Params.Rd
+++ b/man/Lun2Params.Rd
@@ -20,10 +20,10 @@ The Lun2 simulation uses the following parameters:
\item{\emph{Gene parameters}}{
\describe{
\item{\code{gene.params}}{A \code{data.frame} containing gene
- parameters with two coloumns: \code{Mean} (mean expression for
+ parameters with two columns: \code{Mean} (mean expression for
each gene) and \code{Disp} (dispersion for each gene).}
\item{\code{zi.params}}{A \code{data.frame} containing
- zero-inflated gene parameters with three coloumns: \code{Mean}
+ zero-inflated gene parameters with three columns: \code{Mean}
(mean expression for each gene), \code{Disp} (dispersion for
each, gene), and \code{Prop} (zero proportion for each gene).}
}
@@ -31,7 +31,7 @@ The Lun2 simulation uses the following parameters:
\item{\code{[nPlates]}}{The number of plates to simulate.}
\item{\emph{Plate parameters}}{
\describe{
- \item{\code{plate.ingroup}}{Character vecotor giving the plates
+ \item{\code{plate.ingroup}}{Character vector giving the plates
considered to be part of the "ingroup".}
\item{\code{plate.mod}}{Plate effect modifier factor. The plate
effect variance is divided by this value.}
diff --git a/man/compareSCEs.Rd b/man/compareSCEs.Rd
index f0408d0bf88b85d896e4a5ec4e32e1c71e930a30..a71896728e93be6ffacf0f8e098704dbf66e170f 100644
--- a/man/compareSCEs.Rd
+++ b/man/compareSCEs.Rd
@@ -40,7 +40,7 @@ The returned list has three items:
\item{\code{Variances}}{Boxplot of variance distribution.}
\item{\code{MeanVar}}{Scatter plot with fitted lines showing the
mean-variance relationship.}
- \item{\code{LibraySizes}}{Boxplot of the library size
+ \item{\code{LibrarySizes}}{Boxplot of the library size
distribution.}
\item{\code{ZerosGene}}{Boxplot of the percentage of each gene
that is zero.}
diff --git a/man/diffSCEs.Rd b/man/diffSCEs.Rd
index 3e75cb60ee85450fa195cfcf22835efca22973bd..97cb53bbf1fb22d06b5fb14435f0d835fc68d903 100644
--- a/man/diffSCEs.Rd
+++ b/man/diffSCEs.Rd
@@ -51,7 +51,7 @@ The returned list has five items:
\item{\code{Variances}}{Boxplot of variance differences.}
\item{\code{MeanVar}}{Scatter plot showing the difference from
the reference variance across expression ranks.}
- \item{\code{LibraySizes}}{Boxplot of the library size
+ \item{\code{LibraeySizes}}{Boxplot of the library size
differences.}
\item{\code{ZerosGene}}{Boxplot of the differences in the
percentage of each gene that is zero.}
diff --git a/man/getPathOrder.Rd b/man/getPathOrder.Rd
index 7d125e77ef9f75165b78d11c626f28a22efe13cd..8b4782f3337303c91f820eafaf0bd2be5762d0a0 100644
--- a/man/getPathOrder.Rd
+++ b/man/getPathOrder.Rd
@@ -7,7 +7,7 @@
getPathOrder(path.from)
}
\arguments{
-\item{path.from}{vector giving the path endpoints that each path orginates
+\item{path.from}{vector giving the path endpoints that each path originates
from.}
}
\value{
diff --git a/man/logistic.Rd b/man/logistic.Rd
index a98711efe8c53579679313ccbefae629e03ed0ab..d424745bdc5f6f9d088e32c6a4a8452b8631c9f0 100644
--- a/man/logistic.Rd
+++ b/man/logistic.Rd
@@ -14,7 +14,7 @@ logistic(x, x0, k)
\item{k}{shape parameter. Gives the slope of the function.}
}
\value{
-Value of logistic funciton with given parameters
+Value of logistic function with given parameters
}
\description{
Implementation of the logistic function
diff --git a/man/lun2Simulate.Rd b/man/lun2Simulate.Rd
index df77ac55ec57956a28bf8b8cb8571087cca5511c..38c9ab3326c08ceace1ed2ce4f5613637539d5ad 100644
--- a/man/lun2Simulate.Rd
+++ b/man/lun2Simulate.Rd
@@ -34,9 +34,9 @@ added between two groups of plates (an "ingroup" and all other plates).
Library size factors are also applied and optionally a zero-inflated
negative-binomial can be used.
-If the number of genes to simulate differs from the number of provied gene
+If the number of genes to simulate differs from the number of provided gene
parameters or the number of cells to simulate differs from the number of
-library sizes the relevant paramters will be sampled with a warning. This
+library sizes the relevant parameters will be sampled with a warning. This
allows any number of genes or cells to be simulated regardless of the
number in the dataset used in the estimation step but has the downside that
some genes or cells may be simulated multiple times.
diff --git a/man/setParam.Rd b/man/setParam.Rd
index 378560f36fab9d73f53da98db53106e2d4f0eb6f..e144b4055269240d5999c4f4376b4532359acc9c 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -39,7 +39,7 @@ setParam(object, name, value)
\item{name}{name of the parameter to set.}
-\item{value}{value to set the paramter to.}
+\item{value}{value to set the parameter to.}
}
\value{
Object with new parameter value.
diff --git a/man/setParamUnchecked.Rd b/man/setParamUnchecked.Rd
index e8d1b40b4ab543c8b2ca227cf9a935ab5f035210..9ebd4825460616d43760857dcbc7673b7588eee7 100644
--- a/man/setParamUnchecked.Rd
+++ b/man/setParamUnchecked.Rd
@@ -15,7 +15,7 @@ setParamUnchecked(object, name, value)
\item{name}{name of the parameter to set.}
-\item{value}{value to set the paramter to.}
+\item{value}{value to set the parameter to.}
}
\value{
Object with new parameter value.
diff --git a/man/sparseDCEstimate.Rd b/man/sparseDCEstimate.Rd
index c9abf4fb5c2318220fef6b2050d54e8486073227..72671dc48112523b4d4beae3d5463bc8395afb17 100644
--- a/man/sparseDCEstimate.Rd
+++ b/man/sparseDCEstimate.Rd
@@ -23,7 +23,7 @@ containing count data to estimate parameters from.}
\item{nclusters}{number of cluster present in the dataset.}
-\item{norm}{logical, whether to libray size normalise counts before
+\item{norm}{logical, whether to library size normalise counts before
estimation. Set this to FALSE if counts is already normalised.}
\item{params}{PhenoParams object to store estimated values in.}
diff --git a/man/splatSimDE.Rd b/man/splatSimDE.Rd
index 257fb1c7d43b6fbf1a6c9fc11f9d8c0864eae720..55f3bcde77f396bffa1f4753d0a6aebe79084902 100644
--- a/man/splatSimDE.Rd
+++ b/man/splatSimDE.Rd
@@ -21,6 +21,6 @@ SingleCellExperiment with simulated differential expression.
\description{
Simulate differential expression. Differential expression factors for each
group are produced using \code{\link{getLNormFactors}} and these are added
-along with updated means for each group. For paths care is taked to make sure
+along with updated means for each group. For paths care is taken to make sure
they are simulated in the correct order.
}
diff --git a/man/splatSimDropout.Rd b/man/splatSimDropout.Rd
index 7f68ba3c5ede69f35e49615d824f8f22df785766..8222b77c648f827bd2d61e436f2b33dc0873409d 100644
--- a/man/splatSimDropout.Rd
+++ b/man/splatSimDropout.Rd
@@ -15,7 +15,7 @@ splatSimDropout(sim, params)
SingleCellExperiment with simulated dropout and observed counts.
}
\description{
-A logistic function is used to form a relationshop between the expression
+A logistic function is used to form a relationship between the expression
level of a gene and the probability of dropout, giving a probability for each
gene in each cell. These probabilities are used in a Bernoulli distribution
to decide which counts should be dropped.
diff --git a/man/zinbEstimate.Rd b/man/zinbEstimate.Rd
index 5c854a4c252594b067af178e675d697056f3ce06..486d620110ec2459077e75749e36829ffc5477f8 100644
--- a/man/zinbEstimate.Rd
+++ b/man/zinbEstimate.Rd
@@ -33,7 +33,7 @@ containing count data to estimate parameters from.}
\item{common.disp}{logical. Whether or not a single dispersion for all
features is estimated.}
-\item{iter.init}{number of iterations to use for initalization.}
+\item{iter.init}{number of iterations to use for initialization.}
\item{iter.opt}{number of iterations to use for optimization.}
diff --git a/tests/spelling.R b/tests/spelling.R
new file mode 100644
index 0000000000000000000000000000000000000000..6713838fc0fa213b458ec6f984a9987f3fb69576
--- /dev/null
+++ b/tests/spelling.R
@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..097b241637da023174b0f2e3715bd0291d9ded37
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/splat-model.png b/vignettes/splat-model.png
new file mode 100644
index 0000000000000000000000000000000000000000..1e5ca99ce1ce487c534d6e849c6643ee73b94a05
Binary files /dev/null and b/vignettes/splat-model.png differ
diff --git a/vignettes/splat_params.Rmd b/vignettes/splat_params.Rmd
new file mode 100644
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+---
+title: "Splat simulation parameters"
+date: "Last updated: 18 April 2019"
+output:
+ BiocStyle::html_document:
+ toc: true
+ toc_float: true
+vignette: >
+ %\VignetteIndexEntry{Splat simulation parameters}
+ %\VignetteEngine{knitr::rmarkdown}
+ %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>"
+)
+```
+
+This vignette describes the Splat simulation model and the parameters it uses
+in more detail.
+
+```{r setup}
+library("splatter")
+library("scater")
+library("ggplot2")
+```
+
+# The base Splat model
+
+This figure, taken from the Splatter publication, describes the core of the
+Splat simulation model.
+
+
+
+The Splat simulation uses a hierarchical probabilistic where different aspects
+of a dataset are generated from appropriate statistical distributions. The
+first stage generates a mean expression level for each gene. These are
+originally chosen from a Gamma distribution. For some genes that are selected
+to be outliers with high expression a factor is generated from a log-normal
+distribution. These factors are then multiplied by the median gene mean to
+create new means for those genes.
+
+The next stage incorporates variation in the counts per cell. An expected
+library size (total counts) is chosen for each cell from a log-normal
+distribution. The library sizes are then used to scale the gene means for each
+cell, resulting in a range a counts per cell in the simulated dataset. The gene
+means are then further adjusted to enforce a relationship between the mean
+expression level and the variability.
+
+The final cell by gene matrix of gene means is then used to generate a count
+matrix using a Poisson distribution. The result is a synthetic dataset
+consisting of counts from a Gamma-Poisson (or negative-binomial) distribution.
+An additional optional step can be used to replicate a "dropout" effect. A
+probability of dropout is generated using a logistic function based on the
+underlying mean expression level. A Bernoulli distribution is then used to
+create a dropout matrix which sets some of the generated counts to zero.
+
+The model described here will generate a single population of cells but the
+Splat simulation has been designed to be as flexible as possible and can
+create scenarios including multiple groups of cells (cell types), continuous
+paths between cell types and multiple experimental batches. The parameters used
+to create these types of simulations and how they interact with the model are
+described below.
+
+# Splat simulation parameters
+
+Within Splatter the parameters for the Splat simulation model are held in the
+`SplatParams` object. Let's create one of these objects and see what it looks
+like.
+
+```{r splat-params}
+params <- newSplatParams()
+params
+```
+
+Like all the parameter objects in Splatter printing this object displays all the
+parameters required for this simulation. As we haven't set any of the parameters
+the default values are shown but if we were to change any of them they would be
+highlighted. We can also see which parameters can be estimated by the Splat
+estimation procedure and which can't. The default values have been chosen to be
+fairly realistic but it is recommended that estimation is used to get a
+simulation that is more like the data you are interested in. Parameters can be
+modified by setting them in the `SplatParams` object or by providing them
+directly to the simulation function.
+
+The rest of this section provides details of all this parameters and explains
+how they can be used with examples.
+
+## Global parameters
+
+These parameters are used in every simulation model and control global features
+of the dataset produced.
+
+### `nGenes` - Number of genes
+
+The number of genes to simulate.
+
+```{r nGenes}
+# Set the number of genes to 1000
+params <- setParam(params, "nGenes", 1000)
+
+sim <- splatSimulate(params, verbose = FALSE)
+dim(sim)
+```
+
+### `nCells` - Number of cells
+
+The number of genes to simulate. In the Splat simulation this cannot be set
+directly but must be controlled using the `batchCells` parameter.
+
+### `seed` - Random seed
+
+Seed to use for generating random numbers including selecting values from
+distributions. By changing this value multiple simulated datasets with the same
+parameters can be produced. Simulations produced using the same set of
+parameters and random seed should be identical but there may be differences
+between operating systems, software versions etc.
+
+## Batch parameters
+
+These parameters control experimental batches in the simulated dataset. The
+overall effect of how batch effects are included in the model is similar to
+technical replicates (i.e. the same biological sample sequenced multiple times).
+This means that the underlying structure is consistent between batches but a
+global technical signature is added may separate them.
+
+### `nBatches` - Number of batches
+
+The number of batches in the simulation. This cannot be set directly but is
+controlled by setting `batchCells`.
+
+### `batchCells` - Cells per batch
+
+A vector specifying the number of cells in each batch. The number of batches
+(`nBatches`) is equal to the length of the vector and the number of cells
+(`nCells`) is equal to the sum.
+
+```{r batches}
+# Simulation with two batches of 100 cells
+sim <- splatSimulate(params, batchCells = c(100, 100), verbose = FALSE)
+
+# PCA plot using scater
+sim <- normalize(sim)
+plotPCA(sim, colour_by = "Batch")
+```
+
+### `batch.facLoc` - Batch factor location and `batch.facScale` - Batch factor scale
+
+Batches are specified by generating a small scaling factor for each gene in
+each batch from a log-normal distribution. These factors are then applied to the
+underlying gene means in each batch. Modifying these parameters affects how
+different the batches are from each other by generating bigger or smaller
+factors.
+
+```{r batch-factors}
+# Simulation with small batch effects
+sim1 <- splatSimulate(params, batchCells = c(100, 100),
+ batch.facLoc = 0.001, batch.facScale = 0.001,
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Batch") + ggtitle("Small batch effects")
+
+# Simulation with big batch effects
+sim2 <- splatSimulate(params, batchCells = c(100, 100),
+ batch.facLoc = 0.5, batch.facScale = 0.5,
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Batch") + ggtitle("Big batch effects")
+```
+
+
+## Mean parameters
+
+These parameters control the distribution that is used to generate the
+underlying original gene means.
+
+### `mean.shape` - Mean shape and `mean.rate` - Mean rate
+
+These parameters control the Gamma distribution that gene means are drawn from.
+The relationship between shape and rate can be complex and it is often better
+to use values estimated from a real dataset than to try and manually set them.
+Although these parameters control the base gene means the means in the final
+simulation will depend upon other parts of the model, particularly the simulated
+total counts per cell (library sizes).
+
+## Library size parameters
+
+These parameters control the expected number of counts for each cell. Note that
+because of sampling the actual counts per cell in the final simulation may be
+different. Turning on the dropout effect will also effect this. We use the term
+"library size" here for consistency but expected total counts would be more
+appropriate.
+
+### `lib.loc` - Library size location and `lib.scale` - Library size scale
+
+These parameters control the shape of the distribution that is used to generate
+library sizes for each cell. Increasing `lib.loc` will lead to more counts per
+cell and increasing `lib.scale` will result in more variability in the counts
+per cell.
+
+### `lib.norm` - Library size distribution
+
+The default (and recommended) distribution used for library sizes in the Splat
+simulation is a log-normal. However, in rare cases a normal distribution might
+be more appropriate. Setting `lib.norm` to `TRUE` will use a normal distribution
+instead of a log-normal.
+
+## Expression outlier parameters
+
+When developing the Splat simulation we found that while the Gamma distribution
+was generally a good match for gene means for some datasets it did not properly
+capture highly expressed genes. For this reason we added expression outliers to
+the Splat model.
+
+### `out.prob` - Expression outlier probability
+
+This parameter controls the probability that genes will be selected to be
+expression outliers. Higher values will results in more outlier genes.
+
+```{r outlier-prob}
+# Few outliers
+sim1 <- splatSimulate(out.prob = 0.001, verbose = FALSE)
+ggplot(as.data.frame(rowData(sim1)),
+ aes(x = log10(GeneMean), fill = OutlierFactor != 1)) +
+ geom_histogram(bins = 100) +
+ ggtitle("Few outliers")
+
+# Lots of outliers
+sim2 <- splatSimulate(out.prob = 0.2, verbose = FALSE)
+ggplot(as.data.frame(rowData(sim2)),
+ aes(x = log10(GeneMean), fill = OutlierFactor != 1)) +
+ geom_histogram(bins = 100) +
+ ggtitle("Lots of outliers")
+```
+
+### `out.facLoc` - Expression outlier factor location and `out.facScale` - Expression outlier factor scale
+
+The expression outlier factors are drawn from a log-normal distribution
+controlled by these parameters. The generated factors are applied to the median
+mean expression rather than the existing mean for the selected genes. This is
+to be consistent with the estimation procedure for these factors and to make
+sure that the final means are outliers. For example to avoid the situation where
+a factor is applied to a lowly expressed gene, making it just moderately
+expressed rather than an expression outlier.
+
+### Group parameters
+
+Up until this stage of the simulation only a single population of cells is
+considered but we often want to simulate datasets with multiple kinds of cells.
+We do this by assigning cells to groups.
+
+### `nGroups` - Number of groups
+
+The number of groups to simulate. This parameter cannot be set directly and is
+controlled using `group.prob`.
+
+### `group.prob` - Group probabilities
+
+A vector giving the probability that cells will be assigned to groups. The
+length of the vector gives the number of groups (`nGroups`) and the
+probabilities must sum to 1. Adjusting the number and relative values of the
+probabilities changes the number and relative sizes of the groups. To simulate
+groups we also need to use the `splatSimulateGroups` function or set
+`method = "groups"`.
+
+```{r groups}
+params.groups <- newSplatParams(batchCells = 500, nGenes = 1000)
+
+# One small group, one big group
+sim1 <- splatSimulateGroups(params.groups, group.prob = c(0.9, 0.1),
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("One small group, one big group")
+
+# Five groups
+sim2 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.2, 0.2, 0.2, 0.2, 0.2),
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Five groups")
+```
+
+**Note:** Once there are more than three or four groups it becomes difficult to
+properly view them in PCA space. We use PCA here for simplicity but generally a
+non-linear dimensionality reduction such as t-SNE or UMAP is a more useful way
+to visualise the groups.
+
+### Differential expression parameters
+
+Different groups are created by modifying the base expression levels of selected
+genes. The process for doing this is to simulate differential expression (DE)
+between each group and a fictional base cell. Altering the differential
+expression parameters controls how similar groups are to each other.
+
+### `de.prob` - DE probability
+
+This parameter controls the probability that a gene will be selected to be
+differentially expressed.
+
+```{r de-prob}
+# Few DE genes
+sim1 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.prob = 0.01, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("Few DE genes")
+
+# Lots of DE genes
+sim2 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.prob = 0.3, verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Lots of DE genes")
+```
+
+### `de.downProb` - Down-regulation probability
+
+A selected DE gene can be either down-regulated (has a factor less than one) or
+up-regulated (has a factor greater than one). This parameter controls the
+probability that a selected gene will be down-regulated.
+
+### `de.facLoc` - DE factor location and `de.facScale` - DE factor scale
+
+Differential expression factors are produced from a log-normal distribution in
+a similar way to batch effect factors and expression outlier factors. Changing
+these parameters can result in more or less extreme differences between groups.
+
+```{r de-factors}
+# Small DE factors
+sim1 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.facLoc = 0.01, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("Small DE factors")
+
+# Big DE factors
+sim2 <- splatSimulateGroups(params.groups, group.prob = c(0.5, 0.5),
+ de.facLoc = 0.3, verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Big DE factors")
+```
+
+Just looking at the PCA plots this effect seems similar to adjusting `de.prob`
+but the effect is achieved in a different way. A higher `de.prob` means that
+more genes are differentially expressed but changing the DE factors changes the
+level of DE for the same number of genes.
+
+### Complex differential expression
+
+Each of the differential expression parameters can be specified for each group
+by providing a vector of values. These vectors must be the same length as
+`group.prob`. Specifying parameters as vectors allows more complex simulations
+where groups are more or less different to each other rather than being equally
+distinct. Here are some examples of different DE scenarios.
+
+```{r complex-de}
+# Different DE probs
+sim1 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.2, 0.2, 0.2, 0.2, 0.2),
+ de.prob = c(0.01, 0.01, 0.1, 0.1, 0.3),
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") +
+ labs(title = "Different DE probabilities",
+ caption = paste("Groups 1 and 2 have very few DE genes,",
+ "Groups 3 and 4 have the default number,",
+ "Group 5 has many DE genes"))
+
+
+# Different DE factors
+sim2 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.2, 0.2, 0.2, 0.2, 0.2),
+ de.facLoc = c(0.01, 0.01, 0.1, 0.1, 0.2),
+ de.facScale = c(0.2, 0.5, 0.2, 0.5, 0.4),
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") +
+ labs(title = "Different DE factors",
+ caption = paste("Group 1 has factors with small location (value),",
+ "and scale (variability),",
+ "Group 2 has small location and greater scale.\n",
+ "Groups 3 and 4 have greater location with small,",
+ "and large scales",
+ "Group 5 has bigger factors with moderate variability"))
+
+# Combination of everything
+sim3 <- splatSimulateGroups(params.groups,
+ group.prob = c(0.05, 0.2, 0.2, 0.2, 0.35),
+ de.prob = c(0.3, 0.1, 0.2, 0.01, 0.1),
+ de.downProb = c(0.1, 0.4, 0.9, 0.6, 0.5),
+ de.facLoc = c(0.6, 0.1, 0.1, 0.01, 0.2),
+ de.facScale = c(0.1, 0.4, 0.2, 0.5, 0.4),
+ verbose = FALSE)
+sim3 <- normalize(sim3)
+plotPCA(sim3, colour_by = "Group") +
+ labs(title = "Different DE factors",
+ caption = paste(
+ "Group 1 is small with many very up-regulated DE genes,",
+ "Group 2 has the default DE parameters,\n",
+ "Group 3 has many down-regulated DE genes,",
+ "Group 4 has very few DE genes,",
+ "Group 5 is large with moderate DE factors")
+ )
+```
+
+## Biological Coefficient of Variation (BCV) parameters
+
+The BCV parameters control the variability of the genes in the simulated
+dataset.
+
+### `bcv.common` - Common BCV
+
+The `bcv.common` parameter controls the underlying common variability across
+all genes in the dataset.
+
+### `bcv.df` - BCV Degrees of Freedom
+
+This parameter sets the degrees of freedom used in the BCV inverse chi-squared
+distribution. Changing this changes the effect of mean expression on the
+variability of a gene.
+
+## Dropout parameters
+
+These parameters control whether additional dropout is added to increase the
+number of zeros in the simulated dataset and if it is how that is applied.
+
+### `dropout.type` - Dropout type
+
+This parameter determines the kind of dropout effect to simulate. Setting it to
+`"none"` means no dropout, "`experiment`" is global dropout using the same set
+of parameters for every cell, `"batch"` uses the same parameters for every cell
+in the same batch, `"group"` uses the same parameters for every cell in the
+same group and `"cell"` uses a different set of parameters for every cell.
+
+### `dropout.mid` - Dropout mid point and `dropout.shape` - Dropout shape
+
+The probability that a particular count in a particular cell is set to zero is
+related to the mean expression of that gene in that cell. This relationship is
+represented using a logistic function with these parameters. The `dropout.mid`
+parameter control the point at which the probability is equal to 0.5 and the
+`dropout.shape` controls how it changes with increasing expression. These
+parameters must be vectors of the appropriate length depending on the selected
+dropout type.
+
+## Path parameters
+
+For many uses simulating groups is sufficient but in some cases it is more
+appropriate to simulate continuous changes between cell types. The number of
+paths and the probability of assigning cells to them is still controlled by the
+`group.prob` parameter and the amount of change along a path is controlled by
+the DE parameters but other aspects of the `splatSimulatePaths` model are
+controlled by these parameters.
+
+### `path.from` - Path origin
+
+This parameter controls the order of differentiation paths. It is a vector the
+same length as `group.prob` giving the starting position of each path. For
+example a `path.from` of `c(0, 1, 1, 3)` would indicate the Path 1 starts at
+the origin (0), Path 2 starts at the end of Path 1, Path 3 also starts at the
+end of Path 1 (a branch point) and Path 4 starts at the end of Path 3.
+
+```{r paths}
+# Linear paths
+sim1 <- splatSimulatePaths(params.groups,
+ group.prob = c(0.25, 0.25, 0.25, 0.25),
+ de.prob = 0.5, de.facLoc = 0.2,
+ path.from = c(0, 1, 2, 3),
+ verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Group") + ggtitle("Linear paths")
+
+# Branching path
+sim2 <- splatSimulatePaths(params.groups,
+ group.prob = c(0.25, 0.25, 0.25, 0.25),
+ de.prob = 0.5, de.facLoc = 0.2,
+ path.from = c(0, 1, 1, 3),
+ verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Group") + ggtitle("Branching path")
+```
+
+### `path.nSteps` - Number of steps
+
+A path is created by using the same differential expression procedure as used
+for groups to generate an end point. Interpolation is then used to create a
+series of steps between the start and end points. This parameter controls the
+number of steps along a path and therefore how discrete or smooth it is.
+
+```{r paths-steps}
+# Few steps
+sim1 <- splatSimulatePaths(params.groups, path.nSteps = 3,
+ de.prob = 0.5, de.facLoc = 0.2, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Step") + ggtitle("Few steps")
+
+# Lots of steps
+sim2 <- splatSimulatePaths(params.groups, path.nSteps = 1000,
+ de.prob = 0.5, de.facLoc = 0.2, verbose = FALSE)
+sim2 <- normalize(sim2)
+plotPCA(sim2, colour_by = "Step") + ggtitle("Lots of steps")
+```
+
+### `path.skew` - Path skew
+
+By default cells are evenly distributed along a path but it sometimes be useful
+to introduce a skew in the distribution, For example you may want to simulate
+a scenario with few stem-like cells and many differentiated cells. Setting
+`path.skew` to 0 will mean that all cells come from the end point while
+higher values up to 1 will skew them towards the start point.
+
+```{r paths-skew}
+# Skew towards the end
+sim1 <- splatSimulatePaths(params.groups, path.skew = 0.1,
+ de.prob = 0.5, de.facLoc = 0.2, verbose = FALSE)
+sim1 <- normalize(sim1)
+plotPCA(sim1, colour_by = "Step") + ggtitle("Skewed towards the end")
+```
+
+### `path.nonlinearProb` - Non-linear probability
+
+Most genes are interpolated in a linear way along a path but in reality this
+may not always be the case. For example it is easy to imagine a gene that
+is lowly-expressed at the start of a process, highly-expressed in the middle
+and lowly-expressed again at the end. The `path.nonlinearProb` parameter
+controls the probability that a gene will change in a non-linear way along a
+path.
+
+### `path.sigmaFac` - Path skew
+
+Non-linear changes along a path are achieved by building a Brownian bridge
+between the two end points. A Brownian bridge is Brownian motion controlled in
+such a way that the end points are fixed. The `path.sigmaFac` parameter controls
+how extreme each step in the Brownian motion is and therefore how much the
+interpolation differs from a linear path.
diff --git a/vignettes/splatter-logo-small.png b/vignettes/splatter-logo-small.png
index cd78c46e70f630623a5916269309b09f5f438e0b..0c606de481f139402d10d5b10dbb07394aa51260 100644
Binary files a/vignettes/splatter-logo-small.png and b/vignettes/splatter-logo-small.png differ
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index b92584956930bde9ac10e87e101235398fa40a99..f73d3a97e072dda86eba72686945538817db7bdf 100644
--- a/vignettes/splatter.Rmd
+++ b/vignettes/splatter.Rmd
@@ -84,71 +84,6 @@ types of cells or differentiation paths between different cells types where
expression changes in a continuous way. These are described further in the
[simulating counts] section.
-## Parameters
-
-The parameters required for the Splat simulation are briefly described here:
-
-* **Global parameters**
- * `nGenes` - The number of genes to simulate.
- * `nCells` - The number of cells to simulate.
- * `seed` - Seed to use for generating random numbers.
-* **Batch parameters**
- * `nBatches` - The number of batches to simulate.
- * `batchCells` - The number of cells in each batch.
- * `batch.facLoc` - Location (meanlog) parameter for the batch effects factor
- log-normal distribution.
- * `batch.facScale` - Scale (sdlog) parameter for the batch effects factor
- log-normal distribution.
-* **Mean parameters**
- * `mean.shape` - Shape parameter for the mean gamma distribution.
- * `mean.rate` - Rate parameter for the mean gamma distribution.
-* **Library size parameters**
- * `lib.loc` - Location (meanlog) parameter for the library size log-normal
- distribution, or mean for the normal distribution.
- * `lib.scale` - Scale (sdlog) parameter for the library size log-normal
- distribution, or sd for the normal distribution.
- * `lib.norm` - Whether to use a normal distribution instead of the usual
- log-normal distribution.
-* **Expression outlier parameters**
- * `out.prob` - Probability that a gene is an expression outlier.
- * `out.facLoc` - Location (meanlog) parameter for the expression outlier
- factor log-normal distribution.
- * `out.facScale` - Scale (sdlog) parameter for the expression outlier factor
- log-normal distribution.
-* **Group parameters**
- * `nGroups` - The number of groups or paths to simulate.
- * `group.prob` - The probabilities that cells come from particular groups.
-* **Differential expression parameters**
- * `de.prob` - Probability that a gene is differentially expressed in each
- group or path.
- * `de.downProb` - Probability that a differentially expressed gene is
- down-regulated.
- * `de.facLoc` - Location (meanlog) parameter for the differential expression
- factor log-normal distribution.
- * `de.facScale` - Scale (sdlog) parameter for the differential expression
- factor log-normal distribution.
-* **Biological Coefficient of Variation parameters**
- * `bcv.common` - Underlying common dispersion across all genes.
- * `bcv.df` - Degrees of Freedom for the BCV inverse chi-squared
- distribution.
-* **Dropout parameters**
- * `dropout.type` - Type of dropout to simulate.
- * `dropout.mid` - Midpoint parameter for the dropout logistic function.
- * `dropout.shape` - Shape parameter for the dropout logistic function.
-* **Differentiation path parameters**
- * `path.from` - Vector giving the originating point of each path.
- * `path.steps` - Vector giving the number of steps to simulate along each
- path.
- * `path.skew` - Vector giving the skew of each path.
- * `path.nonlinearProb` - Probability that a gene changes expression in a
- non-linear way along the differentiation path.
- * `path.sigmaFac` - Sigma factor for non-linear gene paths.
-
-While this may look like a lot of parameters Splatter attempts to make it easy
-for the user, both by providing sensible defaults and making it easy to estimate
-many of the parameters from real data. For more details on the parameters see
-`?SplatParams`.
-
# The `SplatParams` object
All the parameters for the Splat simulation are stored in a `SplatParams`
@@ -164,7 +99,8 @@ As well as telling us what type of object we have ("A `Params` object of class
some extra information. We can see which parameters can be estimated by the
`splatEstimate` function (those in parentheses), which can't be estimated
(those in brackets) and which have been changed from their default values (those
-in ALL CAPS).
+in ALL CAPS). For more details about the parameters of the Splat simulation
+refer to the [Splat parameters vignette](splat_params.html).
## Getting and setting
@@ -259,7 +195,7 @@ Looking at the output of `splatSimulate` we can see that `sim` is
`r ncol(sim)` samples (cells). The main part of this object is a features
by samples matrix containing the simulated counts (accessed using `counts`),
although it can also hold other expression measures such as FPKM or TPM.
-Additionaly a `SingleCellExperiment` contains phenotype information about
+Additionally a `SingleCellExperiment` contains phenotype information about
each cell (accessed using `colData`) and feature information about each gene
(accessed using `rowData`). Splatter uses these slots, as well as `assays`, to
store information about the intermediate values of the simulation.
@@ -347,9 +283,9 @@ sim.groups <- normalize(sim.groups)
plotPCA(sim.groups, colour_by = "Group")
```
-As we have set both the group probabilites to 0.5 we should get approximately
+As we have set both the group probabilities to 0.5 we should get approximately
equal numbers of cells in each group (around 50 in this case). If we wanted
-uneven groups we could set `group.prob` to any set of probabilites that sum to
+uneven groups we could set `group.prob` to any set of probabilities that sum to
1.
## Simulating paths
@@ -408,7 +344,7 @@ made the batch effects dominate.
Each of the Splatter simulation methods has it's own convenience function.
To simulate a single population use `splatSimulateSingle()` (equivalent to
-`splatSimulate(method = "single")`), to simulate grops use
+`splatSimulate(method = "single")`), to simulate groups use
`splatSimulateGroups()` (equivalent to `splatSimulate(method = "groups")`) or to
simulate paths use `splatSimulatePaths()` (equivalent to
`splatSimulate(method = "paths")`).
@@ -424,12 +360,6 @@ the available simulations run the `listSims()` function:
listSims()
```
-(or more conveniently for the vignette as a table)
-
-```{r listSims-table}
-knitr::kable(listSims(print = FALSE))
-```
-
Each simulation has it's own prefix which gives the name of the functions
associated with that simulation. For example the prefix for the simple
simulation is `simple` so it would store it's parameters in a `SimpleParams`