From 51db1e57667b8b9739e34d37cf70b4ac40496d80 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 13 Oct 2016 23:14:40 +1100
Subject: [PATCH] Add splatParams object
---
DESCRIPTION | 2 +-
NAMESPACE | 7 +
R/AllClasses.R | 174 +++++++++++++++++++++++--
R/AllGenerics.R | 28 +++-
R/Params-methods.R | 20 ++-
R/SplatParams-methods.R | 166 +++++++++++++++++++++++
R/params-functions.R | 5 +-
R/splat-estimate.R | 0
man/SimpleParams.Rd | 14 +-
man/SplatParams.Rd | 111 ++++++++++++++++
man/expandParams-SplatParams-method.Rd | 29 +++++
man/expandParams.Rd | 28 ++++
man/newSplatParams.Rd | 21 +++
man/setParam.Rd | 11 +-
man/setParams.Rd | 4 +-
tests/testthat/test-SplatParams.R | 7 +
16 files changed, 597 insertions(+), 30 deletions(-)
create mode 100644 R/SplatParams-methods.R
create mode 100644 R/splat-estimate.R
create mode 100644 man/SplatParams.Rd
create mode 100644 man/expandParams-SplatParams-method.Rd
create mode 100644 man/expandParams.Rd
create mode 100644 man/newSplatParams.Rd
create mode 100644 tests/testthat/test-SplatParams.R
diff --git a/DESCRIPTION b/DESCRIPTION
index 812c8ab..6dd8764 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.6.4
+Version: 0.6.5
Date: 2016-10-13
Author: Luke Zappia
Authors@R: as.person(c(
diff --git a/NAMESPACE b/NAMESPACE
index 40e112a..897a8ca 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,10 +6,17 @@ export(estimateSimpleParams)
export(getParam)
export(getParams)
export(newSimpleParams)
+export(newSplatParams)
export(setParam)
export(setParams)
export(simpleSimulate)
exportClasses(SimpleParams)
+exportClasses(SplatParams)
+importFrom(checkmate,checkFlag)
+importFrom(checkmate,checkInt)
+importFrom(checkmate,checkIntegerish)
+importFrom(checkmate,checkNumber)
+importFrom(checkmate,checkNumeric)
importFrom(scater,newSCESet)
importFrom(stats,median)
importFrom(stats,rgamma)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 7f058b5..fc595f9 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -34,18 +34,18 @@ setClass("Params",
#' The simple simulation uses the following parameters:
#'
#' \describe{
-#' \item{\code{[nGenes]}}{The number of genes to simulate.}
-#' \item{\code{[nCells]}}{The number of cells to simulate.}
-#' \item{\code{seed}}{Seed to use for generating random numbers.}
-#' \item{\code{[mean.shape]}}{The shape parameter for the mean gamma
+#' \item{\code{nGenes}}{The number of genes to simulate.}
+#' \item{\code{nCells}}{The number of cells to simulate.}
+#' \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#' \item{\code{mean.shape}}{The shape parameter for the mean gamma
#' distribution.}
-#' \item{\code{[mean.rate]}}{The rate parameter for the mean gamma
+#' \item{\code{mean.rate}}{The rate parameter for the mean gamma
#' distribution.}
-#' \item{\code{count.disp}}{The dispersion parameter for the counts negative
+#' \item{\code{[count.disp]}}{The dispersion parameter for the counts negative
#' binomial distribution.}
#' }
#'
-#' The parameters shown in brackets can be estimated from real data using
+#' The parameters not shown in brackets can be estimated from real data using
#' \code{\link{estimateSimpleParams}}. For details of the simple simulation
#' see \code{\link{simpleSimulate}}.
#'
@@ -59,4 +59,162 @@ setClass("SimpleParams",
mean.rate = "numeric",
count.disp = "numeric"),
prototype = prototype(mean.shape = 0.4, mean.rate = 0.3,
- count.disp = 0.1))
\ No newline at end of file
+ count.disp = 0.1))
+
+#' The SplatParams class
+#'
+#' S4 class that holds parameters for the Splatter simulation.
+#'
+#' @section Parameters:
+#'
+#' The Splatter simulation requires the following parameters:
+#'
+#' \describe{
+#' \item{\code{nGenes}}{The number of genes to simulate.}
+#' \item{\code{nCells}}{The number of cells to simulate.}
+#' \item{\code{[groupCells]}}{Vector giving the number of cells in each
+#' simulation group/path.}
+#' \item{\code{[seed]}}{Seed to use for generating random numbers.}
+#' \item{\emph{Mean parameters}}{
+#' \describe{
+#' \item{\code{mean.shape}}{Shape parameter for the mean gamma
+#' distribution.}
+#' \item{\code{mean.rate}}{Rate parameter for the mean gamma
+#' distribution.}
+#' }
+#' }
+#' \item{\emph{Library size parameters}}{
+#' \describe{
+#' \item{\code{lib.loc}}{Location (meanlog) parameter for the library
+#' size log-normal distribution.}
+#' \item{\code{lib.scale}}{Scale (sdlog) parameter for the library size
+#' log-normal distribution.}
+#' }
+#' }
+#' \item{\emph{Expression outlier parameters}}{
+#' \describe{
+#' \item{\code{out.prob}}{Probability that a gene is an expression
+#' outlier.}
+#' \item{\code{out.loProb}}{Probability that an expression outlier gene
+#' is lowly expressed.}
+#' \item{\code{out.facLoc}}{Location (meanlog) parameter for the
+#' expression outlier factor log-normal distribution.}
+#' \item{\code{out.facScale}}{Scale (sdlog) parameter for the expression
+#' outlier factor log-normal distribution.}
+#' }
+#' }
+#' \item{\emph{Differential expression parameters}}{
+#' \describe{
+#' \item{\code{[de.prob]}}{Probability that a gene is differentially
+#' expressed in a group. Can be a vector.}
+#' \item{\code{[de.loProb]}}{Probability that differentially expressed
+#' gene is down-regulated. Can be a vector.}
+#' \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
+#' differential expression factor log-normal distribution. Can be a
+#' vector.}
+#' \item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
+#' differential expression factor log-normal distribution. Can be a
+#' vector.}
+#' }
+#' }
+#' \item{\emph{Biological Coefficient of Variation parameters}}{
+#' \describe{
+#' \item{\code{bcv.common}}{Underlying common dispersion across all
+#' genes.}
+#' \item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse chi-squared
+#' distribution.}
+#' }
+#' }
+#' \item{\emph{Dropout parameters}}{
+#' \describe{
+#' \item{\code{dropout.present}}{Logical. Whether to simulate dropout.}
+#' \item{\code{dropout.mid}}{Midpoint parameter for the dropout logistic
+#' function.}
+#' \item{\code{dropout.shape}}{Shape parameter for the dropout logistic
+#' function.}
+#' }
+#' }
+#' \item{\emph{Differentiation path parameters}}{
+#' \describe{
+#' \item{\code{[path.from]}}{Vector giving the originating point of each
+#' path. This allows path structure such as a cell type which
+#' differentiates into an intermediate cell type that then differentiates
+#' into two mature cell types. A path structure of this form would have a
+#' "from" parameter of c(0, 1, 1) (where 0 is the origin). If no vector is
+#' given all paths will start at the origin.}
+#' \item{\code{[path.length]}}{Vector giving the number of steps to
+#' simulate along each path. If a single value is given it will be applied
+#' to all paths.}
+#' \item{\code{[path.skew]}}{Vector giving the skew of each path. Values
+#' closer to 1 will give more cells towards the starting population,
+#' values closer to 0 will give more cells towards the final population.
+#' If a single value is given it will be applied to all paths.}
+#' \item{\code{[path.nonlinearProb]}}{Probability that a gene follows a
+#' non-linear path along the differentiation path. This allows more
+#' complex gene patterns such as a gene being equally expressed at the
+#' beginning an end of a path but lowly expressed in the middle.}
+#' \item{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene paths.
+#' A higher value will result in more extreme non-linear variations along
+#' a path.}
+#' }
+#' }
+#' }
+#'
+#' The parameters not shown in brackets can be estimated from real data using
+#' \code{\link{estimateSplatParams}}. For details of the Splatter simulation
+#' see \code{\link{splatSimulate}}.
+#'
+#' @name SplatParams
+#' @rdname SplatParams
+#' @aliases SplatParams-class
+#' @exportClass SplatParams
+setClass("SplatParams",
+ contains = "Params",
+ slots = c(nGroups = "numeric",
+ groupCells = "numeric",
+ mean.shape = "numeric",
+ mean.rate = "numeric",
+ lib.loc = "numeric",
+ lib.scale = "numeric",
+ out.prob = "numeric",
+ out.loProb = "numeric",
+ out.facLoc = "numeric",
+ out.facScale = "numeric",
+ de.prob = "numeric",
+ de.downProb = "numeric",
+ de.facLoc = "numeric",
+ de.facScale = "numeric",
+ bcv.common = "numeric",
+ bcv.df = "numeric",
+ dropout.present = "logical",
+ dropout.mid = "numeric",
+ dropout.shape = "numeric",
+ path.from = "numeric",
+ path.length = "numeric",
+ path.skew = "numeric",
+ path.nonlinearProb = "numeric",
+ path.sigmaFac = "numeric"),
+ prototype = prototype(nGroups = 1,
+ groupCells = 100,
+ mean.rate = 0.3,
+ mean.shape = 0.4,
+ lib.loc = 10,
+ lib.scale = 0.5,
+ out.prob = 0.1,
+ out.loProb = 0.5,
+ out.facLoc = 4,
+ out.facScale = 1,
+ de.prob = 0.1,
+ de.downProb = 0.5,
+ de.facLoc = 4,
+ de.facScale = 1,
+ bcv.common = 0.1,
+ bcv.df = 25,
+ dropout.present = TRUE,
+ dropout.mid = 0,
+ dropout.shape = -1,
+ path.from = 0,
+ path.length = 100,
+ path.skew = 0.5,
+ path.nonlinearProb = 0.1,
+ path.sigmaFac = 0.8))
\ No newline at end of file
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 00639fd..ca77aea 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -18,16 +18,32 @@ 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 checkValid logical. Check object is valid after setting.
#'
#' @return Object with new parameter value.
#'
#' @rdname setParam
#' @export
setGeneric("setParam",
- function(object, name, value) {standardGeneric("setParam")})
+ function(object, name, value, checkValid) {
+ standardGeneric("setParam")
+})
-#' #@name arrange
-#' #@rdname arrange
-#' #@docType methods
-#' #@export
-#setGeneric("expandParams", function(object) {standardGeneric("expandParams")})
\ No newline at end of file
+#' Expand parameters
+#'
+#' Expand the parameters that can be vectors so that they are the same length as
+#' the number of groups.
+#'
+#' @param object splatParams object to expand.
+#' @param ... additional arguments.
+#'
+#' @return Expanded splatParams object.
+#' @examples
+#' params <- newSplatParams()
+#' params <- setParams(params, groupCells = c(10, 10))
+#' params
+#' params <- expandParams(params)
+#' params
+setGeneric("expandParams", function(object, ...) {
+ standardGeneric("expandParams")
+})
\ No newline at end of file
diff --git a/R/Params-methods.R b/R/Params-methods.R
index 558da5d..3f0796f 100644
--- a/R/Params-methods.R
+++ b/R/Params-methods.R
@@ -4,10 +4,11 @@ setMethod("getParam", "Params", function(object, name) {
})
#' @rdname setParam
-setMethod("setParam", "Params", function(object, name, value) {
+setMethod("setParam", "Params",
+ function(object, name, value, checkValid = TRUE) {
checkmate::assertString(name)
slot(object, name) <- value
- validObject(object)
+ if (checkValid) {validObject(object)}
return(object)
})
@@ -22,4 +23,19 @@ setMethod("show", "Params", function(object) {
"'Default' or 'NOT DEFAULT'", "\n\n")
showPP(object, pp)
cat(length(slotNames(object)) - 3, "additional parameters", "\n\n")
+})
+
+setMethod("expandParams", "Params", function(object, vectors, n) {
+
+ update <- list()
+ for (parameter in vectors) {
+ value <- getParam(object, parameter)
+ if (length(value) == 1) {
+ update[[parameter]] <- rep(value, n)
+ }
+ }
+
+ object <- setParams(object, update, checkValid = FALSE)
+
+ return(object)
})
\ No newline at end of file
diff --git a/R/SplatParams-methods.R b/R/SplatParams-methods.R
new file mode 100644
index 0000000..a3f1268
--- /dev/null
+++ b/R/SplatParams-methods.R
@@ -0,0 +1,166 @@
+#' New SplatParams
+#'
+#' Create a new SplatParams object.
+#'
+#' @param ... additional parameters passed to \code{\link{setParams}}.
+#'
+#' @return SplatParams object.
+#' @examples
+#' params <- newSplatParams()
+#' @export
+newSplatParams <- function(...) {
+
+ params <- new("SplatParams")
+ params <- setParams(params, ...)
+
+ return(params)
+}
+
+#' @importFrom checkmate checkInt checkIntegerish checkNumber checkNumeric
+#' checkFlag
+setValidity("SplatParams", function(object) {
+
+ object <- expandParams(object)
+ v <- getParams(object, c(slotNames(object)))
+
+ nGroups <- v$nGroups
+ checks <- c(nGenes = checkInt(v$nGenes, lower = 1),
+ nCells = checkInt(v$nCells, lower = 1),
+ nGroups = checkInt(v$nGroups, lower = 1),
+ groupCells = checkIntegerish(v$groupCells, lower = 1,
+ len = nGroups),
+ mean.rate = checkNumber(v$mean.rate, lower = 0),
+ mean.shape = checkNumber(v$mean.shape, lower = 0),
+ lib.loc = checkNumber(v$lib.loc),
+ lib.scale = checkNumber(v$lib.scale, lower = 0),
+ out.prob = checkNumber(v$out.prob, lower = 0, upper = 1),
+ out.loProb = checkNumber(v$out.loProb, lower = 0, upper = 1),
+ out.facLoc = checkNumber(v$lib.loc),
+ out.facScale = checkNumber(v$lib.scale, lower = 0),
+ out.prob = checkNumber(v$out.prob, lower = 0, upper = 1),
+ out.loProb = checkNumber(v$out.loProb, lower = 0, upper = 1),
+ out.facLoc = checkNumber(v$out.facLoc),
+ out.facScale = checkNumber(v$out.facScale, lower = 0),
+ de.prob = checkNumeric(v$de.prob, lower = 0, upper = 1,
+ len = nGroups),
+ de.downProb = checkNumeric(v$de.downProb, lower = 0, upper = 1,
+ len = nGroups),
+ de.facLoc = checkNumeric(v$de.facLoc, len = nGroups),
+ de.facScale = checkNumeric(v$de.facScale, lower = 0,
+ len = nGroups),
+ bcv.common = checkNumber(v$bcv.common, lower = 0),
+ bcv.df = checkNumber(v$bcv.df, lower = 0),
+ dropout.present = checkFlag(v$dropout.present),
+ dropout.mid = checkNumber(v$dropout.mid),
+ dropout.shape = checkNumber(v$dropout.shape),
+ path.from = checkIntegerish(v$path.from, lower = 0,
+ upper = nGroups, len = nGroups),
+ path.length = checkIntegerish(v$path.length, lower = 1,
+ len = nGroups),
+ path.skew = checkNumeric(v$path.skew, lower = 0, upper = 1,
+ len = nGroups),
+ path.nonlinearProb = checkNumber(v$path.nonlinearProb,
+ lower = 0, upper = 1),
+ path.sigmaFac = checkNumber(v$path.sigmaFac, lower = 0),
+ seed = checkInt(v$seed, lower = 0))
+
+ # Check groupCells matches nCells, nGroups
+ if (v$nCells != sum(v$groupCells) || nGroups != length(v$groupCells)) {
+ checks <- c(checks,
+ "nCells, nGroups and groupCells are not consistent")
+ }
+
+ # Check path.from
+ if (!(0 %in% v$path.from)) {
+ checks <- c(checks, path.from = "origin must be specified in path.from")
+ } else if (any(v$path.from == 1:nGroups)) {
+ checks <- c(checks, stop("path cannot begin at itself"))
+ }
+
+ if (all(checks == TRUE)) {
+ valid <- TRUE
+ } else {
+ valid <- checks[checks != TRUE]
+ valid <- paste(names(valid), valid, sep = ": ")
+ }
+
+ return(valid)
+})
+
+#' @rdname setParam
+setMethod("setParam", "SplatParams",
+ function(object, name, value, checkValid) {
+ checkmate::assertString(name)
+
+ if (name == "nCells" || name == "nGroups") {
+ stop(name, " cannot be set directly, set groupCells instead")
+ }
+
+ if (name == "groupCells") {
+ object <- callNextMethod(object, "nCells", sum(value), checkValid)
+ object <- callNextMethod(object, "nGroups", length(value), checkValid)
+ }
+
+ object <- callNextMethod()
+
+ return(object)
+})
+
+setMethod("show", "SplatParams", function(object) {
+
+ pp <- list("Global:" = c("[Groups]" = "nGroups",
+ "[Group Cells]" = "groupCells"),
+ "Mean:" = c("(Rate)" = "mean.rate",
+ "(Shape)" = "mean.shape"),
+ "Library size:" = c("(Location)" = "lib.loc",
+ "(Scale)" = "lib.scale"),
+ "Exprs outliers:" = c("(Probability)" = "out.prob",
+ "(Lo Prob)" = "out.loProb",
+ "(Location)" = "out.facLoc",
+ "(Scale)" = "out.facScale"),
+ "Diff expr:" = c("[Probability]" = "de.prob",
+ "[Down Prob]" = "de.downProb",
+ "[Location]" = "de.facLoc",
+ "[Scale]" = "de.facScale"),
+ "BCV:" = c("(Common Disp)" = "bcv.common",
+ "(DoF)" = "bcv.df"),
+ "Dropout:" = c("(Present T/F)" = "dropout.present",
+ "(Midpoint)" = "dropout.mid",
+ "(Shape)" = "dropout.shape"),
+ "Paths:" = c("[From]" = "path.from",
+ "[Length]" = "path.length",
+ "[Skew]" = "path.skew",
+ "[Non-linear]" = "path.nonlinearProb",
+ "[Sigma Factor]" = "path.sigmaFac"))
+
+ callNextMethod()
+ showPP(object, pp)
+})
+
+#' Expand parameters
+#'
+#' Expand the parameters that can be vectors so that they are the same length as
+#' the number of groups.
+#'
+#' @param object splatParams object to expand.
+#'
+#' @return Expanded splatParams object.
+#' @examples
+#' \dontrun{
+#' params <- newSplatParams()
+#' params <- setParams(params, groupCells = c(10, 10))
+#' params
+#' params <- expandParams(params)
+#' params
+#' }
+setMethod("expandParams", "SplatParams", function(object) {
+
+ n <- getParam(object, "nGroups")
+
+ vectors <- c("de.prob", "de.downProb", "de.facLoc", "de.facScale",
+ "path.from", "path.length", "path.skew")
+
+ object <- callNextMethod(object, vectors, n)
+
+ return(object)
+})
\ No newline at end of file
diff --git a/R/params-functions.R b/R/params-functions.R
index c795020..f93e8d1 100644
--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -27,6 +27,7 @@ getParams <- function(params, names) {
#' names of the parameters to set and the items in the list are values.
#' @param ... additional parameters to set. These are combined with any
#' parameters specified in \code{update}.
+#' @param checkValid logical. Whether to check set object is valid.
#'
#' @details
#' Each parameter is set by a call to \code{\link{setParam}}. If the same
@@ -46,7 +47,7 @@ getParams <- function(params, names) {
#' params <- setParams(params, list(mean.rate = 0.2, mean.shape = 0.8))
#' params
#' @export
-setParams <- function(params, update = NULL, ...) {
+setParams <- function(params, update = NULL, checkValid = TRUE, ...) {
checkmate::assertClass(params, classes = "Params")
checkmate::assertList(update, null.ok = TRUE)
@@ -56,7 +57,7 @@ setParams <- function(params, update = NULL, ...) {
if (length(update) > 0) {
for (name in names(update)) {
value <- update[[name]]
- params <- setParam(params, name, value)
+ params <- setParam(params, name, value, checkValid)
}
}
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
new file mode 100644
index 0000000..e69de29
diff --git a/man/SimpleParams.Rd b/man/SimpleParams.Rd
index 249888b..787073e 100644
--- a/man/SimpleParams.Rd
+++ b/man/SimpleParams.Rd
@@ -14,18 +14,18 @@ S4 class that holds parameters for the simple simulation.
The simple simulation uses the following parameters:
\describe{
- \item{\code{[nGenes]}}{The number of genes to simulate.}
- \item{\code{[nCells]}}{The number of cells to simulate.}
- \item{\code{seed}}{Seed to use for generating random numbers.}
- \item{\code{[mean.shape]}}{The shape parameter for the mean gamma
+ \item{\code{nGenes}}{The number of genes to simulate.}
+ \item{\code{nCells}}{The number of cells to simulate.}
+ \item{\code{[seed]}}{Seed to use for generating random numbers.}
+ \item{\code{mean.shape}}{The shape parameter for the mean gamma
distribution.}
- \item{\code{[mean.rate]}}{The rate parameter for the mean gamma
+ \item{\code{mean.rate}}{The rate parameter for the mean gamma
distribution.}
- \item{\code{count.disp}}{The dispersion parameter for the counts negative
+ \item{\code{[count.disp]}}{The dispersion parameter for the counts negative
binomial distribution.}
}
-The parameters shown in brackets can be estimated from real data using
+The parameters not shown in brackets can be estimated from real data using
\code{\link{estimateSimpleParams}}. For details of the simple simulation
see \code{\link{simpleSimulate}}.
}
diff --git a/man/SplatParams.Rd b/man/SplatParams.Rd
new file mode 100644
index 0000000..b27e11c
--- /dev/null
+++ b/man/SplatParams.Rd
@@ -0,0 +1,111 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R
+\docType{class}
+\name{SplatParams}
+\alias{SplatParams}
+\alias{SplatParams-class}
+\title{The SplatParams class}
+\description{
+S4 class that holds parameters for the Splatter simulation.
+}
+\section{Parameters}{
+
+
+The Splatter simulation requires the following parameters:
+
+\describe{
+ \item{\code{nGenes}}{The number of genes to simulate.}
+ \item{\code{nCells}}{The number of cells to simulate.}
+ \item{\code{[groupCells]}}{Vector giving the number of cells in each
+ simulation group/path.}
+ \item{\code{[seed]}}{Seed to use for generating random numbers.}
+ \item{\emph{Mean parameters}}{
+ \describe{
+ \item{\code{mean.shape}}{Shape parameter for the mean gamma
+ distribution.}
+ \item{\code{mean.rate}}{Rate parameter for the mean gamma
+ distribution.}
+ }
+ }
+ \item{\emph{Library size parameters}}{
+ \describe{
+ \item{\code{lib.loc}}{Location (meanlog) parameter for the library
+ size log-normal distribution.}
+ \item{\code{lib.scale}}{Scale (sdlog) parameter for the library size
+ log-normal distribution.}
+ }
+ }
+ \item{\emph{Expression outlier parameters}}{
+ \describe{
+ \item{\code{out.prob}}{Probability that a gene is an expression
+ outlier.}
+ \item{\code{out.loProb}}{Probability that an expression outlier gene
+ is lowly expressed.}
+ \item{\code{out.facLoc}}{Location (meanlog) parameter for the
+ expression outlier factor log-normal distribution.}
+ \item{\code{out.facScale}}{Scale (sdlog) parameter for the expression
+ outlier factor log-normal distribution.}
+ }
+ }
+ \item{\emph{Differential expression parameters}}{
+ \describe{
+ \item{\code{[de.prob]}}{Probability that a gene is differentially
+ expressed in a group. Can be a vector.}
+ \item{\code{[de.loProb]}}{Probability that differentially expressed
+ gene is down-regulated. Can be a vector.}
+ \item{\code{[de.facLoc]}}{Location (meanlog) parameter for the
+ differential expression factor log-normal distribution. Can be a
+ vector.}
+ \item{\code{[de.facScale]}}{Scale (sdlog) parameter for the
+ differential expression factor log-normal distribution. Can be a
+ vector.}
+ }
+ }
+ \item{\emph{Biological Coefficient of Variation parameters}}{
+ \describe{
+ \item{\code{bcv.common}}{Underlying common dispersion across all
+ genes.}
+ \item{\code{bcv.df}}{Degrees of Freedom for the BCV inverse chi-squared
+ distribution.}
+ }
+ }
+ \item{\emph{Dropout parameters}}{
+ \describe{
+ \item{\code{dropout.present}}{Logical. Whether to simulate dropout.}
+ \item{\code{dropout.mid}}{Midpoint parameter for the dropout logistic
+ function.}
+ \item{\code{dropout.shape}}{Shape parameter for the dropout logistic
+ function.}
+ }
+ }
+ \item{\emph{Differentiation path parameters}}{
+ \describe{
+ \item{\code{[path.from]}}{Vector giving the originating point of each
+ path. This allows path structure such as a cell type which
+ differentiates into an intermediate cell type that then differentiates
+ into two mature cell types. A path structure of this form would have a
+ "from" parameter of c(0, 1, 1) (where 0 is the origin). If no vector is
+ given all paths will start at the origin.}
+ \item{\code{[path.length]}}{Vector giving the number of steps to
+ simulate along each path. If a single value is given it will be applied
+ to all paths.}
+ \item{\code{[path.skew]}}{Vector giving the skew of each path. Values
+ closer to 1 will give more cells towards the starting population,
+ values closer to 0 will give more cells towards the final population.
+ If a single value is given it will be applied to all paths.}
+ \item{\code{[path.nonlinearProb]}}{Probability that a gene follows a
+ non-linear path along the differentiation path. This allows more
+ complex gene patterns such as a gene being equally expressed at the
+ beginning an end of a path but lowly expressed in the middle.}
+ \item{\code{[path.sigmaFac]}}{Sigma factor for non-linear gene paths.
+ A higher value will result in more extreme non-linear variations along
+ a path.}
+ }
+ }
+}
+
+The parameters not shown in brackets can be estimated from real data using
+\code{\link{estimateSplatParams}}. For details of the Splatter simulation
+see \code{\link{splatSimulate}}.
+}
+
diff --git a/man/expandParams-SplatParams-method.Rd b/man/expandParams-SplatParams-method.Rd
new file mode 100644
index 0000000..aab93c5
--- /dev/null
+++ b/man/expandParams-SplatParams-method.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SplatParams-methods.R
+\docType{methods}
+\name{expandParams,SplatParams-method}
+\alias{expandParams,SplatParams-method}
+\title{Expand parameters}
+\usage{
+\S4method{expandParams}{SplatParams}(object)
+}
+\arguments{
+\item{object}{splatParams object to expand.}
+}
+\value{
+Expanded splatParams object.
+}
+\description{
+Expand the parameters that can be vectors so that they are the same length as
+the number of groups.
+}
+\examples{
+\dontrun{
+params <- newSplatParams()
+params <- setParams(params, groupCells = c(10, 10))
+params
+params <- expandParams(params)
+params
+}
+}
+
diff --git a/man/expandParams.Rd b/man/expandParams.Rd
new file mode 100644
index 0000000..0d4c83b
--- /dev/null
+++ b/man/expandParams.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllGenerics.R
+\name{expandParams}
+\alias{expandParams}
+\title{Expand parameters}
+\usage{
+expandParams(object, ...)
+}
+\arguments{
+\item{object}{splatParams object to expand.}
+
+\item{...}{additional arguments.}
+}
+\value{
+Expanded splatParams object.
+}
+\description{
+Expand the parameters that can be vectors so that they are the same length as
+the number of groups.
+}
+\examples{
+params <- newSplatParams()
+params <- setParams(params, groupCells = c(10, 10))
+params
+params <- expandParams(params)
+params
+}
+
diff --git a/man/newSplatParams.Rd b/man/newSplatParams.Rd
new file mode 100644
index 0000000..9ce99b1
--- /dev/null
+++ b/man/newSplatParams.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SplatParams-methods.R
+\name{newSplatParams}
+\alias{newSplatParams}
+\title{New SplatParams}
+\usage{
+newSplatParams(...)
+}
+\arguments{
+\item{...}{additional parameters passed to \code{\link{setParams}}.}
+}
+\value{
+SplatParams object.
+}
+\description{
+Create a new SplatParams object.
+}
+\examples{
+params <- newSplatParams()
+}
+
diff --git a/man/setParam.Rd b/man/setParam.Rd
index 564ef91..b2418db 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -1,14 +1,17 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/AllGenerics.R, R/Params-methods.R
+% Please edit documentation in R/AllGenerics.R, R/Params-methods.R, R/SplatParams-methods.R
\docType{methods}
\name{setParam}
\alias{setParam}
\alias{setParam,Params-method}
+\alias{setParam,SplatParams-method}
\title{Set a parameter}
\usage{
-setParam(object, name, value)
+setParam(object, name, value, checkValid)
-\S4method{setParam}{Params}(object, name, value)
+\S4method{setParam}{Params}(object, name, value, checkValid = TRUE)
+
+\S4method{setParam}{SplatParams}(object, name, value, checkValid)
}
\arguments{
\item{object}{object to set parameter in.}
@@ -16,6 +19,8 @@ setParam(object, name, value)
\item{name}{name of the parameter to set.}
\item{value}{value to set the paramter to.}
+
+\item{checkValid}{logical. Check object is valid after setting.}
}
\value{
Object with new parameter value.
diff --git a/man/setParams.Rd b/man/setParams.Rd
index a3843db..05e8955 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -4,7 +4,7 @@
\alias{setParams}
\title{Set parameters}
\usage{
-setParams(params, update = NULL, ...)
+setParams(params, update = NULL, checkValid = TRUE, ...)
}
\arguments{
\item{params}{Params object to set parameters in.}
@@ -12,6 +12,8 @@ setParams(params, update = NULL, ...)
\item{update}{list of parameters to set where \code{names(update)} are the
names of the parameters to set and the items in the list are values.}
+\item{checkValid}{logical. Whether to check set object is valid.}
+
\item{...}{additional parameters to set. These are combined with any
parameters specified in \code{update}.}
}
diff --git a/tests/testthat/test-SplatParams.R b/tests/testthat/test-SplatParams.R
new file mode 100644
index 0000000..e524067
--- /dev/null
+++ b/tests/testthat/test-SplatParams.R
@@ -0,0 +1,7 @@
+context("SplatParams")
+
+test_that("nGroups checks work", {
+ params <- newSplatParams()
+ expect_error(setParam(params, "nCells", 1),
+ "nCells cannot be set directly, set groupCells instead")
+})
--
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