From fbf8f8ecb1da6e66b4ca91c99a46b20e14ab9e01 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 16 Jul 2019 14:28:14 +1000
Subject: [PATCH] Add mean parameters
---
DESCRIPTION | 4 +-
NAMESPACE | 4 ++
NEWS.md | 4 ++
R/AllClasses.R | 34 +++++++++---
R/SplotchParams-methods.R | 108 ++++++++++++++++++++++++++++++++++----
R/params-functions.R | 6 ++-
R/splotch-simulate.R | 100 +++++++++++++++++++++++++++++++++++
man/SplatParams.Rd | 6 +--
man/SplotchParams.Rd | 18 ++++++-
man/newParams.Rd | 6 ++-
man/setParam.Rd | 5 +-
man/setParams.Rd | 5 +-
man/showValues.Rd | 4 +-
man/splotchSimulate.Rd | 29 ++++++++++
14 files changed, 303 insertions(+), 30 deletions(-)
create mode 100644 R/splotch-simulate.R
create mode 100644 man/splotchSimulate.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index 8cd1713..39cff9a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.2.9000
-Date: 2019-07-11
+Version: 1.9.2.9001
+Date: 2019-07-16
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NAMESPACE b/NAMESPACE
index c9b65bd..afefae4 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -47,6 +47,7 @@ export(newSCDDParams)
export(newSimpleParams)
export(newSparseDCParams)
export(newSplatParams)
+export(newSplotchParams)
export(newZINBParams)
export(phenoEstimate)
export(phenoSimulate)
@@ -63,6 +64,7 @@ export(splatSimulate)
export(splatSimulateGroups)
export(splatSimulatePaths)
export(splatSimulateSingle)
+export(splotchSimulate)
export(summariseDiff)
export(zinbEstimate)
export(zinbSimulate)
@@ -75,6 +77,7 @@ exportClasses(SCDDParams)
exportClasses(SimpleParams)
exportClasses(SparseDCParams)
exportClasses(SplatParams)
+exportClasses(SplotchParams)
exportClasses(ZINBParams)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
@@ -125,6 +128,7 @@ importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,new)
+importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
diff --git a/NEWS.md b/NEWS.md
index d932de8..b1ae280 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+### Version 1.9.2.9001 (2019-07-16)
+
+* Add mean parameters
+
### Version 1.9.2.9000 (2019-07-11)
* Add SplotchParams object
diff --git a/R/AllClasses.R b/R/AllClasses.R
index a251d3f..d208885 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -267,8 +267,22 @@ setClass("SplatParams",
#' \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{[network.graph]}}{Graph containing the gene network.}
-#' \item{\code{[network.nRegs]}}{Number of regulators in a the network.}
+#' \item{\emph{Mean parameters}}{
+#' \describe{
+#' \item{\code{mean.shape}}{Shape parameter for the mean gamma
+#' distribution.}
+#' \item{\code{mean.rate}}{Rate parameter for the mean gamma
+#' distribution.}
+#' \item{\code{mean.values}}{Vector of means for each gene.}
+#' }
+#' }
+#' \item{\emph{Network parameters}}{
+#' \describe{
+#' \item{\code{[network.graph]}}{Graph containing the gene network.}
+#' \item{\code{[network.nRegs]}}{Number of regulators in the
+#' network.}
+#' }
+#' }
#' }
#'
#' The parameters not shown in brackets can be estimated from real data using
@@ -281,10 +295,18 @@ setClass("SplatParams",
#' @exportClass SplotchParams
setClass("SplotchParams",
contains = "Params",
- slots = c(network.graph = "ANY",
- network.nRegs = "numeric"),
- prototype = prototype(network.graph = NULL,
- network.nRegs = 100))
+ slots = c(mean.shape = "numeric",
+ mean.rate = "numeric",
+ mean.values = "numeric",
+ network.graph = "ANY",
+ network.nRegs = "numeric",
+ network.regsSet = "logical"),
+ prototype = prototype(mean.rate = 0.3,
+ mean.shape = 0.6,
+ mean.values = numeric(),
+ network.graph = NULL,
+ network.nRegs = 100,
+ network.regsSet = FALSE))
#' The LunParams class
#'
diff --git a/R/SplotchParams-methods.R b/R/SplotchParams-methods.R
index b5373f1..9727e82 100644
--- a/R/SplotchParams-methods.R
+++ b/R/SplotchParams-methods.R
@@ -17,13 +17,27 @@ setValidity("SplotchParams", function(object) {
v <- getParams(object, slotNames(object))
- checks <- c(nGenes = checkmate::checkInt(v$nGenes, lower = 1),
+ checks <- c(#nGenes = checkmate::checkInt(v$nGenes, lower = 1),
nCells = checkmate::checkInt(v$nCells, lower = 1),
seed = checkmate::checkInt(v$seed, lower = 0),
+ mean.rate = checkmate::checkNumber(v$mean.rate, lower = 0),
+ mean.shape = checkmate::checkNumber(v$mean.shape, lower = 0),
network.graph = checkmate::checkClass(v$network, "igraph",
null.ok = TRUE),
network.nRegs = checkmate::checkInt(v$network.nRegs,
- lower = 0))
+ lower = 0),
+ network.regsSet = checkmate::checkFlag(v$network.regsSet))
+
+ if (checkmate::testNumeric(v$mean.values, len = 0)) {
+ checks <- c(checks, mean.values = TRUE)
+ } else {
+ checks <- c(checks,
+ mean.values = checkmate::checkNumeric(v$mean.values,
+ lower = 0,
+ finite = TRUE,
+ any.missing = FALSE,
+ len = v$nGenes))
+ }
if (all(checks == TRUE)) {
valid <- TRUE
@@ -35,13 +49,21 @@ setValidity("SplotchParams", function(object) {
return(valid)
})
+#' @importFrom methods show
setMethod("show", "SplotchParams", function(object) {
- pp.network <- list("Network:" = c("[Graph]" = "network.graph",
- "[nRegs]" = "network.nRegs"))
+ pp.top <- list("Mean:" = c("(Rate)" = "mean.rate",
+ "(Shape)" = "mean.shape",
+ "[Values]" = "mean.values"))
+
+ pp.network <- list("Network:" = c("[Graph]" = "network.graph",
+ "[nRegs]" = "network.nRegs",
+ "[regsSet]" = "network.regsSet"))
callNextMethod()
+ showPP(object, pp.top)
+
network.graph <- getParam(object, "network.graph")
if (is.null(network.graph)) {
showPP(object, pp.network)
@@ -53,14 +75,80 @@ setMethod("show", "SplotchParams", function(object) {
igraph::gsize(network.graph), "edges\n"
))))
show(network.graph)
- network.nRegs <- getParam(object, "network.nRegs")
- names(network.nRegs) <- c("[nRegs]")
- if (network.nRegs == 100) {
- showValues(network.nRegs, FALSE)
+ network.values <- list("[nRegs]" = getParam(object, "network.nRegs"),
+ "[regsSet]" = getParam(object,
+ "network.regsSet"))
+ network.default <- c(network.values$`[nRegs]` != 100,
+ network.values$`[regsSet]` != FALSE)
+ showValues(network.values, network.default)
+ }
+})
+
+#' @rdname setParam
+setMethod("setParam", "SplotchParams", function(object, name, value) {
+ checkmate::assertString(name)
+
+ if (name == "nGenes") {
+ if (!is.null(getParam(object, "network.graph"))) {
+ stop("nGenes can not be changed once network.graph is set")
+ }
+ if (!length(getParam(object, "mean.values")) == 0) {
+ stop("nGenes can not be changed once mean.values is set")
+ }
+ }
+
+ if (name == "mean.values") {
+ if (!is.null(getParam(object, "network.graph"))) {
+ if (length(value) != getParam(object, "nGenes")) {
+ stop("new mean.values does not match the number of genes in ",
+ "the network")
+ }
} else {
- showValues(network.nRegs, TRUE)
+ object <- setParam(object, "nGenes", length(value))
}
}
- # showPP(object, pp)
+ if (name == "network.graph") {
+ checkmate::assertClass(value, "igraph")
+ object <- setParamUnchecked(object, "nGenes", igraph::gorder(value))
+ if (!(length(getParam(object, "mean.values")) == 0)) {
+ warning("changing network.graph resets mean.values")
+ object <- setParam(object, "mean.values", numeric())
+ }
+
+ if ("IsReg" %in% igraph::vertex_attr_names(value)) {
+ isReg <- igraph::vertex_attr(value, "IsReg")
+ checkmate::assertLogical(isReg, any.missing = FALSE)
+ object <- setParamUnchecked(object, "network.nRegs", sum(isReg))
+ object <- setParamUnchecked(object, "network.regsSet", TRUE)
+ } else {
+ object <- setParamUnchecked(object, "network.regsSet", FALSE)
+ }
+ }
+
+ if (name == "network.nRegs" && getParam(object, "network.regsSet")) {
+ stop("network.nRegs can not be changed after regulators are set")
+ }
+
+ if (name == "network.regsSet") {
+ stop("network.regsSet can not be set manually")
+ }
+
+ object <- callNextMethod()
+
+ return(object)
+})
+
+#' @rdname setParams
+setMethod("setParams", "SplotchParams", function(object, update = NULL, ...) {
+
+ checkmate::assertList(update, null.ok = TRUE)
+
+ update <- c(update, list(...))
+
+ update <- bringItemsForward(update, c("network.graph"))
+
+ object <- callNextMethod(object, update)
+
+ return(object)
})
diff --git a/R/params-functions.R b/R/params-functions.R
index 316c15a..c969ba8 100644
--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -76,8 +76,10 @@ showPP <- function(params, pp) {
not.default <- sapply(seq_along(values), function(i) {
!identical(values[i], default.values[i])
})
- null.values <- sapply(values, is.null)
- values[null.values] <- "Not set"
+ empty.values <- sapply(values, function(x) {
+ is.null(x) || length(x) == 0
+ })
+ values[empty.values] <- "Not set"
cat(crayon::bold(category), "\n")
if (sum(!is.df) > 0) {
diff --git a/R/splotch-simulate.R b/R/splotch-simulate.R
new file mode 100644
index 0000000..4a7c5eb
--- /dev/null
+++ b/R/splotch-simulate.R
@@ -0,0 +1,100 @@
+#' Splotch simulation
+#'
+#' Simulate counts from...
+#'
+#' @param params SplotchParams object containing simulation parameters.
+#' @param verbose logical. Whether to print progress messages
+#' @param ... any additional parameter settings to override what is provided in
+#' \code{params}.
+#'
+#' @details
+#' Details...
+#'
+#' @return SingleCellExperiment containing simulated counts
+#' @examples
+#' sim <- splotchSimulate()
+#'
+#' @export
+#' @importFrom SingleCellExperiment SingleCellExperiment
+splotchSimulate <- function(params = newSplotchParams(), verbose = TRUE, ...) {
+
+ checkmate::assertClass(params, "SplotchParams")
+ params <- setParams(params, ...)
+
+ # Set random seed
+ seed <- getParam(params, "seed")
+ set.seed(seed)
+
+ # Get the parameters we are going to use
+ nGenes <- getParam(params, "nGenes")
+ network.graph <- getParam(params, "network.graph")
+
+ # Generate network
+ if (is.null(network.graph)) {
+ network.graph <- generateNetwork(nGenes, verbose)
+ params <- setParam(params, "network.graph", network.graph)
+ }
+
+ # Select regulators
+ if (!getParam(params, "network.regsSet")) {
+ network.nRegs <- getParam(params, "network.nRegs")
+ network.graph <- selectRegulators(network.graph, network.nRegs,
+ verbose)
+ params <- setParam(params, "network.graph", network.graph)
+ } else {
+ if (verbose) {message("Using selected regulators...")}
+ }
+
+ if (length(getParam(params, "mean.values")) == 0) {
+ if (verbose) {message("Simulating means...")}
+ mean.shape <- getParam(params, "mean.shape")
+ mean.rate <- getParam(params, "mean.rate")
+ mean.values <- rgamma(nGenes, shape = mean.shape, rate = mean.rate)
+ params <- setParam(params, "mean.values", mean.values)
+ } else {
+ if (verbose) {message("Using defined means...")}
+ }
+
+ # Simulate base gene means
+
+ # sim <- SingleCellExperiment(assays = list(counts = counts),
+ # rowData = features,
+ # colData = cells,
+ # metadata = list(params = params))
+ #
+ # return(sim)
+
+ return(params)
+}
+
+generateNetwork <- function(n.nodes, verbose) {
+
+ if (verbose) {message("Generating gene network...")}
+
+ graph.raw <- igraph::sample_forestfire(n.nodes, 0.1)
+ graph.data <- igraph::get.data.frame(graph.raw)
+ graph.data <- graph.data[, c("from", "to")]
+ graph.data$weight <- rnorm(nrow(graph.data))
+ graph <- igraph::graph.data.frame(graph.data)
+ graph <- igraph::set_vertex_attr(graph, "mean",
+ value = rnorm(igraph::gorder(graph)))
+
+ return(graph)
+}
+
+selectRegulators <- function(graph, nReg, verbose) {
+
+ if (verbose) {message("Selecting regulators...")}
+
+ out.degree <- igraph::degree(graph, mode = "out")
+ in.degree <- igraph::degree(graph, mode = "in")
+ reg.prob <- out.degree - in.degree
+ reg.prob <- reg.prob + rnorm(length(reg.prob))
+ reg.prob[reg.prob <= 0] <- 1e-10
+ reg.prob <- reg.prob / sum(reg.prob)
+ reg.nodes <- names(rev(sort(reg.prob))[1:nReg])
+ is.reg <- igraph::V(graph)$name %in% reg.nodes
+ graph <- igraph::set_vertex_attr(graph, "IsReg", value = is.reg)
+
+ return(graph)
+}
diff --git a/man/SplatParams.Rd b/man/SplatParams.Rd
index bb906f9..f2954c5 100644
--- a/man/SplatParams.Rd
+++ b/man/SplatParams.Rd
@@ -6,12 +6,12 @@
\alias{SplatParams-class}
\title{The SplatParams class}
\description{
-S4 class that holds parameters for the Splatter simulation.
+S4 class that holds parameters for the Splat simulation.
}
\section{Parameters}{
-The Splatter simulation requires the following parameters:
+The Splat simulation requires the following parameters:
\describe{
\item{\code{nGenes}}{The number of genes to simulate.}
@@ -133,7 +133,7 @@ The Splatter simulation requires the following parameters:
}
The parameters not shown in brackets can be estimated from real data using
-\code{\link{splatEstimate}}. For details of the Splatter simulation
+\code{\link{splatEstimate}}. For details of the Splat simulation
see \code{\link{splatSimulate}}.
}
diff --git a/man/SplotchParams.Rd b/man/SplotchParams.Rd
index e851d29..e03a62b 100644
--- a/man/SplotchParams.Rd
+++ b/man/SplotchParams.Rd
@@ -17,8 +17,22 @@ The Splotch simulation uses the following parameters:
\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{[network.graph]}}{Graph containing the gene network.}
- \item{\code{[network.nRegs]}}{Number of regulators in a the network.}
+ \item{\emph{Mean parameters}}{
+ \describe{
+ \item{\code{mean.shape}}{Shape parameter for the mean gamma
+ distribution.}
+ \item{\code{mean.rate}}{Rate parameter for the mean gamma
+ distribution.}
+ \item{\code{mean.values}}{Vector of means for each gene.}
+ }
+ }
+ \item{\emph{Network parameters}}{
+ \describe{
+ \item{\code{[network.graph]}}{Graph containing the gene network.}
+ \item{\code{[network.nRegs]}}{Number of regulators in the
+ network.}
+ }
+ }
}
The parameters not shown in brackets can be estimated from real data using
diff --git a/man/newParams.Rd b/man/newParams.Rd
index 5af67ec..6c31e96 100644
--- a/man/newParams.Rd
+++ b/man/newParams.Rd
@@ -2,7 +2,8 @@
% Please edit documentation in R/AllGenerics.R, R/BASiCSParams-methods.R,
% R/Lun2Params-methods.R, R/LunParams-methods.R, R/MFAParams-methods.R,
% R/PhenoParams-methods.R, R/SCDDParams-methods.R, R/SimpleParams-methods.R,
-% R/SparseDCParams-methods.R, R/SplatParams-methods.R, R/ZINBParams-methods.R
+% R/SparseDCParams-methods.R, R/SplatParams-methods.R,
+% R/SplotchParams-methods.R, R/ZINBParams-methods.R
\name{newParams}
\alias{newParams}
\alias{newBASiCSParams}
@@ -14,6 +15,7 @@
\alias{newSimpleParams}
\alias{newSparseDCParams}
\alias{newSplatParams}
+\alias{newSplotchParams}
\alias{newZINBParams}
\title{New Params}
\usage{
@@ -35,6 +37,8 @@ newSparseDCParams(...)
newSplatParams(...)
+newSplotchParams(...)
+
newZINBParams(...)
}
\arguments{
diff --git a/man/setParam.Rd b/man/setParam.Rd
index e144b40..0aca893 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/AllGenerics.R, R/BASiCSParams-methods.R,
% R/Lun2Params-methods.R, R/LunParams-methods.R, R/Params-methods.R,
% R/PhenoParams-methods.R, R/SCDDParams-methods.R, R/SplatParams-methods.R,
-% R/ZINBParams-methods.R
+% R/SplotchParams-methods.R, R/ZINBParams-methods.R
\docType{methods}
\name{setParam}
\alias{setParam}
@@ -13,6 +13,7 @@
\alias{setParam,PhenoParams-method}
\alias{setParam,SCDDParams-method}
\alias{setParam,SplatParams-method}
+\alias{setParam,SplotchParams-method}
\alias{setParam,ZINBParams-method}
\title{Set a parameter}
\usage{
@@ -32,6 +33,8 @@ setParam(object, name, value)
\S4method{setParam}{SplatParams}(object, name, value)
+\S4method{setParam}{SplotchParams}(object, name, value)
+
\S4method{setParam}{ZINBParams}(object, name, value)
}
\arguments{
diff --git a/man/setParams.Rd b/man/setParams.Rd
index b7265f0..ad217dd 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -1,11 +1,12 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Params-methods.R,
-% R/SplatParams-methods.R
+% R/SplatParams-methods.R, R/SplotchParams-methods.R
\docType{methods}
\name{setParams}
\alias{setParams}
\alias{setParams,Params-method}
\alias{setParams,SplatParams-method}
+\alias{setParams,SplotchParams-method}
\title{Set parameters}
\usage{
setParams(object, update = NULL, ...)
@@ -13,6 +14,8 @@ setParams(object, update = NULL, ...)
\S4method{setParams}{Params}(object, update = NULL, ...)
\S4method{setParams}{SplatParams}(object, update = NULL, ...)
+
+\S4method{setParams}{SplotchParams}(object, update = NULL, ...)
}
\arguments{
\item{object}{Params object to set parameters in.}
diff --git a/man/showValues.Rd b/man/showValues.Rd
index ddd813a..9167cc7 100644
--- a/man/showValues.Rd
+++ b/man/showValues.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/params-functions.R
\name{showValues}
\alias{showValues}
-\title{Show vales}
+\title{Show values}
\usage{
showValues(values, not.default)
}
@@ -12,5 +12,5 @@ showValues(values, not.default)
\item{not.default}{logical vector giving which have changed from the default.}
}
\description{
-Function used for pretty printing scale or vector parameters.
+Function used for pretty printing scalar or vector parameters.
}
diff --git a/man/splotchSimulate.Rd b/man/splotchSimulate.Rd
new file mode 100644
index 0000000..19458d9
--- /dev/null
+++ b/man/splotchSimulate.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splotch-simulate.R
+\name{splotchSimulate}
+\alias{splotchSimulate}
+\title{Splotch simulation}
+\usage{
+splotchSimulate(params = newSplotchParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{SplotchParams object containing simulation parameters.}
+
+\item{verbose}{logical. Whether to print progress messages}
+
+\item{...}{any additional parameter settings to override what is provided in
+\code{params}.}
+}
+\value{
+SingleCellExperiment containing simulated counts
+}
+\description{
+Simulate counts from...
+}
+\details{
+Details...
+}
+\examples{
+sim <- splotchSimulate()
+
+}
--
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