Add single mode to splat

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.3.21
-Date: 2016-10-11
+Version: 0.3.22
+Date: 2016-10-12
 Author: Luke Zappia
 Authors@R: as.person(c(
     "Luke Zappia <luke.zappia@mcri.edu.au> [aut, cre]",

NAMESPACE

@@ -13,6 +13,7 @@ export(splat)
 export(splatGroups)
 export(splatParams)
 export(splatPaths)
+export(splatSingle)
 importFrom(Biobase,"assayData<-")
 importFrom(Biobase,"fData<-")
 importFrom(Biobase,"pData<-")

R/simulate.R

@@ -15,9 +15,10 @@
 #'
 #' @param params splatParams object containing parameters for the simulation.
 #'        See \code{\link{splatParams}} for details.
-#' @param method which simulation method to use. Options are "groups" which
-#'        produces distinct groups (eg. cell types) or "paths" which selects
-#'        cells from a continuous trajectory (eg. differentiation process).
+#' @param method which simulation method to use. Options are "single" which
+#'        produces a single population, "groups" which produces distinct groups
+#'        (eg. cell types) or "paths" which selects cells from continuous
+#'        trajectories (eg. differentiation process).
 #' @param verbose logical. Whether to print progress messages.
 #' @param ... any additional parameter settings to override what is provided in
 #'        \code{params}.
@@ -106,7 +107,8 @@
 #' @importFrom Biobase fData pData pData<- assayData
 #' @importFrom scater newSCESet counts
 #' @export
-splat <- function(params = defaultParams(), method = c("groups", "paths"),
+splat <- function(params = defaultParams(),
+                  method = c("single", "groups", "paths"),
                   verbose = TRUE, ...) {
 
     method <- match.arg(method)
@@ -126,6 +128,11 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
     nGroups <- getParams(params, "nGroups")
     group.cells <- getParams(params, "groupCells")
 
+    if (nGroups == 1 && method == "groups") {
+        warning("nGroups is 1, switching to single mode")
+        method <- "single"
+    }
+
     if (verbose) {message("Creating simulation object...")}
     # Set up name vectors
     cell.names <- paste0("Cell", 1:nCells)
@@ -149,16 +156,20 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
 
     # Make groups vector which is the index of param$groupCells repeated
     # params$groupCells[index] times
-    groups <- lapply(1:nGroups, function(i, g) {rep(i, g[i])},
-                     g = group.cells)
-    groups <- unlist(groups)
-    pData(sim)$Group <- group.names[groups]
+    if (method != "single") {
+        groups <- lapply(1:nGroups, function(i, g) {rep(i, g[i])},
+                         g = group.cells)
+        groups <- unlist(groups)
+        pData(sim)$Group <- group.names[groups]
+    }
 
     if (verbose) {message("Simulating library sizes...")}
     sim <- simLibSizes(sim, params)
     if (verbose) {message("Simulating gene means...")}
     sim <- simGeneMeans(sim, params)
-    if (method == "groups") {
+    if (method == "single") {
+        sim <- simSingleCellMeans(sim, params)
+    } else if (method == "groups") {
         if (verbose) {message("Simulating group DE...")}
         sim <- simGroupDE(sim, params)
         if (verbose) {message("Simulating cell means...")}
@@ -193,11 +204,17 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
     return(sce)
 }
 
+#' @rdname splat
+#' @export
+splatSingle <- function(params = defaultParams(), verbose = TRUE, ...) {
+    sim <- splat(params = params, method = "single", verbose = verbose, ...)
+    return(sim)
+}
+
 #' @rdname splat
 #' @export
 splatGroups <- function(params = defaultParams(), verbose = TRUE, ...) {
     sim <- splat(params = params, method = "groups", verbose = verbose, ...)
-
     return(sim)
 }
 
@@ -205,7 +222,6 @@ splatGroups <- function(params = defaultParams(), verbose = TRUE, ...) {
 #' @export
 splatPaths <- function(params = defaultParams(), verbose = TRUE, ...) {
     sim <- splat(params = params, method = "paths", verbose = verbose, ...)
-
     return(sim)
 }
 
@@ -346,6 +362,35 @@ simPathDE <- function(sim, params) {
     return(sim)
 }
 
+#' Simulate single population cell means
+#'
+#' Simulate a gene by cell matrix giving the mean expression for each gene in
+#' each cell.
+#'
+#' @param sim SCESet to add cell means to.
+#' @param params splatParams object with simulation parameters.
+#'
+#' @return SCESet with added cell means.
+#'
+#' @importFrom Biobase fData pData assayData assayData<-
+simSingleCellMeans <- function(sim, params) {
+
+    nCells <- getParams(params, "nCells")
+    cell.names <- pData(sim)$Cell
+    gene.names <- fData(sim)$Gene
+    exp.lib.sizes <- pData(sim)$ExpLibSize
+
+    cell.means.gene <- as.matrix(fData(sim)[, rep("GeneMean", nCells)])
+    cell.props.gene <- t(t(cell.means.gene) / colSums(cell.means.gene))
+    base.means.cell <- t(t(cell.props.gene) * exp.lib.sizes)
+    colnames(base.means.cell) <- cell.names
+    rownames(base.means.cell) <- gene.names
+
+    assayData(sim)$BaseCellMeans <- base.means.cell
+
+    return(sim)
+}
+
 #' Simulate group cell means
 #'
 #' Simulate a gene by cell matrix giving the mean expression for each gene in
@@ -368,10 +413,6 @@ simGroupCellMeans <- function(sim, params) {
     exp.lib.sizes <- pData(sim)$ExpLibSize
 
     group.means.gene <- fData(sim)[, paste0("GeneMean", group.names)]
-    if (nGroups == 1) {
-        group.means.gene <- matrix(group.means.gene)
-        colnames(group.means.gene) <- "GeneMeanGroup1"
-    }
     cell.means.gene <- as.matrix(group.means.gene[, factor(groups)])
     cell.props.gene <- t(t(cell.means.gene) / colSums(cell.means.gene))
     base.means.cell <- t(t(cell.props.gene) * exp.lib.sizes)

man/simSingleCellMeans.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simulate.R
+\name{simSingleCellMeans}
+\alias{simSingleCellMeans}
+\title{Simulate single population cell means}
+\usage{
+simSingleCellMeans(sim, params)
+}
+\arguments{
+\item{sim}{SCESet to add cell means to.}
+
+\item{params}{splatParams object with simulation parameters.}
+}
+\value{
+SCESet with added cell means.
+}
+\description{
+Simulate a gene by cell matrix giving the mean expression for each gene in
+each cell.
+}
+

man/splat.Rd

@@ -4,11 +4,14 @@
 \alias{splat}
 \alias{splatGroups}
 \alias{splatPaths}
+\alias{splatSingle}
 \title{Simulate scRNA-seq data}
 \usage{
-splat(params = defaultParams(), method = c("groups", "paths"),
+splat(params = defaultParams(), method = c("single", "groups", "paths"),
   verbose = TRUE, ...)
 
+splatSingle(params = defaultParams(), verbose = TRUE, ...)
+
 splatGroups(params = defaultParams(), verbose = TRUE, ...)
 
 splatPaths(params = defaultParams(), verbose = TRUE, ...)
@@ -17,9 +20,10 @@ splatPaths(params = defaultParams(), verbose = TRUE, ...)
 \item{params}{splatParams object containing parameters for the simulation.
 See \code{\link{splatParams}} for details.}
 
-\item{method}{which simulation method to use. Options are "groups" which
-produces distinct groups (eg. cell types) or "paths" which selects
-cells from a continuous trajectory (eg. differentiation process).}
+\item{method}{which simulation method to use. Options are "single" which
+produces a single population, "groups" which produces distinct groups
+(eg. cell types) or "paths" which selects cells from continuous
+trajectories (eg. differentiation process).}
 
 \item{verbose}{logical. Whether to print progress messages.}
 

tests/testthat/test-simulate.R

+context("splatter simulations")
+
+test_that("one group switches to single mode", {
+  expect_warning(splat(method = "groups"),
+                 "nGroups is 1, switching to single mode")
+  expect_silent(splat(method = "paths", verbose = FALSE))
+})