From 790a051bb7c14af44b70f92688dc5f9b21505a40 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 24 Sep 2019 12:16:13 +1000
Subject: [PATCH] Add ambient expression and empty cells to Splotch
---
DESCRIPTION | 5 +-
NAMESPACE | 6 --
NEWS.md | 4 ++
R/AllClasses.R | 19 +++++-
R/SplotchParams-methods.R | 16 ++++-
R/splotch-simulate.R | 123 +++++++++++++++++++++++++++++++-------
man/SplotchParams.Rd | 11 +++-
7 files changed, 150 insertions(+), 34 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 0ceb4d8..908dc2d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.7.9012
+Version: 1.9.7.9014
Date: 2019-09-19
Author: Luke Zappia
Authors@R:
@@ -63,7 +63,8 @@ Suggests:
SparseDC,
BiocManager,
spelling,
- igraph
+ igraph,
+ DropletUtils
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
diff --git a/NAMESPACE b/NAMESPACE
index d0fd874..08a786f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -66,11 +66,8 @@ export(splatSimulate)
export(splatSimulateGroups)
export(splatSimulatePaths)
export(splatSimulateSingle)
-<<<<<<< HEAD
export(splotchEstimate)
export(splotchSimulate)
-=======
->>>>>>> master
export(summariseDiff)
export(zinbEstimate)
export(zinbSimulate)
@@ -142,11 +139,8 @@ importFrom(methods,validObject)
importFrom(stats,aggregate)
importFrom(stats,approxfun)
importFrom(stats,cor)
-<<<<<<< HEAD
importFrom(stats,dbeta)
importFrom(stats,density)
-=======
->>>>>>> master
importFrom(stats,dnbinom)
importFrom(stats,ks.test)
importFrom(stats,median)
diff --git a/NEWS.md b/NEWS.md
index 48494f7..495471a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+### Version 1.9.7.9014 (2019-09-24)
+
+* Add ambient expression and empty cells to SplotchSimulate
+
### Version 1.9.7.9013 (2019-09-19)
* Merge master into splotch branch
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 18d6b62..e603805 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -325,12 +325,21 @@ setClass("SplatParams",
#' "density" to sample from the provided density object.}
#' }
#' }
-#' \item{\emph{Paths parameters}}{
+#' \item{\emph{Design parameters}}{
#' \describe{
#' \item{\code{[cells.design]}}{data.frame describing cell
#' structure.}
#' }
#' }
+#' \item{\emph{Ambient parameters}}{
+#' \describe{
+#' \item{\code{[ambient.scale]}}{Scaling factor for the library
+#' size log-normal distribution when generating ambient library
+#' sizes.}
+#' \item{\code{[ambient.nEmpty]}}{Number of empty cells to
+#' simulate.}
+#' }
+#' }
#' }
#'
#' The parameters not shown in brackets can be estimated from real data using
@@ -363,7 +372,9 @@ setClass("SplotchParams",
lib.scale = "numeric",
lib.dens = "density",
lib.method = "character",
- cells.design = "data.frame"),
+ cells.design = "data.frame",
+ ambient.scale = "numeric",
+ ambient.nEmpty = "numeric"),
prototype = prototype(mean.rate = 0.3,
mean.shape = 0.6,
mean.outProb = 0.05,
@@ -394,7 +405,9 @@ setClass("SplotchParams",
Probability = 1,
Alpha = 0,
Beta = 1
- )))
+ ),
+ ambient.scale = 0.05,
+ ambient.nEmpty = 0))
#' The LunParams class
#'
diff --git a/R/SplotchParams-methods.R b/R/SplotchParams-methods.R
index 2f84c91..17d6227 100644
--- a/R/SplotchParams-methods.R
+++ b/R/SplotchParams-methods.R
@@ -7,6 +7,10 @@ newSplotchParams <- function(...) {
stop("The Splotch simulation requires the 'igraph' package.")
}
+ if (!requireNamespace("DropletUtils", quietly = TRUE)) {
+ stop("The Splotch simulation requires the 'DropletUtils' package.")
+ }
+
params <- new("SplotchParams")
params <- setParams(params, ...)
@@ -52,7 +56,13 @@ setValidity("SplotchParams", function(object) {
any.missing = FALSE,
nrows = nrow(
v$paths.design),
- ncols = 4))
+ ncols = 4),
+ ambient.scale = checkmate::check_number(v$ambient.scale,
+ lower = 0,
+ upper = 1),
+ ambient.nEmpty = checkmate::check_number(v$ambient.nEmpty,
+ lower = 0,
+ finite = TRUE))
if (!checkmate::testNumeric(v$mean.values, len = 0)) {
checks <- c(checks,
@@ -148,7 +158,9 @@ setMethod("show", "SplotchParams", function(object) {
"(Scale)" = "lib.scale",
"(Density)" = "lib.dens",
"[Method]" = "lib.method"),
- "Cells:" = c("[Design]" = "cells.design"))
+ "Cells:" = c("[Design]" = "cells.design"),
+ "Ambient:" = c("[Scale]" = "ambient.scale",
+ "[Empty]" = "ambient.nEmpty"))
paths.means <- getParam(object, "paths.means")
if (length(paths.means) == 0) {
diff --git a/R/splotch-simulate.R b/R/splotch-simulate.R
index faa73f9..7082165 100644
--- a/R/splotch-simulate.R
+++ b/R/splotch-simulate.R
@@ -69,13 +69,25 @@ splotchSample <- function(params, verbose = TRUE) {
cell.names <- paste0("Cell", seq_len(nCells))
gene.names <- paste0("Gene", seq_len(nGenes))
- cells <- data.frame(Cell = cell.names, row.names = cell.names)
- features <- data.frame(Gene = gene.names, row.names = gene.names)
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ if (nEmpty > 0) {
+ empty.names <- paste0("Empty", seq_len(nEmpty))
+ cell.names <- c(cell.names, empty.names)
+ }
+
+ cells <- data.frame(Cell = cell.names,
+ Type = rep(c("Cell", "Empty"), c(nCells, nEmpty)),
+ row.names = cell.names)
+ features <- data.frame(Gene = gene.names,
+ BaseMean = getParam(params, "mean.values"),
+ row.names = gene.names)
sim <- SingleCellExperiment(rowData = features, colData = cells,
metadata = list(Params = params))
sim <- splotchSimLibSizes(sim, params, verbose)
sim <- splotchSimCellMeans(sim, params, verbose)
+ sim <- splotchSimCellCounts(sim, params, verbose)
+ sim <- splotchSimAmbientCounts(sim, params, verbose)
sim <- splotchSimCounts(sim, params, verbose)
return(sim)
@@ -252,6 +264,7 @@ splotchSimLibSizes <- function(sim, params, verbose) {
if (verbose) {message("Simulating library sizes...")}
nCells <- getParam(params, "nCells")
+ nEmpty <- getParam(params, "ambient.nEmpty")
lib.method <- getParam(params, "lib.method")
if (lib.method == "fit") {
@@ -259,15 +272,24 @@ splotchSimLibSizes <- function(sim, params, verbose) {
lib.loc <- getParam(params, "lib.loc")
lib.scale <- getParam(params, "lib.scale")
- exp.lib.sizes <- rlnorm(nCells, lib.loc, lib.scale)
+ cell.lib.sizes <- rlnorm(nCells, lib.loc, lib.scale)
} else if (lib.method == "density") {
if (verbose) {message("Sampling from density object...")}
lib.dens <- getParam(params, "lib.dens")
- exp.lib.sizes <- sampleDensity(nCells, lib.dens)
+ cell.lib.sizes <- sampleDensity(nCells, lib.dens)
}
- colData(sim)$ExpLibSize <- exp.lib.sizes
+ cell.lib.sizes <- c(cell.lib.sizes, rep(0, nEmpty))
+ colData(sim)$CellLibSize <- cell.lib.sizes
+
+ ambient.scale <- getParam(params, "ambient.scale")
+ if (ambient.scale > 0) {
+ ambient.loc <- log(exp(lib.loc) * ambient.scale)
+
+ ambient.lib.sizes <- rlnorm(nCells + nEmpty, ambient.loc, 0.3)
+ colData(sim)$AmbientLibSize <- ambient.lib.sizes
+ }
return(sim)
}
@@ -281,7 +303,9 @@ splotchSimCellMeans <- function(sim, params, verbose) {
cells.design <- getParam(params, "cells.design")
paths.design <- getParam(params, "paths.design")
paths.means <- getParam(params, "paths.means")
- exp.lib.sizes <- colData(sim)$ExpLibSize
+ cell.lib.sizes <- colData(sim)$CellLibSize
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ not.empty <- colData(sim)$Type != "Empty"
if (verbose) {message("Assigning cells to paths...")}
cells.paths <- sample(cells.design$Path, nCells, replace = TRUE,
@@ -316,10 +340,7 @@ splotchSimCellMeans <- function(sim, params, verbose) {
# Adjust mean based on library size
cells.props <- t(t(cells.means) / colSums(cells.means))
- cells.means <- t(t(cells.props) * exp.lib.sizes)
-
- colnames(cells.means) <- cell.names
- rownames(cells.means) <- gene.names
+ cells.means <- t(t(cells.props) * cell.lib.sizes[not.empty])
nGenes <- getParam(params, "nGenes")
bcv.common <- getParam(params, "bcv.common")
@@ -338,30 +359,92 @@ splotchSimCellMeans <- function(sim, params, verbose) {
shape = 1 / (bcv ^ 2), scale = cells.means * (bcv ^ 2)),
nrow = nGenes, ncol = nCells)
- colData(sim)$Path <- cells.paths
- colData(sim)$Step <- cells.steps
+ empty.means <- matrix(0, nrow = nGenes, ncol = nEmpty)
+ cells.means <- cbind(cells.means, empty.means)
+
+ colnames(cells.means) <- cell.names
+ rownames(cells.means) <- gene.names
+
+ colData(sim)$Path <- c(cells.paths, rep(NA, nEmpty))
+ colData(sim)$Step <- c(cells.steps, rep(NA, nEmpty))
assays(sim)$CellMeans <- cells.means
return(sim)
}
-splotchSimCounts <- function(sim, params, verbose) {
+splotchSimCellCounts <- function(sim, params, verbose) {
- if (verbose) {message("Simulating counts...")}
+ if (verbose) {message("Simulating cell counts...")}
cell.names <- colData(sim)$Cell
gene.names <- rowData(sim)$Gene
nGenes <- getParam(params, "nGenes")
nCells <- getParam(params, "nCells")
+ nEmpty <- getParam(params, "ambient.nEmpty")
cells.means <- assays(sim)$CellMeans
- true.counts <- matrix(rpois(
- as.numeric(nGenes) * as.numeric(nCells),
+ cell.counts <- matrix(rpois(
+ as.numeric(nGenes) * as.numeric(nCells + nEmpty),
lambda = cells.means),
- nrow = nGenes, ncol = nCells)
+ nrow = nGenes, ncol = nCells + nEmpty)
+
+ colnames(cell.counts) <- cell.names
+ rownames(cell.counts) <- gene.names
+ assays(sim)$CellCounts <- cell.counts
+
+ return(sim)
+}
+
+splotchSimAmbientCounts <- function(sim, params, verbose) {
+
+ if (verbose) {message("Simulating ambient counts...")}
+ cell.names <- colData(sim)$Cell
+ gene.names <- rowData(sim)$Gene
+ nGenes <- getParam(params, "nGenes")
+ nCells <- getParam(params, "nCells")
+ nEmpty <- getParam(params, "ambient.nEmpty")
+ cell.counts <- assays(sim)$CellCounts
+ not.empty <- colData(sim)$Type != "Empty"
+ ambient.lib.sizes <- colData(sim)$AmbientLibSize
+
+ not.empty.means <- rowMeans(cell.counts[, not.empty])
+ ambient.props <- not.empty.means / sum(not.empty.means)
+
+ ambient.means <- ambient.props %*% t(ambient.lib.sizes)
+
+ ambient.counts <- matrix(rpois(
+ as.numeric(nGenes) * as.numeric(nCells + nEmpty),
+ lambda = ambient.means),
+ nrow = nGenes, ncol = nCells + nEmpty)
+
+ colnames(ambient.counts) <- cell.names
+ rownames(ambient.counts) <- gene.names
+ assays(sim)$AmbientCounts <- ambient.counts
+ rowData(sim)$AmbientMean <- not.empty.means
+
+ return(sim)
+}
+
+splotchSimCounts <- function(sim, params, verbose) {
+
+ if (verbose) {message("Simulating final counts...")}
+ cell.lib.sizes <- colData(sim)$CellLibSize
+ ambient.lib.sizes <- colData(sim)$AmbientLibSize
+ empty <- colData(sim)$Type == "Empty"
+ cell.counts <- assays(sim)$CellCounts
+ ambient.counts <- assays(sim)$AmbientCounts
+
+ lib.sizes <- cell.lib.sizes
+ lib.sizes[empty] <- ambient.lib.sizes[empty]
+
+ counts <- cell.counts + ambient.counts
+
+ down.prop <- lib.sizes / colSums(counts)
+ # Avoid proportion creeping over 1 for empty cells
+ down.prop <- min(down.prop, 1)
+
+ counts <- DropletUtils::downsampleMatrix(counts, down.prop)
- colnames(true.counts) <- cell.names
- rownames(true.counts) <- gene.names
- assays(sim)$counts <- true.counts
+ assays(sim)$counts <- counts
return(sim)
}
diff --git a/man/SplotchParams.Rd b/man/SplotchParams.Rd
index ec9b689..07dc3ba 100644
--- a/man/SplotchParams.Rd
+++ b/man/SplotchParams.Rd
@@ -75,12 +75,21 @@ The Splotch simulation uses the following parameters:
"density" to sample from the provided density object.}
}
}
- \item{\emph{Paths parameters}}{
+ \item{\emph{Design parameters}}{
\describe{
\item{\code{[cells.design]}}{data.frame describing cell
structure.}
}
}
+ \item{\emph{Ambient parameters}}{
+ \describe{
+ \item{\code{[ambient.scale]}}{Scaling factor for the library
+ size log-normal distribution when generating ambient library
+ sizes.}
+ \item{\code{[ambient.nEmpty]}}{Number of empty cells to
+ simulate.}
+ }
+ }
}
The parameters not shown in brackets can be estimated from real data using
--
GitLab