From de7cf89093e84b2ac16fcba67f3b69538240f41d Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 26 Sep 2019 14:33:41 +1000
Subject: [PATCH] Add doublets to SplotchSimulate
Might need a bit more work...
---
DESCRIPTION | 4 +-
NEWS.md | 4 ++
R/AllClasses.R | 8 ++++
R/SplotchParams-methods.R | 4 ++
R/splotch-simulate.R | 79 +++++++++++++++++++++++++++++++++++----
man/SplotchParams.Rd | 6 +++
6 files changed, 95 insertions(+), 10 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 908dc2d..9eaece6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.7.9014
-Date: 2019-09-19
+Version: 1.9.7.9015
+Date: 2019-09-26
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 495471a..3cb698f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+### Version 1.9.7.9015 (2019-09-26)
+
+* Add doublets to SplotchSimulate
+
### Version 1.9.7.9014 (2019-09-24)
* Add ambient expression and empty cells to SplotchSimulate
diff --git a/R/AllClasses.R b/R/AllClasses.R
index e603805..11c05ca 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -331,6 +331,12 @@ setClass("SplatParams",
#' structure.}
#' }
#' }
+#' \item{\emph{Doublet parameters}}{
+#' \describe{
+#' \item{\code{[doublet.prop]}}{Proportion of cells that are
+#' doublets.}
+#' }
+#' }
#' \item{\emph{Ambient parameters}}{
#' \describe{
#' \item{\code{[ambient.scale]}}{Scaling factor for the library
@@ -373,6 +379,7 @@ setClass("SplotchParams",
lib.dens = "density",
lib.method = "character",
cells.design = "data.frame",
+ doublet.prop = "numeric",
ambient.scale = "numeric",
ambient.nEmpty = "numeric"),
prototype = prototype(mean.rate = 0.3,
@@ -406,6 +413,7 @@ setClass("SplotchParams",
Alpha = 0,
Beta = 1
),
+ doublet.prop = 0,
ambient.scale = 0.05,
ambient.nEmpty = 0))
diff --git a/R/SplotchParams-methods.R b/R/SplotchParams-methods.R
index 17d6227..c3a51cc 100644
--- a/R/SplotchParams-methods.R
+++ b/R/SplotchParams-methods.R
@@ -57,6 +57,9 @@ setValidity("SplotchParams", function(object) {
nrows = nrow(
v$paths.design),
ncols = 4),
+ doublet.prop = checkmate::check_number(v$doublet.prop,
+ lower = 0,
+ upper = 1),
ambient.scale = checkmate::check_number(v$ambient.scale,
lower = 0,
upper = 1),
@@ -159,6 +162,7 @@ setMethod("show", "SplotchParams", function(object) {
"(Density)" = "lib.dens",
"[Method]" = "lib.method"),
"Cells:" = c("[Design]" = "cells.design"),
+ "Doublets:" = c("[Prop]" = "doublet.prop"),
"Ambient:" = c("[Scale]" = "ambient.scale",
"[Empty]" = "ambient.nEmpty"))
diff --git a/R/splotch-simulate.R b/R/splotch-simulate.R
index 7082165..8096a1f 100644
--- a/R/splotch-simulate.R
+++ b/R/splotch-simulate.R
@@ -65,10 +65,19 @@ splotchSample <- function(params, verbose = TRUE) {
if (verbose) {message("Creating simulation object...")}
nGenes <- getParam(params, "nGenes")
- nCells <- getParam(params, "nCells")
- cell.names <- paste0("Cell", seq_len(nCells))
gene.names <- paste0("Gene", seq_len(nGenes))
+ nCells <- getParam(params, "nCells")
+ doublet.prop <- getParam(params, "doublet.prop")
+ nDoublets <- floor(nCells * doublet.prop)
+ if (doublet.prop > 0) {
+ nCells <- nCells - nDoublets
+ cell.names <- c(paste0("Cell", seq_len(nCells)),
+ paste0("Doublet", seq_len(nDoublets)))
+ } else {
+ cell.names <- paste0("Cell", seq_len(nCells))
+ }
+
nEmpty <- getParam(params, "ambient.nEmpty")
if (nEmpty > 0) {
empty.names <- paste0("Empty", seq_len(nEmpty))
@@ -76,7 +85,8 @@ splotchSample <- function(params, verbose = TRUE) {
}
cells <- data.frame(Cell = cell.names,
- Type = rep(c("Cell", "Empty"), c(nCells, nEmpty)),
+ Type = rep(c("Cell", "Doublet", "Empty"),
+ c(nCells, nDoublets, nEmpty)),
row.names = cell.names)
features <- data.frame(Gene = gene.names,
BaseMean = getParam(params, "mean.values"),
@@ -265,6 +275,7 @@ splotchSimLibSizes <- function(sim, params, verbose) {
if (verbose) {message("Simulating library sizes...")}
nCells <- getParam(params, "nCells")
nEmpty <- getParam(params, "ambient.nEmpty")
+ is.doublet <- colData(sim)$Type == "Doublet"
lib.method <- getParam(params, "lib.method")
if (lib.method == "fit") {
@@ -281,6 +292,7 @@ splotchSimLibSizes <- function(sim, params, verbose) {
}
cell.lib.sizes <- c(cell.lib.sizes, rep(0, nEmpty))
+ cell.lib.sizes[is.doublet] <- 1.5 * cell.lib.sizes[is.doublet]
colData(sim)$CellLibSize <- cell.lib.sizes
ambient.scale <- getParam(params, "ambient.scale")
@@ -299,7 +311,8 @@ splotchSimCellMeans <- function(sim, params, verbose) {
cell.names <- colData(sim)$Cell
gene.names <- rowData(sim)$Gene
- nCells <- getParam(params, "nCells")
+ nDoublets <- sum(colData(sim)$Type == "Doublet")
+ nCells <- getParam(params, "nCells") - nDoublets
cells.design <- getParam(params, "cells.design")
paths.design <- getParam(params, "paths.design")
paths.means <- getParam(params, "paths.means")
@@ -338,10 +351,47 @@ splotchSimCellMeans <- function(sim, params, verbose) {
return(means)
})
+ if (nDoublets > 0) {
+ if (verbose) {message("Assigning doublets...")}
+ doublet.paths1 <- sample(cells.design$Path, nDoublets, replace = TRUE,
+ prob = cells.design$Probability)
+ doublet.paths2 <- sample(cells.design$Path, nDoublets, replace = TRUE,
+ prob = cells.design$Probability)
+
+ doublet.steps1 <- sapply(doublet.paths1, function(path) {
+ probs <- steps.probs[[path]]
+ step <- sample(1:length(probs), 1, prob = probs)
+ return(step)
+ })
+ doublet.steps2 <- sapply(doublet.paths2, function(path) {
+ probs <- steps.probs[[path]]
+ step <- sample(1:length(probs), 1, prob = probs)
+ return(step)
+ })
+
+ if (verbose) {message("Simulating doublet means...")}
+ doublet.means1 <- sapply(seq_len(nDoublets), function(doublet) {
+ path <- doublet.paths1[doublet]
+ step <- doublet.steps1[doublet]
+ means <- paths.means[[path]][, step]
+ return(means)
+ })
+ doublet.means2 <- sapply(seq_len(nDoublets), function(doublet) {
+ path <- doublet.paths2[doublet]
+ step <- doublet.steps2[doublet]
+ means <- paths.means[[path]][, step]
+ return(means)
+ })
+ doublet.means <- (doublet.means1 + doublet.means2) * 0.5
+
+ cells.means <- cbind(cells.means, doublet.means)
+ }
+
# Adjust mean based on library size
cells.props <- t(t(cells.means) / colSums(cells.means))
cells.means <- t(t(cells.props) * cell.lib.sizes[not.empty])
+ if (verbose) {message("Applying BCV adjustment...")}
nGenes <- getParam(params, "nGenes")
bcv.common <- getParam(params, "bcv.common")
bcv.df <- getParam(params, "bcv.df")
@@ -355,9 +405,9 @@ splotchSimCellMeans <- function(sim, params, verbose) {
}
cells.means <- matrix(rgamma(
- as.numeric(nGenes) * as.numeric(nCells),
+ as.numeric(nGenes) * as.numeric(nCells + nDoublets),
shape = 1 / (bcv ^ 2), scale = cells.means * (bcv ^ 2)),
- nrow = nGenes, ncol = nCells)
+ nrow = nGenes, ncol = nCells + nDoublets)
empty.means <- matrix(0, nrow = nGenes, ncol = nEmpty)
cells.means <- cbind(cells.means, empty.means)
@@ -365,8 +415,21 @@ splotchSimCellMeans <- function(sim, params, verbose) {
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))
+ colData(sim)$Path <- factor(c(cells.paths, rep(NA, nDoublets),
+ rep(NA, nEmpty)))
+ colData(sim)$Step <- c(cells.steps, rep(NA, nDoublets), rep(NA, nEmpty))
+
+ if (nDoublets > 0) {
+ colData(sim)$Path1 <- factor(c(rep(NA, nCells), doublet.paths1,
+ rep(NA, nEmpty)))
+ colData(sim)$Step1 <- c(rep(NA, nCells), doublet.steps1,
+ rep(NA, nEmpty))
+ colData(sim)$Path2 <- factor(c(rep(NA, nCells), doublet.paths2,
+ rep(NA, nEmpty)))
+ colData(sim)$Step2 <- c(rep(NA, nCells), doublet.steps2,
+ rep(NA, nEmpty))
+ }
+
assays(sim)$CellMeans <- cells.means
return(sim)
diff --git a/man/SplotchParams.Rd b/man/SplotchParams.Rd
index 07dc3ba..7fb9c84 100644
--- a/man/SplotchParams.Rd
+++ b/man/SplotchParams.Rd
@@ -81,6 +81,12 @@ The Splotch simulation uses the following parameters:
structure.}
}
}
+ \item{\emph{Doublet parameters}}{
+ \describe{
+ \item{\code{[doublet.prop]}}{Proportion of cells that are
+ doublets.}
+ }
+ }
\item{\emph{Ambient parameters}}{
\describe{
\item{\code{[ambient.scale]}}{Scaling factor for the library
--
GitLab