From 6f488ee2bd266db2e1ef638736bac8b765a5ece2 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Wed, 4 Oct 2017 14:06:32 +1100
Subject: [PATCH] Add phenoSimulate
---
NAMESPACE | 3 +
R/pheno-simulate.R | 84 ++++++++++++++++++++++++++++
man/PhenoParams.Rd | 34 +++++++++++
man/newParams.Rd | 7 ++-
man/phenoSimulate.Rd | 43 ++++++++++++++
man/setParam.Rd | 7 ++-
tests/testthat/test-pheno-simulate.R | 5 ++
7 files changed, 179 insertions(+), 4 deletions(-)
create mode 100644 R/pheno-simulate.R
create mode 100644 man/PhenoParams.Rd
create mode 100644 man/phenoSimulate.Rd
create mode 100644 tests/testthat/test-pheno-simulate.R
diff --git a/NAMESPACE b/NAMESPACE
index 5017918..b97422b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -31,9 +31,11 @@ export(mfaSimulate)
export(newLun2Params)
export(newLunParams)
export(newMFAParams)
+export(newPhenoParams)
export(newSCDDParams)
export(newSimpleParams)
export(newSplatParams)
+export(phenoSimulate)
export(scDDEstimate)
export(scDDSimulate)
export(setParam)
@@ -49,6 +51,7 @@ export(summariseDiff)
exportClasses(Lun2Params)
exportClasses(LunParams)
exportClasses(MFAParams)
+exportClasses(PhenoParams)
exportClasses(SCDDParams)
exportClasses(SimpleParams)
exportClasses(SplatParams)
diff --git a/R/pheno-simulate.R b/R/pheno-simulate.R
new file mode 100644
index 0000000..70042e4
--- /dev/null
+++ b/R/pheno-simulate.R
@@ -0,0 +1,84 @@
+#' PhenoPath simulation
+#'
+#' Simulate counts from a pseudotime trajectory using the PhenoPath method.
+#'
+#' @param params PhenoParams 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
+#' This function is just a wrapper around
+#' \code{\link[phenopath]{simulate_phenopath}} that takes a
+#' \code{\link{PhenoParams}}, runs the simulation then converts the
+#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+#' See \code{\link[phenopath]{simulate_phenopath}} and the PhenoPath paper for
+#' more details about how the simulation works.
+#'
+#' @return SingleCellExperiment containing simulated counts
+#'
+#' @references
+#' Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
+#' and environmental backgrounds across single-cells and populations. bioRxiv
+#' (2017).
+#'
+#' Paper: \url{10.1101/159913}
+#'
+#' Code: \url{https://github.com/kieranrcampbell/phenopath}
+#'
+#' @examples
+#' sim <- phenoSimulate()
+#'
+#' @export
+#' @importFrom SingleCellExperiment SingleCellExperiment
+phenoSimulate <- function(params = newPhenoParams(), verbose = TRUE, ...) {
+
+ checkmate::assertClass(params, "PhenoParams")
+ params <- setParams(params, ...)
+
+ # Set random seed
+ seed <- getParam(params, "seed")
+ set.seed(seed)
+
+ # Get the parameters we are going to use
+ nCells <- getParam(params, "nCells")
+ nGenes <- getParam(params, "nGenes")
+ n.de <- getParam(params, "n.de")
+ n.pst <- getParam(params, "n.pst")
+ n.pst.beta <- getParam(params, "n.pst.beta")
+ n.de.pst.beta <- getParam(params, "n.de.pst.beta")
+
+ if (verbose) {message("Simulating counts...")}
+ pheno.sim <- phenopath::simulate_phenopath(N = nCells,
+ G_de = n.de,
+ G_pst = n.pst,
+ G_pst_beta = n.pst.beta,
+ G_de_pst_beta = n.de.pst.beta)
+
+ if (verbose) {message("Creating final dataset...")}
+ cell.names <- paste0("Cell", seq_len(nCells))
+ gene.names <- paste0("Gene", seq_len(nGenes))
+
+ counts <- t(pheno.sim$y)
+ rownames(counts) <- gene.names
+ colnames(counts) <- cell.names
+
+ cells <- data.frame(Cell = cell.names,
+ Covariate = pheno.sim$x,
+ Pseudotime = pheno.sim$z)
+ rownames(cells) <- cell.names
+
+ features <- data.frame(Gene = gene.names,
+ Alpha = pheno.sim$parameters$alpha,
+ Lambda = pheno.sim$parameters$lambda,
+ Beta = pheno.sim$parameters$beta,
+ Regime = pheno.sim$parameters$regime)
+ rownames(features) <- gene.names
+
+ sim <- SingleCellExperiment(assays = list(counts = counts),
+ rowData = features,
+ colData = cells,
+ metadata = list(params = params))
+
+ return(sim)
+}
diff --git a/man/PhenoParams.Rd b/man/PhenoParams.Rd
new file mode 100644
index 0000000..b1e135f
--- /dev/null
+++ b/man/PhenoParams.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R
+\docType{class}
+\name{PhenoParams}
+\alias{PhenoParams}
+\alias{PhenoParams-class}
+\title{The PhenoParams class}
+\description{
+S4 class that holds parameters for the PhenoPath simulation.
+}
+\section{Parameters}{
+
+
+The PhenoPath 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{[n.de]}}{Number of genes to simulate from the differential
+ expression regime}
+ \item{\code{[n.pst]}}{Number of genes to simulate from the pseudotime
+ regime}
+ \item{\code{[n.pst.beta]}}{Number of genes to simulate from the
+ pseudotime + beta interactions regime}
+ \item{\code{[n.de.pst.beta]}}{Number of genes to simulate from the
+ differential expression + pseudotime + interactions regime}
+}
+
+The parameters not shown in brackets can be estimated from real data using
+\code{\link{phenoEstimate}}. For details of the PhenoPath simulation
+see \code{\link{phenoSimulate}}.
+}
+
diff --git a/man/newParams.Rd b/man/newParams.Rd
index de3e6b8..106202a 100644
--- a/man/newParams.Rd
+++ b/man/newParams.Rd
@@ -1,12 +1,13 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Lun2Params-methods.R,
-% R/LunParams-methods.R, R/MFAParams-methods.R, R/SCDDParams-methods.R,
-% R/SimpleParams-methods.R, R/SplatParams-methods.R
+% R/LunParams-methods.R, R/MFAParams-methods.R, R/PhenoParams-methods.R,
+% R/SCDDParams-methods.R, R/SimpleParams-methods.R, R/SplatParams-methods.R
\name{newParams}
\alias{newParams}
\alias{newLun2Params}
\alias{newLunParams}
\alias{newMFAParams}
+\alias{newPhenoParams}
\alias{newSCDDParams}
\alias{newSimpleParams}
\alias{newSplatParams}
@@ -18,6 +19,8 @@ newLunParams(...)
newMFAParams(...)
+newPhenoParams(...)
+
newSCDDParams(...)
newSimpleParams(...)
diff --git a/man/phenoSimulate.Rd b/man/phenoSimulate.Rd
new file mode 100644
index 0000000..2effe20
--- /dev/null
+++ b/man/phenoSimulate.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pheno-simulate.R
+\name{phenoSimulate}
+\alias{phenoSimulate}
+\title{PhenoPath simulation}
+\usage{
+phenoSimulate(params = newPhenoParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{PhenoParams 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 a pseudotime trajectory using the PhenoPath method.
+}
+\details{
+This function is just a wrapper around
+\code{\link[phenopath]{simulate_phenopath}} that takes a
+\code{\link{PhenoParams}}, runs the simulation then converts the
+output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+See \code{\link[phenopath]{simulate_phenopath}} and the PhenoPath paper for
+more details about how the simulation works.
+}
+\examples{
+sim <- phenoSimulate()
+
+}
+\references{
+Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic
+and environmental backgrounds across single-cells and populations. bioRxiv
+(2017).
+
+Paper: \url{10.1101/159913}
+
+Code: \url{https://github.com/kieranrcampbell/phenopath}
+}
diff --git a/man/setParam.Rd b/man/setParam.Rd
index 9c1ba53..ce8a32c 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -1,13 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Lun2Params-methods.R,
-% R/LunParams-methods.R, R/Params-methods.R, R/SCDDParams-methods.R,
-% R/SplatParams-methods.R
+% R/LunParams-methods.R, R/Params-methods.R, R/PhenoParams-methods.R,
+% R/SCDDParams-methods.R, R/SplatParams-methods.R
\docType{methods}
\name{setParam}
\alias{setParam}
\alias{setParam,Lun2Params-method}
\alias{setParam,LunParams-method}
\alias{setParam,Params-method}
+\alias{setParam,PhenoParams-method}
\alias{setParam,SCDDParams-method}
\alias{setParam,SplatParams-method}
\title{Set a parameter}
@@ -20,6 +21,8 @@ setParam(object, name, value)
\S4method{setParam}{Params}(object, name, value)
+\S4method{setParam}{PhenoParams}(object, name, value)
+
\S4method{setParam}{SCDDParams}(object, name, value)
\S4method{setParam}{SplatParams}(object, name, value)
diff --git a/tests/testthat/test-pheno-simulate.R b/tests/testthat/test-pheno-simulate.R
new file mode 100644
index 0000000..f67a25e
--- /dev/null
+++ b/tests/testthat/test-pheno-simulate.R
@@ -0,0 +1,5 @@
+context("PhenoPath simulation")
+
+test_that("PhenoPath simulation output is valid", {
+ expect_true(validObject(phenoSimulate()))
+})
--
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