From dd3df053fc57c0a523eae5cd331cd6e165a79752 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Sun, 1 Oct 2017 15:57:58 +1100
Subject: [PATCH] Add mfaSimulate

---
 NAMESPACE          |  1 +
 R/mfa-simulate.R   | 84 ++++++++++++++++++++++++++++++++++++++++++++++
 man/mfaSimulate.Rd | 41 ++++++++++++++++++++++
 3 files changed, 126 insertions(+)
 create mode 100644 R/mfa-simulate.R
 create mode 100644 man/mfaSimulate.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 64df61f..6620b22 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,6 +26,7 @@ export(makeCompPanel)
 export(makeDiffPanel)
 export(makeOverallPanel)
 export(mfaEstimate)
+export(mfaSimulate)
 export(newLun2Params)
 export(newLunParams)
 export(newMFAParams)
diff --git a/R/mfa-simulate.R b/R/mfa-simulate.R
new file mode 100644
index 0000000..70d171d
--- /dev/null
+++ b/R/mfa-simulate.R
@@ -0,0 +1,84 @@
+#' MFA simulation
+#'
+#' Simulate a bifurcating pseudotime path using the mfa method.
+#'
+#' @param params MFAParams 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[mfa]{create_synthetic}}
+#' that takes a \code{\link{MFAParams}}, runs the simulation then converts the
+#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+#' See \code{\link[mfa]{create_synthetic}} and the mfa paper for more details
+#' about how the simulation works.
+#'
+#' @return SingleCellExperiment containing simulated counts
+#'
+#' @references
+#' Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell
+#' gene expression data using a Bayesian mixture of factor analyzers. Wellcome
+#' Open Research (2017).
+#'
+#' Paper: \url{10.12688/wellcomeopenres.11087.1}
+#'
+#' Code: \url{https://github.com/kieranrcampbell/mfa}
+#'
+#' @examples
+#' sim <- mfaSimulate()
+#' @export
+mfaSimulate <- function(params = newMFAParams(), verbose = TRUE, ...) {
+
+    checkmate::assertClass(params, "MFAParams")
+    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")
+    trans.prop <- getParam(params, "trans.prop")
+    zero.neg <- getParam(params, "zero.neg")
+    dropout.present <- getParam(params, "dropout.present")
+    dropout.lambda <- getParam(params, "dropout.lambda")
+
+    if (verbose) {message("Simulating counts...")}
+    mfa.sim <- mfa::create_synthetic(C = nCells,
+                                     G = nGenes,
+                                     p_transient = trans.prop,
+                                     zero_negative = zero.neg,
+                                     model_dropout = dropout.present,
+                                     lambda = dropout.lambda)
+
+    if (verbose) {message("Creating final dataset...")}
+    cell.names <- paste0("Cell", seq_len(nCells))
+    gene.names <- paste0("Gene", seq_len(nGenes))
+
+    counts <- t(mfa.sim$X)
+    rownames(counts) <- gene.names
+    colnames(counts) <- cell.names
+
+    cells <- data.frame(Cell = cell.names,
+                        Branch = mfa.sim$branch,
+                        Pseudotime = mfa.sim$pst)
+    rownames(cells) <- cell.names
+
+    features <- data.frame(Gene = gene.names,
+                           KBranch1 = mfa.sim$k[, 1],
+                           KBranch2 = mfa.sim$k[, 2],
+                           PhiBranch1 = mfa.sim$phi[, 1],
+                           PhiBranch2 = mfa.sim$phi[, 2],
+                           DeltaBranch1 = mfa.sim$delta[, 1],
+                           DeltaBranch2 = mfa.sim$delta[, 2])
+    rownames(features) <- gene.names
+
+    sim <- SingleCellExperiment(assays = list(counts = counts),
+                                rowData = features,
+                                colData = cells,
+                                metadata = list(params = params))
+
+    return(sim)
+}
diff --git a/man/mfaSimulate.Rd b/man/mfaSimulate.Rd
new file mode 100644
index 0000000..7f7e356
--- /dev/null
+++ b/man/mfaSimulate.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mfa-simulate.R
+\name{mfaSimulate}
+\alias{mfaSimulate}
+\title{MFA simulation}
+\usage{
+mfaSimulate(params = newMFAParams(), verbose = TRUE, ...)
+}
+\arguments{
+\item{params}{MFAParams 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 a bifurcating pseudotime path using the mfa method.
+}
+\details{
+This function is just a wrapper around \code{\link[mfa]{create_synthetic}}
+that takes a \code{\link{MFAParams}}, runs the simulation then converts the
+output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+See \code{\link[mfa]{create_synthetic}} and the mfa paper for more details
+about how the simulation works.
+}
+\examples{
+sim <- mfaSimulate()
+}
+\references{
+Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell
+gene expression data using a Bayesian mixture of factor analyzers. Wellcome
+Open Research (2017).
+
+Paper: \url{10.12688/wellcomeopenres.11087.1}
+
+Code: \url{https://github.com/kieranrcampbell/mfa}
+}
-- 
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