From d173ae09c328fb39f9b2c6626778bee8eb108e5a Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 29 Sep 2017 18:14:47 +1000
Subject: [PATCH] Add MFAParams
---
DESCRIPTION | 3 ++-
NAMESPACE | 2 ++
R/AllClasses.R | 48 +++++++++++++++++++++++++++++++++++----
R/MFAParams-methods.R | 52 +++++++++++++++++++++++++++++++++++++++++++
man/MFAParams.Rd | 35 +++++++++++++++++++++++++++++
man/Params.Rd | 8 +++----
man/newParams.Rd | 7 ++++--
7 files changed, 144 insertions(+), 11 deletions(-)
create mode 100644 R/MFAParams-methods.R
create mode 100644 man/MFAParams.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index 73a36d7..68a958e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -51,7 +51,8 @@ Suggests:
rmarkdown,
S4Vectors,
scDD,
- scran
+ scran,
+ mfa
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software
URL: https://github.com/Oshlack/splatter
diff --git a/NAMESPACE b/NAMESPACE
index 216436b..dedc870 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,6 +25,7 @@ export(makeDiffPanel)
export(makeOverallPanel)
export(newLun2Params)
export(newLunParams)
+export(newMFAParams)
export(newSCDDParams)
export(newSimpleParams)
export(newSplatParams)
@@ -42,6 +43,7 @@ export(splatSimulateSingle)
export(summariseDiff)
exportClasses(Lun2Params)
exportClasses(LunParams)
+exportClasses(MFAParams)
exportClasses(SCDDParams)
exportClasses(SimpleParams)
exportClasses(SplatParams)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 59432fe..47b8233 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -7,12 +7,12 @@
#' The Params class defines 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{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.}
#' }
#'
-#' The parameters shown in brackets can be estimated from real data.
+#' The parameters not shown in brackets can be estimated from real data.
#'
#' @name Params
#' @rdname Params
@@ -460,3 +460,43 @@ setClass("SCDDParams",
modeFC = c(2, 3, 4),
varInflation = c(1, 1),
condition = "condition"))
+
+#' The MFAParams class
+#'
+#' S4 class that holds parameters for the mfa simulation.
+#'
+#' @section Parameters:
+#'
+#' The mfa 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{[trans.prop]}}{Proportion of genes that show transient
+#' expression. These genes are briefly up or down-regulated before returning
+#' to their initial state}
+#' \item{\code{[zero.neg]}}{Logical. Whether to set negative expression
+#' values to zero. This will zero-inflate the data.}
+#' \item{\code{[dropout.present]}}{Logical. Whether to simulate dropout.}
+#' \item{\code{dropout.lambda}}{Lambda parameter for the exponential
+#' dropout function.}
+#' }
+#'
+#' The parameters not shown in brackets can be estimated from real data using
+#' \code{\link{mfaEstimate}}. See \code{\link[mfa]{create_synthetic}} for more
+#' details about the parameters. For details of the Splatter implementation of
+#' the mfa simulation see \code{\link{mfaSimulate}}.
+#'
+#' @name MFAParams
+#' @rdname MFAParams
+#' @aliases MFAParams-class
+#' @exportClass MFAParams
+setClass("MFAParams",
+ contains = "Params",
+ slots = c(trans.prop = "numeric",
+ zero.neg = "logical",
+ dropout.present = "logical",
+ dropout.lambda = "numeric"),
+ prototype = prototype(trans.prop = 0, zero.neg = TRUE,
+ dropout.present = FALSE, dropout.lambda = 1))
diff --git a/R/MFAParams-methods.R b/R/MFAParams-methods.R
new file mode 100644
index 0000000..2ff3e54
--- /dev/null
+++ b/R/MFAParams-methods.R
@@ -0,0 +1,52 @@
+#' @rdname newParams
+#' @importFrom methods new
+#' @export
+newMFAParams <- function(...) {
+
+ if (!requireNamespace("mfa", quietly = TRUE)) {
+ stop("The mfa simulation requires the 'mfa' package.")
+ }
+
+ params <- new("MFAParams")
+ params <- setParams(params, ...)
+
+ return(params)
+}
+
+setValidity("MFAParams", function(object) {
+
+ v <- getParams(object, slotNames(object))
+
+ checks <- c(nGenes = checkmate::checkInt(v$nGenes, lower = 1),
+ nCells = checkmate::checkInt(v$nCells, lower = 1),
+ trans.prop = checkmate::checkNumber(v$trans.prop, lower = 0,
+ upper = 1),
+ zero.neg = checkmate::checkLogical(v$zero.neg,
+ any.missing = FALSE,
+ len = 1),
+ dropout.present = checkmate::checkLogical(v$dropout.present,
+ any.missing = FALSE,
+ len = 1),
+ dropout.lambda = checkmate::checkNumber(v$dropout.lambda),
+ seed = checkmate::checkInt(v$seed, lower = 0))
+
+ if (all(checks == TRUE)) {
+ valid <- TRUE
+ } else {
+ valid <- checks[checks != TRUE]
+ valid <- paste(names(valid), valid, sep = ": ")
+ }
+
+ return(valid)
+})
+
+setMethod("show", "MFAParams", function(object) {
+
+ pp <- list("Transient:" = c("[Proportion]" = "trans.prop"),
+ "Negative:" = c("[Zero]" = "zero.neg"),
+ "Dropout:" = c("[Present]" = "dropout.present",
+ "(Lambda)" = "dropout.lambda"))
+
+ callNextMethod()
+ showPP(object, pp)
+})
diff --git a/man/MFAParams.Rd b/man/MFAParams.Rd
new file mode 100644
index 0000000..9851398
--- /dev/null
+++ b/man/MFAParams.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R
+\docType{class}
+\name{MFAParams}
+\alias{MFAParams}
+\alias{MFAParams-class}
+\title{The MFAParams class}
+\description{
+S4 class that holds parameters for the mfa simulation.
+}
+\section{Parameters}{
+
+
+The mfa 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{[trans.prop]}}{Proportion of genes that show transient
+ expression. These genes are briefly up or down-regulated before returning
+ to their initial state}
+ \item{\code{[zero.neg]}}{Logical. Whether to set negative expression
+ values to zero. This will zero-inflate the data.}
+ \item{\code{[dropout.present]}}{Logical. Whether to simulate dropout.}
+ \item{\code{dropout.lambda}}{Lambda parameter for the exponential
+ dropout function.}
+}
+
+The parameters not shown in brackets can be estimated from real data using
+\code{\link{mfaEstimate}}. See \code{\link[mfa]{create_synthetic}} for more
+details about the parameters. For details of the Splatter implementation of
+the mfa simulation see \code{\link{mfaSimulate}}.
+}
+
diff --git a/man/Params.Rd b/man/Params.Rd
index c8fbe45..156c6c4 100644
--- a/man/Params.Rd
+++ b/man/Params.Rd
@@ -14,11 +14,11 @@ Virtual S4 class that all other Params classes inherit from.
The Params class defines 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{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.}
}
-The parameters shown in brackets can be estimated from real data.
+The parameters not shown in brackets can be estimated from real data.
}
diff --git a/man/newParams.Rd b/man/newParams.Rd
index 197dc02..de3e6b8 100644
--- a/man/newParams.Rd
+++ b/man/newParams.Rd
@@ -1,11 +1,12 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Lun2Params-methods.R,
-% R/LunParams-methods.R, R/SCDDParams-methods.R, R/SimpleParams-methods.R,
-% R/SplatParams-methods.R
+% R/LunParams-methods.R, R/MFAParams-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{newSCDDParams}
\alias{newSimpleParams}
\alias{newSplatParams}
@@ -15,6 +16,8 @@ newLun2Params(...)
newLunParams(...)
+newMFAParams(...)
+
newSCDDParams(...)
newSimpleParams(...)
--
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