From aae77a9cea765e50a19651a8b3ae4f9dcbb74529 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Wed, 4 Oct 2017 12:36:34 +1100
Subject: [PATCH] Add PhenoParams
---
DESCRIPTION | 3 +-
R/AllClasses.R | 40 ++++++++++++++++
R/PhenoParams-methods.R | 79 +++++++++++++++++++++++++++++++
tests/testthat/test-PhenoParams.R | 15 ++++++
4 files changed, 136 insertions(+), 1 deletion(-)
create mode 100644 R/PhenoParams-methods.R
create mode 100644 tests/testthat/test-PhenoParams.R
diff --git a/DESCRIPTION b/DESCRIPTION
index 3717687..4be8b4b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -52,7 +52,8 @@ Suggests:
S4Vectors,
scDD,
scran,
- mfa
+ mfa,
+ phenopath
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software
URL: https://github.com/Oshlack/splatter
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 536efce..e9a131c 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -500,3 +500,43 @@ setClass("MFAParams",
dropout.lambda = "numeric"),
prototype = prototype(trans.prop = 0, zero.neg = TRUE,
dropout.present = FALSE, dropout.lambda = 1))
+
+
+#' The PhenoParams class
+#'
+#' 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}}.
+#'
+#' @name PhenoParams
+#' @rdname PhenoParams
+#' @aliases PhenoParams-class
+#' @exportClass PhenoParams
+setClass("PhenoParams",
+ contains = "Params",
+ slots = c(n.de = "numeric",
+ n.pst = "numeric",
+ n.pst.beta = "numeric",
+ n.de.pst.beta = "numeric"),
+ prototype = prototype(n.de = 2500, n.pst = 2500, n.pst.beta = 2500,
+ n.de.pst.beta = 2500))
diff --git a/R/PhenoParams-methods.R b/R/PhenoParams-methods.R
new file mode 100644
index 0000000..2151c52
--- /dev/null
+++ b/R/PhenoParams-methods.R
@@ -0,0 +1,79 @@
+#' @rdname newParams
+#' @importFrom methods new
+#' @export
+newPhenoParams <- function(...) {
+
+ if (!requireNamespace("phenopath", quietly = TRUE)) {
+ stop("The PhenoPath simulation requires the 'phenopath' package.")
+ }
+
+ params <- new("PhenoParams")
+ params <- setParams(params, ...)
+
+ return(params)
+}
+
+setValidity("PhenoParams", function(object) {
+
+ v <- getParams(object, slotNames(object))
+
+ checks <- c(nGenes = checkmate::checkInt(v$nGenes, lower = 1),
+ nCells = checkmate::checkInt(v$nCells, lower = 1),
+ n.de = checkmate::checkInt(v$n.de, lower = 0),
+ n.pst = checkmate::checkInt(v$n.pst, lower = 0),
+ n.pst.beta = checkmate::checkInt(v$n.pst.beta, lower = 0),
+ n.de.pst.beta = checkmate::checkInt(v$n.de.pst.beta, lower = 0),
+ seed = checkmate::checkInt(v$seed, lower = 0))
+
+ if (v$nGenes != (v$n.de + v$n.pst + v$n.pst.beta + v$n.de.pst.beta)) {
+ checks <- c(checks,
+ nGenes = paste("nGenes is not consistent with",
+ "n.de, n.pst, n.pst.beta, n.de.pst.beta"))
+ }
+
+ if (all(checks == TRUE)) {
+ valid <- TRUE
+ } else {
+ valid <- checks[checks != TRUE]
+ valid <- paste(names(valid), valid, sep = ": ")
+ }
+
+ return(valid)
+})
+
+#' @rdname setParam
+setMethod("setParam", "PhenoParams", function(object, name, value) {
+ checkmate::assertString(name)
+
+ if (name == "nGenes") {
+ stop(name, " cannot be set directly, set n.de, n.pst, n.pst.beta or ",
+ "n.de.pst.beta instead")
+ }
+
+ nNames <- c("n.de", "n.pst", "n.pst.beta", "n.de.pst.beta")
+ if (name %in% nNames) {
+ checkmate::assertInt(value, lower = 0)
+ total <- value
+ for (nName in nNames) {
+ if (nName != name) {
+ total <- total + getParam(object, nName)
+ }
+ }
+ object <- setParamUnchecked(object, "nGenes", total)
+ }
+
+ object <- callNextMethod()
+
+ return(object)
+})
+
+setMethod("show", "PhenoParams", function(object) {
+
+ pp <- list("Genes:" = c("[DE]" = "n.de",
+ "[PST]" = "n.pst",
+ "[PST + Beta]" = "n.pst.beta",
+ "[DE + PST + Beta]" = "n.de.pst.beta"))
+
+ callNextMethod()
+ showPP(object, pp)
+})
diff --git a/tests/testthat/test-PhenoParams.R b/tests/testthat/test-PhenoParams.R
new file mode 100644
index 0000000..535724a
--- /dev/null
+++ b/tests/testthat/test-PhenoParams.R
@@ -0,0 +1,15 @@
+context("PhenoParams")
+
+test_that("constructor is valid", {
+ expect_true(validObject(newSCDDParams()))
+})
+
+test_that("nGenes checks work", {
+ params <- newPhenoParams()
+ expect_error(setParam(params, "nGenes", 1),
+ "nGenes cannot be set directly")
+ params <- setParam(params, "n.de", 0)
+ total <- getParam(params, "n.de") + getParam(params, "n.pst") +
+ getParam(params, "n.pst.beta") + getParam(params, "n.de.pst.beta")
+ expect_equal(getParam(params, "nGenes"), total)
+})
--
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