diff --git a/DESCRIPTION b/DESCRIPTION
index af95dd9d2ba8e5d67a90d581d1e4384005b7d3aa..8cd17135922a9d51ed49ac8190d8231a18dcd76e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.2
-Date: 2019-06-13
+Version: 1.9.2.9000
+Date: 2019-07-11
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -62,7 +62,8 @@ Suggests:
zinbwave,
SparseDC,
BiocManager,
- spelling
+ spelling,
+ igraph
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
diff --git a/NEWS.md b/NEWS.md
index ea91789687390d3b095759333f41bec82069c81a..d932de8f2d0d102d129216cb1e1cb12dfe0cba36 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+### Version 1.9.2.9000 (2019-07-11)
+
+* Add SplotchParams object
+
## Version 1.9.2 (2019-06-13)
* Add variable gene correlation plot to compareSCEs
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 1da947a4586fee93e38cf7b87ae43d95ec4c86ed..a251d3f76d61bf0cea9354f270d713bb028e9ec5 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -63,11 +63,11 @@ setClass("SimpleParams",
#' The SplatParams class
#'
-#' S4 class that holds parameters for the Splatter simulation.
+#' S4 class that holds parameters for the Splat simulation.
#'
#' @section Parameters:
#'
-#' The Splatter simulation requires the following parameters:
+#' The Splat simulation requires the following parameters:
#'
#' \describe{
#' \item{\code{nGenes}}{The number of genes to simulate.}
@@ -189,7 +189,7 @@ setClass("SimpleParams",
#' }
#'
#' The parameters not shown in brackets can be estimated from real data using
-#' \code{\link{splatEstimate}}. For details of the Splatter simulation
+#' \code{\link{splatEstimate}}. For details of the Splat simulation
#' see \code{\link{splatSimulate}}.
#'
#' @name SplatParams
@@ -255,6 +255,37 @@ setClass("SplatParams",
path.nonlinearProb = 0.1,
path.sigmaFac = 0.8))
+#' The SplotchParams class
+#'
+#' S4 class that holds parameters for the Splotch simulation.
+#'
+#' @section Parameters:
+#'
+#' The Splotch 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{[network.graph]}}{Graph containing the gene network.}
+#' \item{\code{[network.nRegs]}}{Number of regulators in a the network.}
+#' }
+#'
+#' The parameters not shown in brackets can be estimated from real data using
+#' \code{\link{splotchEstimate}}. For details of the Splotch simulation
+#' see \code{\link{splotchSimulate}}.
+#'
+#' @name SplotchParams
+#' @rdname SplotchParams
+#' @aliases SplotchParams-class
+#' @exportClass SplotchParams
+setClass("SplotchParams",
+ contains = "Params",
+ slots = c(network.graph = "ANY",
+ network.nRegs = "numeric"),
+ prototype = prototype(network.graph = NULL,
+ network.nRegs = 100))
+
#' The LunParams class
#'
#' S4 class that holds parameters for the Lun simulation.
diff --git a/R/SplotchParams-methods.R b/R/SplotchParams-methods.R
new file mode 100644
index 0000000000000000000000000000000000000000..b5373f12cf5e9ec694348d4559c44789c958772a
--- /dev/null
+++ b/R/SplotchParams-methods.R
@@ -0,0 +1,66 @@
+#' @rdname newParams
+#' @importFrom methods new
+#' @export
+newSplotchParams <- function(...) {
+
+ if (!requireNamespace("igraph", quietly = TRUE)) {
+ stop("The Splotch simulation requires the 'igraph' package.")
+ }
+
+ params <- new("SplotchParams")
+ params <- setParams(params, ...)
+
+ return(params)
+}
+
+setValidity("SplotchParams", function(object) {
+
+ v <- getParams(object, slotNames(object))
+
+ checks <- c(nGenes = checkmate::checkInt(v$nGenes, lower = 1),
+ nCells = checkmate::checkInt(v$nCells, lower = 1),
+ seed = checkmate::checkInt(v$seed, lower = 0),
+ network.graph = checkmate::checkClass(v$network, "igraph",
+ null.ok = TRUE),
+ network.nRegs = checkmate::checkInt(v$network.nRegs,
+ lower = 0))
+
+ if (all(checks == TRUE)) {
+ valid <- TRUE
+ } else {
+ valid <- checks[checks != TRUE]
+ valid <- paste(names(valid), valid, sep = ": ")
+ }
+
+ return(valid)
+})
+
+setMethod("show", "SplotchParams", function(object) {
+
+ pp.network <- list("Network:" = c("[Graph]" = "network.graph",
+ "[nRegs]" = "network.nRegs"))
+
+ callNextMethod()
+
+ network.graph <- getParam(object, "network.graph")
+ if (is.null(network.graph)) {
+ showPP(object, pp.network)
+ } else {
+ cat(crayon::bold("Network:"), "\n")
+ cat(crayon::bold(crayon::blue("[GRAPH]\n")))
+ cat(crayon::bold(crayon::green(paste(
+ "Graph with", igraph::gorder(network.graph), "nodes and",
+ igraph::gsize(network.graph), "edges\n"
+ ))))
+ show(network.graph)
+ network.nRegs <- getParam(object, "network.nRegs")
+ names(network.nRegs) <- c("[nRegs]")
+ if (network.nRegs == 100) {
+ showValues(network.nRegs, FALSE)
+ } else {
+ showValues(network.nRegs, TRUE)
+ }
+ }
+
+ # showPP(object, pp)
+})
diff --git a/R/params-functions.R b/R/params-functions.R
index cfdb02c4a37f676c12131bfa7f2601c37c3709b6..316c15a61cecdff07e2591cf9c145782d84c9215 100644
--- a/R/params-functions.R
+++ b/R/params-functions.R
@@ -76,6 +76,8 @@ showPP <- function(params, pp) {
not.default <- sapply(seq_along(values), function(i) {
!identical(values[i], default.values[i])
})
+ null.values <- sapply(values, is.null)
+ values[null.values] <- "Not set"
cat(crayon::bold(category), "\n")
if (sum(!is.df) > 0) {
@@ -88,9 +90,9 @@ showPP <- function(params, pp) {
}
}
-#' Show vales
+#' Show values
#'
-#' Function used for pretty printing scale or vector parameters.
+#' Function used for pretty printing scalar or vector parameters.
#'
#' @param values list of values to show.
#' @param not.default logical vector giving which have changed from the default.
diff --git a/man/SplotchParams.Rd b/man/SplotchParams.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..e851d290727adda37e18b8a53f586d855e3ffaf4
--- /dev/null
+++ b/man/SplotchParams.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R
+\docType{class}
+\name{SplotchParams}
+\alias{SplotchParams}
+\alias{SplotchParams-class}
+\title{The SplotchParams class}
+\description{
+S4 class that holds parameters for the Splotch simulation.
+}
+\section{Parameters}{
+
+
+The Splotch 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{[network.graph]}}{Graph containing the gene network.}
+ \item{\code{[network.nRegs]}}{Number of regulators in a the network.}
+}
+
+The parameters not shown in brackets can be estimated from real data using
+\code{\link{splotchEstimate}}. For details of the Splotch simulation
+see \code{\link{splotchSimulate}}.
+}
+