Add SplotchParams object

Basic skeleton so far

DESCRIPTION

 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

NEWS.md

+### 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

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.

R/SplotchParams-methods.R

+#' @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)
+})

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.

man/SplotchParams.Rd

+% 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}}.
+}
+