From e0017803dd772ecfd0fa71bc491bfa6a19b0ba3f Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Wed, 4 Oct 2017 16:09:55 +1100
Subject: [PATCH] Add ZINBParams
---
DESCRIPTION | 3 +-
NAMESPACE | 2 +
R/AllClasses.R | 33 ++++++++++++
R/ZINBParams-methods.R | 119 +++++++++++++++++++++++++++++++++++++++++
man/ZINBParams.Rd | 31 +++++++++++
man/newParams.Rd | 6 ++-
man/setParam.Rd | 5 +-
7 files changed, 196 insertions(+), 3 deletions(-)
create mode 100644 R/ZINBParams-methods.R
create mode 100644 man/ZINBParams.Rd
diff --git a/DESCRIPTION b/DESCRIPTION
index 4be8b4b..af80af7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -53,7 +53,8 @@ Suggests:
scDD,
scran,
mfa,
- phenopath
+ phenopath,
+ zinbwave
biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software
URL: https://github.com/Oshlack/splatter
diff --git a/NAMESPACE b/NAMESPACE
index e388c47..a45acec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -37,6 +37,7 @@ export(newPhenoParams)
export(newSCDDParams)
export(newSimpleParams)
export(newSplatParams)
+export(newZINBParams)
export(phenoEstimate)
export(phenoSimulate)
export(scDDEstimate)
@@ -58,6 +59,7 @@ exportClasses(PhenoParams)
exportClasses(SCDDParams)
exportClasses(SimpleParams)
exportClasses(SplatParams)
+exportClasses(ZINBParams)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(SingleCellExperiment,"cpm<-")
diff --git a/R/AllClasses.R b/R/AllClasses.R
index e9a131c..00f74fc 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -540,3 +540,36 @@ setClass("PhenoParams",
n.de.pst.beta = "numeric"),
prototype = prototype(n.de = 2500, n.pst = 2500, n.pst.beta = 2500,
n.de.pst.beta = 2500))
+
+
+#' The ZINBParams class
+#'
+#' S4 class that holds parameters for the ZINB-WaVE simulation.
+#'
+#' @section Parameters:
+#'
+#' The ZINB-WaVE 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{model}}{Object describing a ZINB model.}
+#' }
+#'
+#' The majority of the parameters for this simulation are stored in a
+#' \code{\link[zinbwave]{ZinbModel}} object. Please refer to the documentation
+#' for this class for details about all the parameters.
+#'
+#' The parameters not shown in brackets can be estimated from real data using
+#' \code{\link{zinbEstimate}}. For details of the ZINB-WaVE simulation
+#' see \code{\link{zinbSimulate}}.
+#'
+#' @name ZINBParams
+#' @rdname ZINBParams
+#' @aliases ZINBParams-class
+#' @exportClass ZINBParams
+setClass("ZINBParams",
+ contains = "Params",
+ slots = c(model = "ZinbModel"),
+ prototype = prototype(model = zinbwave::zinbModel()))
diff --git a/R/ZINBParams-methods.R b/R/ZINBParams-methods.R
new file mode 100644
index 0000000..391b34b
--- /dev/null
+++ b/R/ZINBParams-methods.R
@@ -0,0 +1,119 @@
+#' @rdname newParams
+#' @importFrom methods new
+#' @export
+newZINBParams <- function(...) {
+
+ if (!requireNamespace("zinbwave", quietly = TRUE)) {
+ stop("The ZINB-WaVE simulation requires the 'zinbwave' package.")
+ }
+
+ params <- new("ZINBParams")
+
+ params <- setParams(params, ...)
+
+ return(params)
+}
+
+setValidity("ZINBParams", 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$seed, lower = 0),
+ model = checkmate::checkClass(v$model, "ZinbModel"),
+ model_valid = validObject(v$model, test = TRUE))
+
+ if (all(checks == TRUE)) {
+ valid <- TRUE
+ } else {
+ valid <- checks[checks != TRUE]
+ valid <- paste(names(valid), valid, sep = ": ")
+ }
+
+ return(valid)
+})
+
+#' @rdname setParam
+setMethod("setParam", "ZINBParams", function(object, name, value) {
+ checkmate::assertString(name)
+
+ if (name %in% names(getSlots("ZinbModel"))) {
+ model <- getParam(object, "model")
+ slot(model, name) <- value
+ object <- setParam(object, "model", model)
+ } else {
+ object <- callNextMethod()
+ }
+
+ return(object)
+})
+
+setMethod("show", "ZINBParams", function(object) {
+
+ pp <- list("Design:" = c("(Samples)" = "X",
+ "(Genes)" = "V"),
+ "Offsets:" = c("(Mu)" = "O_mu",
+ "(Pi)" = "O_pi"),
+ "Indices:" = c("(Sample Mu)" = "which_X_mu",
+ "(Gene Mu)" = "which_V_mu",
+ "(Sample Pi)" = "which_X_pi",
+ "(Gene Pi)" = "which_V_pi"),
+ "Intercepts:" = c("(Sample Mu)" = "X_mu_intercept",
+ "(Gene Mu)" = "V_mu_intercept",
+ "(Sample Pi)" = "X_pi_intercept",
+ "(Gene Pi)" = "V_pi_intercept"),
+ "Latent factors:" = c("(W)" = "W"),
+ "Coefficients:" = c("(Sample Mu)" = "beta_mu",
+ "(Gene Mu)" = "gamma_mu",
+ "(Latent Mu)" = "alpha_mu",
+ "(Sample Pi)" = "beta_pi",
+ "(Gene Pi)" = "gamma_pi",
+ "(Latent Pi)" = "alpha_pi"),
+ "Regularisation:" = c("(Sample Mu)" = "epsilon_beta_mu",
+ "(Gene Mu)" = "epsilon_gamma_mu",
+ "(Sample Pi)" = "epsilon_beta_pi",
+ "(Gene Pi)" = "epsilon_gamma_pi",
+ "(Latent)" = "epsilon_W",
+ "(Latent coeffs)" = "epsilon_alpha",
+ "(Zeta)" = "epsilon_zeta",
+ "(Logit)" = "epsilon_min_logit"))
+
+ callNextMethod()
+
+ model <- getParam(object, "model")
+ cat("Model:", "\n")
+ cat("ZinbModel with", zinbwave::nFeatures(model), "features,",
+ zinbwave::nSamples(model), "samples,", zinbwave::nFactors(model),
+ "factors and", zinbwave::nParams(model), "parameters", "\n\n")
+
+ default <- zinbwave::zinbModel()
+ for (category in names(pp)) {
+ parameters <- pp[[category]]
+ values <- lapply(parameters, function(x) {slot(model, x)})
+ short.values <- sapply(values, function(x) {
+ if ("matrix" %in% class(x)) {
+ if (nrow(x) == 1) {
+ paste0(paste(head(x[1, ], n = 4), collapse = ", "), ",...")
+ } else if (ncol(x) == 1) {
+ paste0(paste(head(x[, 1], n = 4), collapse = ", "), ",...")
+ } else {
+ paste(nrow(x), "x", ncol(x), "matrix")
+ }
+ } else if (length(x) > 4) {
+ paste0(paste(head(x, n = 4), collapse = ", "), ",...")
+ } else {
+ paste(x, collapse = ", ")
+ }
+ })
+ values <- sapply(values, paste, collapse = ", ")
+ default.values <- lapply(parameters, function(x) {slot(default, x)})
+ default.values <- sapply(default.values, paste, collapse = ", ")
+ not.default <- values != default.values
+ names(short.values)[not.default] <- toupper(names(values[not.default]))
+ cat("Model", category, "\n")
+ print(noquote(short.values), print.gap = 2)
+ cat("\n")
+ }
+
+})
diff --git a/man/ZINBParams.Rd b/man/ZINBParams.Rd
new file mode 100644
index 0000000..1b6db33
--- /dev/null
+++ b/man/ZINBParams.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AllClasses.R
+\docType{class}
+\name{ZINBParams}
+\alias{ZINBParams}
+\alias{ZINBParams-class}
+\title{The ZINBParams class}
+\description{
+S4 class that holds parameters for the ZINB-WaVE simulation.
+}
+\section{Parameters}{
+
+
+The ZINB-WaVE 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{model}}{Object describing a ZINB model.}
+}
+
+The majority of the parameters for this simulation are stored in a
+\code{\link[zinbwave]{ZinbModel}} object. Please refer to the documentation
+for this class for details about all the parameters.
+
+The parameters not shown in brackets can be estimated from real data using
+\code{\link{zinbEstimate}}. For details of the ZINB-WaVE simulation
+see \code{\link{zinbSimulate}}.
+}
+
diff --git a/man/newParams.Rd b/man/newParams.Rd
index 106202a..bac4731 100644
--- a/man/newParams.Rd
+++ b/man/newParams.Rd
@@ -1,7 +1,8 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Lun2Params-methods.R,
% R/LunParams-methods.R, R/MFAParams-methods.R, R/PhenoParams-methods.R,
-% R/SCDDParams-methods.R, R/SimpleParams-methods.R, R/SplatParams-methods.R
+% R/SCDDParams-methods.R, R/SimpleParams-methods.R, R/SplatParams-methods.R,
+% R/ZINBParams-methods.R
\name{newParams}
\alias{newParams}
\alias{newLun2Params}
@@ -11,6 +12,7 @@
\alias{newSCDDParams}
\alias{newSimpleParams}
\alias{newSplatParams}
+\alias{newZINBParams}
\title{New Params}
\usage{
newLun2Params(...)
@@ -26,6 +28,8 @@ newSCDDParams(...)
newSimpleParams(...)
newSplatParams(...)
+
+newZINBParams(...)
}
\arguments{
\item{...}{additional parameters passed to \code{\link{setParams}}.}
diff --git a/man/setParam.Rd b/man/setParam.Rd
index ce8a32c..3958a59 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -1,7 +1,7 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Lun2Params-methods.R,
% R/LunParams-methods.R, R/Params-methods.R, R/PhenoParams-methods.R,
-% R/SCDDParams-methods.R, R/SplatParams-methods.R
+% R/SCDDParams-methods.R, R/SplatParams-methods.R, R/ZINBParams-methods.R
\docType{methods}
\name{setParam}
\alias{setParam}
@@ -11,6 +11,7 @@
\alias{setParam,PhenoParams-method}
\alias{setParam,SCDDParams-method}
\alias{setParam,SplatParams-method}
+\alias{setParam,ZINBParams-method}
\title{Set a parameter}
\usage{
setParam(object, name, value)
@@ -26,6 +27,8 @@ setParam(object, name, value)
\S4method{setParam}{SCDDParams}(object, name, value)
\S4method{setParam}{SplatParams}(object, name, value)
+
+\S4method{setParam}{ZINBParams}(object, name, value)
}
\arguments{
\item{object}{object to set parameter in.}
--
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