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Luke Zappia authoredLuke Zappia authored
params.R 16.07 KiB
#' Create splatParams object
#'
#' S3 class for holding Splatter simulation parameters.
#'
#' @param ... parameters to set in the new params object, passed to
#' \code{\link{setParams}}.
#'
#' @details
#' The splatParams object is a list based S3 object for holding simulation
#' parameters. It has the following sections and values:
#'
#' \itemize{
#' \item nGenes - Number of genes to simulate.
#' \item nCells - Number of cells to simulate.
#' \item [groupCells] - Vector giving the number of cells in each simulation
#' group/path.
#' \item mean (mean parameters)
#' \itemize{
#' \item rate - Rate parameter for the mean gamma simulation.
#' \item shape - Shape parameter for the mean gamma simulation.
#' }
#' \item lib (library size parameters)
#' \itemize{
#' \item loc - Location (meanlog) parameter for the library size
#' log-normal distribution.
#' \item scale - Scale (sdlog) parameter for the library size log-normal
#' distribution.
#' }
#' \item out (expression outlier parameters)
#' \itemize{
#' \item prob - Probability that a gene is an expression outlier.
#' \item loProb - Probability that an expression outlier gene is lowly
#' expressed.
#' \item facLoc - Location (meanlog) parameter for the expression outlier
#' factor log-normal distribution.
#' \item facScale - Scale (sdlog) parameter for the expression outlier
#' factor log-normal distribution.
#' }
#' \item de (differential expression parameters)
#' \itemize{
#' \item [prob] - Probability that a gene is differentially expressed
#' between groups or paths.
#' \item [downProb] - Probability that differentially expressed gene is
#' down-regulated.
#' \item [facLoc] - Location (meanlog) parameter for the differential
#' expression factor log-normal distribution.
#' \item [facScale] - Scale (sdlog) parameter for the differential
#' expression factor log-normal distribution.
#' }
#' \item bcv (Biological Coefficient of Variation parameters)
#' \itemize{
#' \item common - Underlying common dispersion across all genes.
#' \item DF - Degrees of Freedom for the BCV inverse chi-squared
#' distribution.
#' }
#' \item dropout (dropout parameters)
#' \itemize{
#' \item present - Logical. Whether to simulate dropout.
#' \item mid - Midpoint parameter for the dropout logistic function.
#' \item shape - Shape parameter for the dropout logistic function.
#' }
#' \item path (differentiation path parameters)
#' \itemize{
#' \item [from] - Vector giving the originating point of each path. This
#' allows path structure such as a cell type which differentiates
#' into an intermediate cell type that then differentiates into two
#' mature cell types. A path structure of this form would have a
#' "from" parameter of c(0, 1, 1) (where 0 is the origin). If no
#' vector is given all paths will start at the origin.
#' \item [length] - Vector giving the number of steps to simulate along#' each path. If a single value is given it will be applied to all
#' paths.
#' \item [skew] - Vector giving the skew of each path. Values closer to 1
#' will give more cells towards the starting population, values
#' closer to 0 will give more cells towards the final population.
#' If a single value is given it will be applied to all paths.
#' \item [nonlinearProb] - Probability that a gene follows a non-linear
#' path along the differentiation path. This allows more complex
#' gene patterns such as a gene being equally expressed at the
#' beginning an end of a path but lowly expressed in the middle.
#' \item [sigmaFac] - Sigma factor for non-linear gene paths. A higher
#' value will result in more extreme non-linear variations along a
#' path.
#' }
#' }
#'
#' Those shown in brackets cannot currently be easily estimated from a real
#' dataset by Splatter. This is also shown when a splatParams object is printed
#' with parameters labelled as either (estimatable) or [not estimatable].
#'
#' @return List based S3 splatParams object
#' @examples
#' params <- splatParams()
#' params
#' @export
splatParams <- function(...) {
params <- list(nGenes = NA, nCells = NA, groupCells = NA,
mean = list(rate = NA, shape = NA),
lib = list(loc = NA, scale = NA),
out = list(prob = NA, loProb = NA, facLoc = NA,
facScale = NA),
de = list(prob = NA, downProb = NA, facLoc = NA,
facScale = NA),
bcv = list(common = NA, DF = NA),
dropout = list(present = NA, mid = NA, shape = NA),
path = list(from = NA, length = NA, skew = NA,
nonlinearProb = NA, sigmaFac = NA))
class(params) <- "splatParams"
params <- setParams(params, ...)
return(params)
}
#' Print splatParams object
#'
#' Pretty print the parameters stored in a splatParams object. Parameters are
#' labelled as either (estimatable) or [not estimatable].
#'
#' @param x splatParams object to print.
#' @param ... further arguments passed to or from other methods.
#'
#' @return Invisibly returns x (via \code{\link{invisible}(x)})
#'
#' @examples
#' params <- defaultParams()
#' print(params)
#' @export
print.splatParams <- function(x, ...) {
pp <- list("Global:" = c("(Genes)" = "nGenes",
"(Cells)" = "nCells",
"[Group Cells]" = "groupCells"),
"Mean:" = c("(Rate)" = "mean.rate",
"(Shape)" = "mean.shape"),
"Library size:" = c("(Location)" = "lib.loc",
"(Scale)" = "lib.scale"),
"Exprs outliers:" = c("(Probability)" = "out.prob",
"(Lo Prob)" = "out.loProb", "(Location)" = "out.facLoc",
"(Scale)" = "out.facScale"),
"Differential exprs:" = c("[Probability]" = "de.prob",
"[Down Prob]" = "de.downProb",
"[Location]" = "de.facLoc",
"[Scale]" = "de.facScale"),
"BCV:" = c("(Common Disp)" = "bcv.common",
"(DoF)" = "bcv.DF"),
"Dropout:" = c("(Present T/F)" = "dropout.present",
"(Midpoint)" = "dropout.mid",
"(Shape)" = "dropout.shape"),
"Paths:" = c("[From]" = "path.from",
"[Length]" = "path.length",
"[Skew]" = "path.skew",
"[Non-linear]" = "path.nonlinearProb",
"[Sigma Factor]" = "path.sigmaFac"))
for (category in names(pp)) {
parameters <- getParams(x, pp[[category]])
parameters <- sapply(parameters, paste, collapse = ", ")
names(parameters) <- names(pp[[category]])
cat(category, "\n")
print(noquote(parameters), print.gap = 2)
cat("\n")
}
invisible(x)
}
#' Update a splatParams object
#'
#' Set any of the parameters in a splatParams object to have a new value.
#'
#' @param params the splatParams object to update.
#' @param ... Any parameters to set.
#'
#' @details
#' This function allows multiple parameters to be updated or set using a single
#' simple function call. Parameters to update are specified by supplying
#' additional arguments that follow the levels of the splatParams data structure
#' separated by the "." character. For example
#' \code{setParams(params, nGenes = 100)} is equivalent to
#' \code{params$nGenes <- 100} and \code{update(params, mean.rate = 1)} is
#' equivalent to \code{params$mean$rate <- 1}. For more details of the available
#' parameters and the splatParams data structure see \code{\link{splatParams}}.
#'
#' @return splatParms object with updated parameters
#' @examples
#' params <- defaultParams()
#' params
#' # Set nGenes and nCells
#' params <- setParams(params, nGenes = 1000, nCells = 200)
#' params
#' # Set mean rate paramater and library size location parameter
#' params <- setParams(params, mean.rate = 1, lib.loc = 12)
#' params
#' @export
setParams <- function(params, ...) {
update <- list(...)
if (length(update) == 0) {
return(params)
}
names <- strsplit(names(update), ".", fixed = TRUE)
for (idx in seq_along(names)) {
name <- names[[idx]]
value <- update[[idx]] if (length(name) == 1) {
params[[name]] <- value
} else {
params[[name[1]]][[name[2]]] <- value
}
}
checkParams(params)
return(params)
}
#' Get parameters from splatParams object
#'
#' Get values for the parameters in a splatParams object. Uses the same pattern
#' (category.parameter) as \code{\link{setParams}}.
#'
#' @param params splatParams object to get parameters from.
#' @param names vector of parameter names to extract.
#'
#' @return Vector if all selected parameters are single values, otherwise a
#' list.
#' @examples
#' params <- defaultParams()
#' # Get the number of genes
#' getParams(params, "nGenes")
#' # Get the number of genes and the mean rate parameter
#' getParams(params, c("nGenes", "mean.rate"))
#' # Returns a list if one of the selected parameters is a vector
#' params <- setParams(params, groupCells = c(100, 200))
#' getParams(params, c("nGenes", "mean.rate", "groupCells"))
#' @export
getParams <- function(params, names) {
if (length(names) == 0) {
return(NULL)
}
output <- list()
keep.list <- FALSE
for (idx in seq_along(names)) {
name <- names[[idx]]
name.split <- strsplit(name, ".", fixed = TRUE)[[1]]
if (length(name) == 1) {
value <- params[[name.split]]
} else {
value <- params[[name.split[1]]][[name.split[2]]]
}
output[[name]] <- value
if (length(value) > 1) {
keep.list <- TRUE
}
}
if (!keep.list) {
output <- unlist(output)
} else if (length(output) == 1) {
output <- output[[1]]
}
return(output)
}
#' Check splatParams object
#'
#' Check that a splatParams object has valid parameter values.
#'
#' @param params splatParams object to check
#'
#' @details#' The following checks are made:
#' \itemize{
#' \item{Input has "splatParams" class}
#' \item{Logical parameters are logical}
#' \item{Numeric parameters are numeric}
#' \item{Positive numeric parameters are positive}
#' \item{Integer parameters are integers}
#' \item{Probability parameters are in the range 0-1}
#' \item{Vector parameters are the correct length}
#' \item{Vector parameters do not contain NAs}
#' \item{Non-vector parameters are single values}
#' }
#'
#' @return Produces error if not valid otherwise nothing
#' @examples
#' checkParams(defaultParams())
#' @export
checkParams <- function(params) {
# Check class before anything else
if (!("splatParams" %in% class(params))) {
stop("params does not belong to the splatParams class")
}
# Define what values each parameter can take
# NUM = Numeric
# POS = Positive numeric
# INT = Positive integer
# PROB = Positive numeric in range 0-1
# LOG = Logical
types <- c(nGenes = "INT", nCells = "INT", groupCells = "INT",
mean.rate = "POS", mean.shape = "POS", lib.loc = "NUM",
lib.scale = "POS", out.prob = "PROB", out.loProb = "PROB",
out.facLoc = "NUM", out.facScale = "POS", de.prob = "PROB",
de.downProb = "PROB", de.facLoc = "NUM", de.facScale = "POS",
bcv.common = "POS", bcv.DF = "POS", dropout.present = "LOG",
dropout.mid = "NUM", dropout.shape = "NUM", path.from = "INT",
path.length = "INT", path.skew = "PROB",
path.nonlinearProb = "PROB", path.sigmaFac = "POS")
# Define which parameters are allowed to be vectors
vectors <- c("groupCells", "path.from", "path.length", "path.skew")
n.groups <- length(getParams(params, "groupCells"))
for (idx in seq_along(types)) {
name <- names(types)[idx]
type <- types[idx]
value <- getParams(params, name)
# Check vector properties first so we can exclude vectors with an NA
# before the next section
if (length(value) > 1) {
if (name %in% vectors) {
if (any(is.na(value))) {
stop(name, " is a vector and contains NA values")
} else if (length(value) != n.groups) {
stop("length of ", name, " must be 1 or the length of ",
"the groupCells parameter")
}
} else {
stop(name, " should be a single value")
}
}
# Missing values are allowed so we skip anything that is NA
if (!all(is.na(value))) {
if (type %in% c("NUM", "INT", "POS", "PROB") &&
!(is.numeric(value))) {
stop(name, " must be numeric") }
if (type %in% c("INT", "POS", "PROB") && value < 0) {
stop(name, " must be positive")
}
if (type == "INT" && value %% 1 != 0) {
stop(name, " must be an integer")
}
if (type == "PROB" && (value < 0 || value > 1)) {
stop(paste(name, "must be in the range 0-1"))
}
if (type == "LOG" && !(is.logical(value))) {
stop(name, " must be logical (TRUE/FALSE)")
}
}
}
}
#' Merge two splatParams objects
#'
#' Merge two splatParams objects. Any parameters that are NA in the first
#' splatParams object are replaced by the value in the second splatParams
#' object.
#'
#' @param params1 first splatParams object to merge.
#' @param params2 second splatParams object to merge.
#'
#' @return Merged splatParams object.
#' @examples
#' params <- splatParams(nGenes = 1000, nCells = 50)
#' params
#' # Replace unset parameters with default parameters
#' params <- mergeParams(params, defaultParams())
#' params
#' @export
mergeParams <- function(params1, params2) {
for (i in 1:length(params1)) {
for (j in 1:length(params1[[i]])) {
if (is.na(params1[[i]][[j]])) {
params1[[i]][[j]] <- params2[[i]][[j]]
}
}
}
checkParams(params1)
return(params1)
}
#' Get default simulation parameters
#'
#' Get a splatParams object with a set of default parameters that will produce a
#' resonable simulation of single-cell RNA-seq count data.
#'
#' @return A splatParams object containing default parameters
#' @examples
#' params <- defaultParams()
#' params
#' @export
defaultParams <- function() {
params <- splatParams()
params <- setParams(params, nGenes = 10000, nCells = 100,
groupCells = 100, mean.rate = 0.3, mean.shape = 0.4,
lib.loc = 10, lib.scale = 0.5, out.prob = 0.1, out.loProb = 0.5, out.facLoc = 4, out.facScale = 1,
de.prob = 0.1, de.downProb = 0.5, de.facLoc = 4,
de.facScale = 1, bcv.common = 0.1, bcv.DF = 25,
dropout.present = TRUE, dropout.mid = 0,
dropout.shape = -1, path.from = 0, path.length = 100,
path.skew = 0.5, path.nonlinearProb = 0.1,
path.sigmaFac = 0.8)
return(params)
}