swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 9d22f91094fccc93fee647614ed2db2b8e15cbd3 authored by David Collins on 14 March 2024, 13:43:14 UTC
Update cran-comments
Update cran-comments
Tip revision: 9d22f91
zzz.R
#' @importFrom progressr progressor
#' @importFrom methods slot slot<-
#' @importFrom lifecycle deprecated deprecate_soft deprecate_stop
#' deprecate_warn is_present
#' @importFrom rlang !!!
#' abort
#' arg_match
#' arg_match0
#' as_name
#' caller_env
#' check_installed
#' enquo
#' inform
#' is_integerish
#' is_na
#' is_quosure
#' is_scalar_integerish
#' quo_get_env
#' quo_get_expr
#' warn
#'
NULL
#' @section Package options:
#'
#' Seurat uses the following [options()] to configure behaviour:
#'
#' \describe{
#' \item{\code{Seurat.memsafe}}{global option to call gc() after many operations.
#' This can be helpful in cleaning up the memory status of the R session and
#' prevent use of swap space. However, it does add to the computational overhead
#' and setting to FALSE can speed things up if you're working in an environment
#' where RAM availability is not a concern.}
#' \item{\code{Seurat.warn.umap.uwot}}{Show warning about the default backend
#' for \code{\link{RunUMAP}} changing from Python UMAP via reticulate to UWOT}
#' \item{\code{Seurat.checkdots}}{For functions that have ... as a parameter,
#' this controls the behavior when an item isn't used. Can be one of warn,
#' stop, or silent.}
#' \item{\code{Seurat.limma.wilcox.msg}}{{Show message about more efficient
#' Wilcoxon Rank Sum test available via the limma package}}
#' \item{\code{Seurat.Rfast2.msg}}{{Show message about more efficient
#' Moran's I function available via the Rfast2 package}}
#' \item{\code{Seurat.warn.vlnplot.split}}{Show message about changes to
#' default behavior of split/multi violin plots}
#' }
#'
#' @docType package
#' @rdname Seurat-package
#' @name Seurat-package
#'
"_PACKAGE"
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Options
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
seurat_default_options <- list(
Seurat.memsafe = FALSE,
Seurat.warn.umap.uwot = TRUE,
Seurat.checkdots = "warn",
Seurat.presto.wilcox.msg = TRUE, #CHANGE
Seurat.Rfast2.msg = TRUE,
Seurat.warn.vlnplot.split = TRUE,
Seurat.object.assay.version = "v5"
)
#' @importFrom methods setClassUnion
#' @importClassesFrom Matrix dgCMatrix
#'
NULL
setClassUnion(name = 'V3Matrix', members = c('matrix', 'dgCMatrix'))
AttachDeps <- function(deps) {
for (d in deps) {
if (!paste0('package:', d) %in% search()) {
packageStartupMessage("Attaching ", d)
attachNamespace(ns = d)
}
}
}
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Hooks
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#' @importFrom SeuratObject AttachDeps
#'
.onAttach <- function(libname, pkgname) {
AttachDeps(deps = c('SeuratObject'))
return(invisible(x = NULL))
}
.onLoad <- function(libname, pkgname) {
toset <- setdiff(
x = names(x = seurat_default_options),
y = names(x = options())
)
# toset <- names(x = seurat_default_options)
if (length(x = toset)) {
options(seurat_default_options[toset])
}
return(invisible(x = NULL))
}