swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 9b3892961c9e1bf418af3bbb1bc79950adb481d7 authored by Paul Hoffman on 11 June 2021, 19:17:45 UTC
Merge pull request #4608 from satijalab/develop
Merge pull request #4608 from satijalab/develop
Tip revision: 9b38929
zzz.R
#' @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"
seurat_default_options <- list(
Seurat.memsafe = FALSE,
Seurat.warn.umap.uwot = TRUE,
Seurat.checkdots = "warn",
Seurat.limma.wilcox.msg = TRUE,
Seurat.Rfast2.msg = TRUE,
Seurat.warn.vlnplot.split = TRUE
)
AttachDeps <- function(deps) {
for (d in deps) {
if (!paste0('package:', d) %in% search()) {
packageStartupMessage("Attaching ", d)
attachNamespace(ns = d)
}
}
}
.onAttach <- function(libname, pkgname) {
AttachDeps(deps = 'SeuratObject')
}
.onLoad <- function(libname, pkgname) {
op <- options()
toset <- !(names(x = seurat_default_options) %in% names(x = op))
if (any(toset)) options(seurat_default_options[toset])
invisible(x = NULL)
}