swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 74905f1be2f14438e55b8cd3c96e89e6d13b4857 authored by Gesmira on 10 January 2024, 16:15:10 UTC
exclude tests for v4 compatability
exclude tests for v4 compatability
Tip revision: 74905f1
zzz.R
#' @importFrom progressr progressor
#'
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.limma.wilcox.msg = TRUE,
Seurat.Rfast2.msg = TRUE,
Seurat.warn.vlnplot.split = TRUE
)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# 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())
)
if (length(x = toset)) {
options(seurat_default_options[toset])
}
return(invisible(x = NULL))
}