clustering_volcanos: Title

In Close-your-eyes/scexpr: Lots of helpers and wrappers to analyze scRNAseq data sets

Title

Description

Title

Usage

clustering_volcanos(
  SO,
  assay = c("RNA", "SCT"),
  cluster.meta.cols,
  reduction = "UMAP",
  clustree.prefix = NULL,
  save.path = NULL,
  lapply_fun = lapply,
  ...
)

Arguments

SO	Seurat object, with cluster annotations in meta.data columns
assay	which assay to obtain expression values from
cluster.meta.cols	column names in meta.data of SO that contain different clusterings (e.g. increasing resolutions)
reduction	which reduction to plot cluster identities on, must be present in SO
clustree.prefix	the common prefix-string of clusterings, passed to clustree::clustree; if missing will be guessed based on cluster.meta.cols.
save.path	path to a folder on disk where to save results to; if it does not exist yet it will be created
lapply_fun	function name without quotes; lapply, pbapply::pblapply or parallel::mclapply are suggested
...	additional argument to the lapply function; e.g. mc.cores may be passed when parallel::mclapply is chosen above

Close-your-eyes/scexpr documentation built on April 21, 2023, 10:27 a.m.