plotTheSoup: plotTheSoup

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

plotTheSoup

Description

Plot stats about the ambient RNA content in a 10X experiment.

Usage

plotTheSoup(
  CellRanger_outs_Dir = "~/Data/114593/114593",
  library_name = basename(gsub("/outs", "", CellRanger_outs_Dir)),
  out_dir_prefix = "SoupStatistics",
  add_custom_class = FALSE,
  pattern_custom = "\\.RabV$",
  ls.Alpha = 1
)

Arguments

CellRanger_outs_Dir	CellRanger 'outs' (output) directory, Default: '~/Data/114593/114593'
library_name	Aka SampleName (the folder above 'outs;).
out_dir_prefix	Prefix for the output directory. Default: 'SoupStatistics'
add_custom_class	Add a custom class of genes, matched by apattern in gene symbol. Default: TRUE.
pattern_custom	The pattern to match in gene symbol. Default: NA.
ls.Alpha	The alpha value for the label text. Default: 0.5.

See Also

colSums rownames geom_label_repel

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.