scCustomize (version 3.1.3)

Percent_Expressing: Calculate percent of expressing cells

Description

Calculates the percent of cells that express a given set of features by various grouping factors

Usage

Percent_Expressing(
  seurat_object,
  features,
  threshold = 0,
  group_by = deprecated(),
  group.by = NULL,
  split_by = deprecated(),
  split.by = NULL,
  entire_object = FALSE,
  layer = "data",
  assay = NULL
)

Value

A data.frame

Arguments

seurat_object

Seurat object name.

features

Feature(s) to plot.

threshold

Expression threshold to use for calculation of percent expressing (default is 0).

group_by

soft-deprecated. See group.by.

group.by

Factor to group the cells by.

split_by

soft-deprecated. See split.by.

split.by

Factor to split the groups by.

entire_object

logical (default = FALSE). Whether to calculate percent of expressing cells across the entire object as opposed to by cluster or by group.by variable.

layer

Which layer to pull expression data from? Default is "data".

assay

Assay to pull feature data from. Default is active assay.

References

Part of code is modified from Seurat package as used by DotPlot to generate values to use for plotting. Source code can be found here: https://github.com/satijalab/seurat/blob/4e868fcde49dc0a3df47f94f5fb54a421bfdf7bc/R/visualization.R#L3391 (License: GPL-3).

Examples

if (FALSE) {
percent_stats <- Percent_Expressing(seurat_object = object, features = "Cx3cr1", threshold = 0)
}