Percent_Expressing: Calculate percent of expressing cells

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

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 = NULL,
  split_by = NULL,
  entire_object = FALSE,
  layer = "data",
  assay = NULL
)

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	Factor to group the cells 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.

Value

A data.frame

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

## Not run: 
percent_stats <- Percent_Expressing(seurat_object = object, features = "Cx3cr1", threshold = 0)

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.