scBarplot.CellsPerCluster: Barplot of Fraction of Cells per Cluster

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

Barplot of Fraction of Cells per Cluster

Description

Visualizes the fraction of cells within each cluster through a barplot.

Usage

scBarplot.CellsPerCluster(
  obj = combined.obj,
  ident = GetOrderedClusteringRuns(obj = obj)[1],
  sort = FALSE,
  plotname = "Cells per Identity Group",
  sub = ident,
  label = list(TRUE, "percent")[[1]],
  suffix = if (label == "percent") "percent" else NULL,
  palette = c("alphabet", "alphabet2", "glasbey", "polychrome", "stepped")[3],
  return_table = FALSE,
  ylab_adj = 1.1,
  min.cells = round(ncol(obj)/100),
  ...
)

Arguments

obj	Seurat object for analysis. Default: combined.obj.
ident	Cluster identity. Used to specify which clustering results to visualize. Default: First entry from ordered clustering runs.
sort	If TRUE, sorts clusters by size. Default: FALSE.
sub	Subtitle for the plot. Default: "identity".
label	If TRUE, shows cell count or percentage based on the label vector. Default: TRUE.
suffix	Optional suffix for file naming. Used in conjunction with kpp.
palette	Color palette for the barplot. Default: 'glasbey'.
return_table	If TRUE, returns the data used for plotting instead of the plot itself. Default: FALSE.
ylab_adj	Adjustment factor for y-axis label positioning. Default: 1.1.
min.cells	Minimum cell count threshold for categories. Adjusted by data size.
...	Additional parameters for internal function calls.
title	Title for the plot. Default: "Cells per Identity Group".

Examples

## Not run: 
scBarplot.CellsPerCluster()
scBarplot.CellsPerCluster(sort = TRUE)

## End(Not run)

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