Proportion_Plot: Cell Proportion Plot

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

Cell Proportion Plot

Description

Plots the proportion of cells belonging to each identity in active.ident of Seurat object. Can plot either the totals or split by a variable in meta.data.

Usage

Proportion_Plot(
  seurat_object,
  plot_type = "bar",
  plot_scale = "percent",
  group_by_var = "ident",
  split.by = NULL,
  num_columns = NULL,
  x_lab_rotate = FALSE,
  colors_use = NULL,
  ggplot_default_colors = FALSE,
  color_seed = 123
)

Arguments

seurat_object	Seurat object name.
plot_type	whether to plot a pie chart or bar chart; value must be one of "bar" or "pie". Default is "bar"
plot_scale	whether to plot bar chart as total cell counts or percents, value must be one of "percent" or "count". Default is "percent".
group_by_var	meta data column to classify samples (default = "ident" and will use active.ident.
split.by	meta data variable to use to split plots. Default is NULL which will plot across entire object.
num_columns	number of columns in plot. Only valid if split.by is not NULL.
x_lab_rotate	Rotate x-axis labels 45 degrees (Default is FALSE). Only valid if plot_type = "bar".
colors_use	color palette to use for plotting.
ggplot_default_colors	logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
color_seed	random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Value

ggplot2 or patchwork object

Examples

#' library(Seurat)
Proportion_Plot(seurat_object = pbmc_small)

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