scCustomize (version 3.2.4)

Proportion_Plot: 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 = "ident",
  split.by = NULL,
  num_columns = NULL,
  x_lab_rotate = TRUE,
  colors_use = NULL,
  ggplot_default_colors = FALSE,
  color_seed = 123
)

Value

ggplot2 or patchwork object

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

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.

Examples

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