ClusterDistrPlot: Cluster proportion boxplot by condition

In huayc09/SeuratExtend: SeuratExtend

Cluster proportion boxplot by condition

Description

Plot the percentage/absolute cell count of each cluster grouped by condition

Usage

ClusterDistrPlot(
  origin,
  cluster,
  condition = NULL,
  rev = F,
  normalize = rev,
  percent = T,
  plot = T,
  flip = T,
  reverse_order = T,
  stack = T,
  cols = "light",
  border = "white",
  violin = F,
  box = T,
  width = 0.9,
  pt = T,
  pt.style = "quasirandom",
  pt.size = 1,
  pt.alpha = 1,
  style = "outline",
  ncol = NULL,
  nrow = NULL,
  stat.method = "wilcox.test",
  p.adjust.method = "none",
  label = "p.signif",
  hide.ns = TRUE,
  ...
)

Arguments

origin	factor/vector of sample
cluster	factor/vector of cluster
condition	factor/vector of condition, should have the same number of unique values as origin. If provided, will create boxplots instead of bar plots, Default: NULL
rev	If TRUE, plot the proportion of sample in each cluster, Default: F
normalize	Normalize sample size to 100, Default: rev
percent	If FALSE, plot absolute cell number instead of percentage, Default: T
plot	Generate plot (TRUE) or matrix (FALSE), Default: T
flip	If plot bars horizontally (only used when condition is NULL), Default: T
reverse_order	If TRUE, will reverse the default stacking order (only used when condition is NULL), Default: T
stack	If TRUE, plot stacked bars (only used when condition is NULL), Default: T
cols	Colors to use for plotting. Default: "light"
border	Border color for bar plots (only used when condition is NULL), Default: "white"
violin	Indicates whether to generate a violin plot (only used when condition is not NULL), Default: FALSE
box	Indicates whether to depict a box plot (only used when condition is not NULL), Default: TRUE
width	Width parameter. When condition is NULL, controls bar width; when condition is provided, controls box plot width. Default: 0.9
pt	Indicates if points should be plotted (only used when condition is not NULL), Default: TRUE
pt.style	Position adjustment. Default choices: "quasirandom", "jitter" (only used when condition is not NULL)
pt.size	Point size setting (only used when condition is not NULL), Default: 1
pt.alpha	Adjusts the transparency of points (only used when condition is not NULL), Default: 1
style	Plot style: "fill" or "outline" (only used when condition is not NULL). Default: "outline"
ncol	Number of columns for multi-panel plots. Default: NULL
nrow	Number of rows for multi-panel plots. Default: NULL
stat.method	Determines if pairwise statistics are added to the plot. Either "wilcox.test" or "t.test", Default: "wilcox.test"
p.adjust.method	Method for adjusting p-values, Default: "none"
label	Specifies label type. Options include "p.signif", "p", "p.adj", "p.format", Default: "p.signif"
hide.ns	If TRUE, the 'ns' symbol is concealed when displaying significance levels, Default: TRUE
...	Additional arguments passed to VlnPlot2

Details

This function extends ClusterDistrBar to allow grouping by condition, creating boxplots instead of bar plots. When condition is NULL, it behaves exactly like ClusterDistrBar, supporting all its parameters and returning a stacked bar plot. When condition is provided, it transforms the distribution data into a boxplot format using VlnPlot2, with each box representing the distribution of a cluster's proportion across samples within the same condition. This is particularly useful for comparing cluster distributions between experimental conditions.

All styling parameters from VlnPlot2 are supported, including violin/box display options, point styles, colors, and statistical testing. For detailed formatting options, refer to the VlnPlot2 documentation. Common customizations include:

- Changing point display: pt=TRUE/FALSE, pt.size, pt.alpha, pt.style

- Adjusting plot style: style="fill"/"outline", violin=TRUE/FALSE

- Adding statistical tests: stat.method="wilcox.test"/"t.test", p.adjust.method

- Controlling layout: ncol, nrow for multi-cluster displays

Value

ggplot object or matrix

Examples

# Example with condition
ClusterDistrPlot(
  origin = pbmc$sample_id,
  cluster = pbmc$cluster,
  condition = pbmc$condition
)

huayc09/SeuratExtend documentation built on July 5, 2025, 1:41 a.m.