cell_bar_plot: Visualize Cell Fractions as Stacked Bar Chart

In IOBR: Immune Oncology Biological Research

Visualize Cell Fractions as Stacked Bar Chart

Description

Creates stacked bar charts to visualize tumor microenvironment (TME) cell fractions. Supports batch visualization of deconvolution results from methods such as CIBERSORT, EPIC, and quanTIseq.

Usage

cell_bar_plot(
  input,
  id = "ID",
  title = "Cell Fraction",
  features = NULL,
  pattern = NULL,
  legend.position = "bottom",
  coord_flip = TRUE,
  palette = 3,
  show_col = FALSE,
  cols = NULL
)

Arguments

input	Data frame containing deconvolution results.
id	Character string specifying the column name containing sample identifiers. Default is "ID".
title	Character string specifying the plot title. Default is "Cell Fraction".
features	Character vector specifying column names representing cell types to plot. If NULL, columns are selected based on 'pattern'. Default is NULL.
pattern	Character string or regular expression to match column names for automatic feature selection. Used when 'features' is NULL. Default is NULL.
legend.position	Character string specifying legend position ("bottom", "top", "left", "right"). Default is "bottom".
coord_flip	Logical indicating whether to flip plot coordinates using 'coord_flip()'. Default is TRUE.
palette	Integer specifying the color palette to use. Default is 3.
show_col	Logical indicating whether to display color information. Default is FALSE.
cols	Character vector of custom colors. If NULL, palette is used. Default is NULL.

Value

A ggplot2 object representing the stacked bar chart.

Author(s)

Dongqiang Zeng

Examples

set.seed(123)
input_data <- data.frame(
  ID = paste0("Sample", 1:10),
  Cell_A = runif(10, 0, 0.4),
  Cell_B = runif(10, 0, 0.3),
  Cell_C = runif(10, 0, 0.3)
)
cell_bar_plot(input = input_data, id = "ID", features = c("Cell_A", "Cell_B", "Cell_C"))

IOBR documentation built on May 30, 2026, 5:07 p.m.