sig_heatmap: Signature Heatmap with Optional Annotations

In IOBR: Immune Oncology Biological Research

Signature Heatmap with Optional Annotations

Description

Generates a heatmap of selected features grouped by a categorical variable, with optional conditional (annotation) bars. Supports palette customization, scaling, size controls, and output saving.

Usage

sig_heatmap(
  input,
  id = "ID",
  features,
  group,
  condition = NULL,
  id_condition = "vars",
  col_condition = "condition",
  cols_condition = NULL,
  scale = FALSE,
  palette = 2,
  cols_heatmap = NULL,
  palette_group = "jama",
  show_col = FALSE,
  show_palettes = FALSE,
  cols_group = NULL,
  show_plot = TRUE,
  width = 8,
  height = NULL,
  size_col = 10,
  size_row = 8,
  angle_col = 90,
  column_title = NULL,
  row_title = NULL,
  show_heatmap_col_name = FALSE,
  path = NULL,
  index = NULL
)

Arguments

input	Data frame containing ID, grouping variable, and feature columns.
id	Character string. Column name for sample identifier. Default is '"ID"'.
features	Character vector. Feature (column) names to include in the heatmap.
group	Character string. Grouping variable column name.
condition	Data frame or 'NULL'. Optional annotation table with variable-condition mapping. Default is 'NULL'.
id_condition	Character string. Column name in 'condition' for feature IDs. Default is '"vars"'.
col_condition	Character string. Column name in 'condition' for condition labels. Default is '"condition"'.
cols_condition	Character vector. Colors for conditions.
scale	Logical indicating whether to scale values by row. Default is 'FALSE'.
palette	Integer or character. Palette index/name for heatmap colors. Default is '2'.
cols_heatmap	Character vector. Custom colors for heatmap gradient.
palette_group	Character string. Palette name for group colors. Default is '"jama"'.
show_col	Logical indicating whether to display the color vector. Default is 'FALSE'.
show_palettes	Logical indicating whether to print palette options. Default is 'FALSE'.
cols_group	Character vector. Custom colors for groups.
show_plot	Logical indicating whether to print the heatmap. Default is 'TRUE'.
width	Numeric. Plot width in inches. Default is '8'.
height	Numeric or 'NULL'. Plot height in inches. Auto-calculated if 'NULL'.
size_col	Numeric. Font size for column labels. Default is '10'.
size_row	Numeric. Font size for row labels. Default is '8'.
angle_col	Numeric. Rotation angle for column labels in degrees. Default is '90'.
column_title	Character string or 'NULL'. Title for column annotation.
row_title	Character string or 'NULL'. Title for row annotation.
show_heatmap_col_name	Logical indicating whether to show column names. Default is 'FALSE'.
path	Character string or 'NULL'. Output directory for saving the heatmap.
index	Integer or 'NULL'. Index appended to filename. Default is 'NULL'.

Value

A tidyHeatmap object. Saves PDF only when 'path' is provided.

Author(s)

Dongqiang Zeng

Examples

set.seed(123)
test_input <- data.frame(
  ID = paste0("Sample", 1:20),
  subtype = sample(c("TypeA", "TypeB"), 20, replace = TRUE),
  Sig1 = rnorm(20),
  Sig2 = rnorm(20)
)
sig_heatmap(input = test_input, features = c("Sig1", "Sig2"), group = "subtype", scale = TRUE)

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