sig_pheatmap: Generate Heatmap for Signature Data

In IOBR: Immune Oncology Biological Research

Generate Heatmap for Signature Data

Description

Creates a heatmap from signature data with grouping variables, offering flexible options for colors, clustering, and output formats using ComplexHeatmap.

Usage

sig_pheatmap(
  input,
  feas,
  group,
  group2 = NULL,
  group3 = NULL,
  ID = "ID",
  path = NULL,
  cols1 = "random",
  cols2 = "random",
  cols3 = "random",
  seed = 54321,
  show_col = FALSE,
  palette1 = 1,
  palette2 = 2,
  palette3 = 3,
  cluster_cols = TRUE,
  palette_for_heatmape = 6,
  scale.matrix = TRUE,
  cellwidth = 1,
  cellheight = 9,
  show_colnames = FALSE,
  fig.type = "pdf",
  width = 6,
  height = NULL,
  file_name_prefix = 1
)

Arguments

input	Data frame with variables in columns.
feas	Character vector. Feature names (columns) to include in heatmap.
group	Character string. Column name for primary grouping variable.
group2	Character string or 'NULL'. Optional secondary grouping variable.
group3	Character string or 'NULL'. Optional tertiary grouping variable.
ID	Character string. Column name for sample identifiers. Default is '"ID"'.
path	Character string or 'NULL'. Directory to save output files. If 'NULL', the heatmap is not saved. Default is 'NULL'.
cols1	Character vector or '"random"' or '"normal"'. Colors for primary group. Default is '"random"'.
cols2	Character vector or '"random"' or '"normal"'. Colors for secondary group. Default is '"random"'.
cols3	Character vector or '"random"' or '"normal"'. Colors for tertiary group. Default is '"random"'.
seed	Integer. Random seed for color generation. Default is '54321'.
show_col	Logical indicating whether to display colors. Default is 'FALSE'.
palette1	Integer. Palette for primary group. Default is '1'.
palette2	Integer. Palette for secondary group. Default is '2'.
palette3	Integer. Palette for tertiary group. Default is '3'.
cluster_cols	Logical indicating whether to cluster columns. Default is 'TRUE'.
palette_for_heatmape	Integer. Palette number for heatmap. Default is '6'.
scale.matrix	Logical indicating whether to scale the matrix. Default is 'TRUE'.
cellwidth	Numeric. Width of each cell in points. Default is '1'.
cellheight	Numeric. Height of each cell in points. Default is '9'.
show_colnames	Logical indicating whether to show column names. Default is 'FALSE'.
fig.type	Character string. File format for saving. Default is '"pdf"'.
width	Numeric. Width of saved figure in inches. Default is '6'.
height	Numeric or 'NULL'. Height of saved figure in inches. Calculated if 'NULL'.
file_name_prefix	Character or numeric. Prefix for saved file name. Default is '1'.

Value

A list containing:

p_anno

Annotation data frame

p_cols

List of cluster colors

plot

ComplexHeatmap object

eset

Transformed expression matrix

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_pheatmap(
  input = test_input,
  feas = c("Sig1", "Sig2"),
  group = "subtype"
)

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