Create a ComplexHeatmap with row annotation

Generates a heatmap using the ComplexHeatmap package with a single-color row annotation. Designed to stack several heatmaps (for example, one per cell type) with consistent formatting.

Usage

create_heatmap(
  mat,
  color,
  split,
  common_names = rownames(mat),
  use_raster_flag = FALSE
)

Arguments

mat

A numeric matrix representing the heatmap values (e.g., Z-scores).

color

A character string specifying the annotation color (e.g., "black", "gold1").

split

A factor, character vector or data frame used to split the columns of the heatmap. NULL for no split.

common_names

A character vector of row names, used to size the annotation. By default, the row names of mat.

use_raster_flag

Logical. If TRUE, rasterization is enabled for faster rendering of large matrices (requires the magick package and a working Cairo/X11 installation). Default FALSE.

Value

A Heatmap object from ComplexHeatmap, ready to be combined or drawn.

Details

Requires the Bioconductor package ComplexHeatmap, which is not installed with GeneExprLupusMx. If it is missing, the function stops and shows how to install it:

install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")

Note

Other packages (e.g., RplotterPkg and wilson) also have a function called create_heatmap(). If you load one of them together with GeneExprLupusMx, the one loaded last is used. To make sure you use this one, call it as GeneExprLupusMx::create_heatmap().

Examples

if (requireNamespace("ComplexHeatmap", quietly = TRUE)) {
  # small simulated Z-score matrix: 50 genes x 20 samples
  # (with the lesson data: zscore_mat <- download_data("zscore_mat"))
  set.seed(1)
  mat <- t(scale(t(matrix(rnorm(50 * 20), nrow = 50))))
  ht <- create_heatmap(mat, color = "black", split = NULL)
  ComplexHeatmap::draw(ht)
}