HeatmapExp: HeatmapExp

In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

HeatmapExp

Description

Plot a heatmap of the top variable genes across samples.

Usage

HeatmapExp(
  x,
  ColorPanel,
  scale,
  cutree_rows,
  cutree_cols,
  cluster,
  show_names,
  NumGenes
)

Arguments

x	Numeric matrix of log-CPM values (genes × samples), e.g., from edgeR::cpm().
ColorPanel	Character. Name of a continuous palette from the paletteer package.
scale	Character. Scaling mode for heatmap: "row", "column", or "none".
cutree_rows	Integer. Number of clusters for rows (genes).
cutree_cols	Integer. Number of clusters for columns (samples).
cluster	Character. One of "both", "row", "column", or "none" to specify clustering.
show_names	Character. One of "both", "row", "column", or "none" to show row/col names.
NumGenes	Integer. Number of top-variance genes to include in the heatmap.

Details

This function selects the highest-variance genes from a log-CPM matrix, transposes the data, and renders a heatmap with customizable clustering, scaling, and color palettes using pheatmap.

1. Compute per-gene variance and select the top "NumGenes".

2. Transpose the subsetted matrix so samples are rows.

3. Apply the specified color palette (n = 50) via paletteer::paletteer_c().

4. Determine clustering and name-display options from "cluster" and "show_names".

5. Render the heatmap with "pheatmap::pheatmap()", saving to a temporary file to suppress autosave.

Value

A "pheatmap" object containing the heatmap and clustering information.

inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.