plotting-heatmaps

name	plotting-heatmaps
description	Generate marker gene heatmaps with hierarchical clustering dendrograms.
allowed-tools	Read, Bash
compatibility	scRNA-seq, snRNA-seq

Heatmap Plots

When to Use

To visualize marker gene expression patterns across clusters for annotation review.

Functions

heatmap(adata, genes, groupby, output_dir=None, dendrogram=True, show_values=False) -> str

Creates marker gene heatmap with optional dendrogram. Saves to {output_dir}/heatmap_{groupby}.png