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Generate marker gene heatmaps with hierarchical clustering dendrograms.
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Correct batch effects in single-cell data using Harmony, BBKNN, or ComBat.
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| name | plotting-heatmaps |
| description | Generate marker gene heatmaps with hierarchical clustering dendrograms. |
| allowed-tools | Read, Bash |
| compatibility | scRNA-seq, snRNA-seq |
To visualize marker gene expression patterns across clusters for annotation review.
heatmap(adata, genes, groupby, output_dir=None, dendrogram=True, show_values=False) -> strCreates marker gene heatmap with optional dendrogram.
Saves to {output_dir}/heatmap_{groupby}.png