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Heatmap

Heatmaps render pairwise co-mutation counts as an NxN matrix so larger co-occurrence sets stay readable.

Supported Commands

  • study co-occurrence --chart heatmap

Examples

biomcp study co-occurrence --study msk_impact_2017 \
  --genes TP53,KRAS,PIK3CA,EGFR --chart heatmap --terminal

biomcp study co-occurrence --study msk_impact_2017 \
  --genes TP53,KRAS,PIK3CA,EGFR --chart heatmap -o cooccurrence-heatmap.svg

Notes

Diagonal cells are placeholders rather than self-co-occurrence measurements.

--palette is not supported for heatmaps in this release. Use --theme and --title; BioMCP applies a fixed continuous colormap to the cells.