sc.pl.heatmap cannot show different colors for more than 20 cell types
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Area - Plotting 🌺
- Dominant language
- Python
- Stars
- 2.6k
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Description
I plot heatmap for normalized gene expression for 34 clusters. The code is as below:
sc.pl.heatmap(adata, marker_genes, use_raw=False, swap_axes=True, show=False, show_gene_labels=True, save=ofile, groupby='louvain', dendrogram=True)
However, there are only 20 colors for the cluster bars. How can I deal with this issue?
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First steps
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Research direction
Start at the sc.pl.heatmap entry point and trace how colors are assigned to the groupby='louvain' categories. Reproduce the reported case with 34 clusters and determine the expected behavior for color bars beyond 20 categories; done means the heatmap can represent all groups distinctly or documents the supported limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100