sc.pl.heatmap show the wrong scale
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Description
Dear, when I use sc.pl.heatmap(adata,markers,groupby='leiden',show_gene_labels=True) to show some marker genes, the colorbar value range is different from that generated by sc.pl.umap(). I am sure that umap show the expression value correctly and there must be something wrong with sc.pl.heatmap(), here are the images:
For example, the expression value of gene 'Sct' is 0-7.5, while it changes to 0-1e7 on the heatmap, the value is so high that it may scale other gene's expression value to almost zero and nothing can be seen on heatmap for other genes. Some other genes have the same issue. Do you know the reason ?
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Research direction
Reproduce the report with sc.pl.heatmap(adata, markers, groupby='leiden', show_gene_labels=True) and compare its colorbar with sc.pl.umap(). Start at the sc.pl.heatmap and sc.pl.umap entry points to trace how expression values and scales are handled. Done means the heatmap uses the correct expression range, such as 0–7.5 for Sct, without suppressing other genes.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100