Allow plotting heatmap with smoothed expressions per cluster
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- Dominant language
- Python
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Description
When dealing with many cells, it can be hard to see expression patterns without smoothing. using the PAGA smoothed version doesn’t respect cluster border, however.
It should be possible to specify a smoothing parameter to sc.pl.heatmap.
cc @sophietr
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the sc.pl.heatmap entry point and trace how the PAGA-smoothed expression is used for plotting. Add a smoothing parameter that preserves cluster borders, then verify that heatmaps for many cells show the intended smoothed patterns without losing cluster separation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100