Use simplified dendrogram for speed
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
Plotting a heatmap with many genes results in the dendrogram being impractical since the drawing of uncountable individual lines slows the plotting process to a crawl.
sc.pl.heatmap should grow a dendrogram resolution parameter that limits the dendrogram levels to a practical amount by default.
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 its dendrogram is drawn. Determine where a resolution parameter could limit dendrogram levels while preserving the heatmap behavior, then add coverage showing the parameter bounds the rendered dendrogram and improves the many-gene case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100