Add persistence diagrams for persistent homology analysis
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- Dominant language
- Python
- Stars
- 598
- Forks
- 121
- Avg merge
- 3d 11h
- Merged PRs (30d)
- 3
Description
Description of feature
Hi, I have worked on persistent homology and persistence diagrams which have been a common technique used for extracting topological features for downstream analysis. I was wondering would you be interested if I added a few functions to squidpy which would allow this? Below is a small example.
Possible MVP:
sq.gr.persistent_homology(...) for computing persistence diagrams from adata.obsm["spatial"]
output stored in adata.uns[...] or returned as a tidy DataFrame
sq.pl.persistence_diagram(...) for visualization
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 by reviewing the proposed sq.gr.persistent_homology(...) and sq.pl.persistence_diagram(...) entry points, using adata.obsm["spatial"] as the input described. Define how persistence diagrams are computed and whether results belong in adata.uns[...] or a tidy DataFrame, then ensure the visualization entry point can display them.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100