sc.tl.dpt(adata, n_branchings=2) sometimes works sometimes doesn't
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Description
A very very strange issue:
I would want to visualize a huge dataset (10000+, 20000+). However, sc.tl.dpt(adata, n_branchings=2) doesn't work. If I happened to select a smaller subgroup, it might work but not all the time.
Thanks in advance for your help.
Allen
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.tl.dpt entry point and reproduce the behavior with datasets larger than 10,000 cells, varying n_branchings=2 and the selected subgroup. Capture the missing error details and identify a minimal dataset that distinguishes the working and failing cases; done means the failure is reproducible and its cause or a verified fix is documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100