Subsample by observations grouping
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
Related to scanpy.pp.subsample, it would be useful to have a subsampling tool that subsamples based on the key of an observations grouping. E.g., if I have an observation key 'MyGroup' with possible values ['A', 'B'], and there are 10,000 cells of type 'A' and 2,000 cells of type 'B' and I want only max 5,000 cells of each type, then this function would subsample 5,000 cells of type 'A' but retain all 2,000 cells of type 'B'.
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 with the existing scanpy.pp.subsample entry point and review how it selects observations. Define the grouping-key behavior described in the issue: retain at most the requested number of observations per group while keeping smaller groups intact. Done means the function supports the example with the MyGroup observation key and preserves all groups below the limit.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100