Allow selection of layer/ raw for methods that use X
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- Python
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Description
I think this could use a consolidated effort for consistent behavior. Especially since testing whether it works will probably have some common patterns. In some cases Raw will need to be an option.
I like the convention of having the arguments use_raw, layers, and (when appropriate) obsm_key/ varm_key. With these at most one of the values can be not None, and if all are None (the default) X is used.
An alternative convention is use_rep: Optional[str]. I’m less a fan of this due to potential key collisions.
Some relevant issues/ prs: #826 #801 #730
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 related issues and pull requests #826, #801, and #730 to identify the affected methods and existing decisions. Define a consistent convention for selecting X, raw data, layers, and applicable obsm_key or varm_key values, then add shared tests for the expected behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100