Linking patient data with cells
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- Dominant language
- Python
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Description
Hey!
I have recently gotten a quite deeply clinically phenotyped dataset and have been pondering how the metadata should best be stored in an anndata object. It feels redundant to duplicate a label for every cell from the same patient. Instead, one could save patient-level data in adata.uns and then have a function that links categories in an obs column to e.g., keys in a dict in adata.uns. This would save quite a lot of space in anndata objects if you have a lot of clinical metadata. I'm thinking of this as a hidden function that plotting functions could use instead of just looking for .obs columns to plot data.
This may be somewhat linked to #619.
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 relationship between cell-level adata.obs categories and patient-level metadata in adata.uns, then read the related discussion in #619. No file, test, or entry point is named, so the intended plotting behavior and completion criteria need to be clarified before implementation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100