scverse / scverse/scanpy

Linking patient data with cells

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#658 3 comments 0 reactions 0 assignees View on GitHub

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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.

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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

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