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chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
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Compartment / Coarse Cell Types #883

Open Yanay1 opened 9 months ago

Yanay1 commented 9 months ago

Description

It would be great if the census had some coarse cell types / compartment information in addition to the fine grained cell types!

Context

For UCE, I wanted to view transferred labels separated by compartment (eg stromal, endothelial, immune etc). Unless pre-made by authors, I end up having to come up with a mapping each time.

Impact

This would be a great feature for label transfer-- you could subset the census to endothelial cells for example and then have a high quality reference to transfer to the endothelial compartment of your new dataset.

Alternatives you've considered

The alternative is to use your own coarse mapping or author provided ones if they exist.

Ideal behavior

There would be some column(s) in the census / standard in the adata reference corresponding to compartment. Maybe this could also just exists as one dictionary (from cell type to compartment).

pablo-gar commented 9 months ago

Thanks Yanay. This is the very similar to https://github.com/chanzuckerberg/cellxgene-census/issues/17 we are currently exploring options on this.

pablo-gar commented 9 months ago

cc @brianraymor

pablo-gar commented 3 months ago

See suggested initial minimal solution https://github.com/chanzuckerberg/cellxgene-census/issues/1029#issuecomment-2108164017