chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
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get_embedding should not be obs biased #1048

Closed ebezzi closed 1 month ago

ebezzi commented 5 months ago

The get_embedding function was designed for obs embedding only (docs, parameters), but it also works for var embeddings. Changes needed:

  1. Rename obs_soma_joinids to soma_joinids. This is a breaking change, so consider whether we want to rename (and break) or do this via deprecation
  2. Change the docs to remove the obs bias.
pablo-gar commented 1 month ago

Superseded by the embedding arguments of get_anddata