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loosing .uns metadata when concatenating

See original GitHub issue

I was facing some problems with metadata in .uns, when I realised that we currently don’t seem to have any mechanism that automatically transfers uns labels into obs before concatenating adatas when calling DatasetGroup.adata

I’m wondering whether we should just by default move all uns to obs before concatenating adatas. Couldn’t we just add a call to self._set_metadata_in_adata(allow_uns=False) before this line: https://github.com/theislab/sfaira/blob/58aadc6f9678f83f37587e1eceb6aaea99faa717/sfaira/data/base/dataset_group.py#L318

what do you think @davidsebfischer ?

Issue Analytics

State:
Created 2 years ago
Comments:6 (6 by maintainers)

Top GitHub Comments

1reaction

le-andercommented, Apr 1, 2021

like have another input argument for .streamline(format==“sfaira”, allow_uns=False)?

0reactions

davidsebfischercommented, Apr 1, 2021

Cellxgene streamlining needs allow_uns=False because the cellxgene object format is narrowly defined on this. I would not optimise this interface too much though because they might be merged in the future: https://github.com/theislab/sfaira/issues/200.