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emdann / milopy

Python implementation of Milo for differential abundance testing on KNN graph
MIT License
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milo.make_nhoods(combined_emb) fails if 'X' was used for nearest neighbors #44

Closed canergen closed 1 year ago

canergen commented 1 year ago

milopy assumes neighbors were calculated on a reduced dimension. Especially for protein assays, this is not always the case:

https://github.com/emdann/milopy/blob/49db7b8354538632a25480c172de0ced3e136db4/milopy/core.py#L65

canergen commented 1 year ago

Thanks for fixing the PR @emdann (I should stop coding on Github directly)