Allow subsetting features when clustering

saeyslab / harpy

https://harpy.readthedocs.io/en/latest/

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Allow subsetting features when clustering #3

Closed berombau closed 5 months ago

berombau commented 6 months ago

Currently, the whole X matrix is used (https://github.com/saeyslab/harpy/blob/main/src/sparrow/table/_clustering.py). A subset of only the lineage markers is needed for good-quality clustering. This should be a list of indices (numerical or string). Adding this as an annotation like a boolean mask "lineage" in the AnnData.var could also be nice.

ArneDefauw commented 5 months ago

https://github.com/saeyslab/harpy/pull/12 should close this issue, unless we still want this "Adding this as an annotation like a boolean mask "lineage" in the AnnData.var could also be nice."