milo.make_nhoods(combined_emb) fails if 'X' was used for nearest neighbors

[canergen]

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

milopy/milopy/core.py

Line 65 in 49db7b8

X_dimred = adata.obsm[use_rep]

[canergen]

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