How does the `tl.get_c_niche` function work?

LiHongCSBLab / SOAPy

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How does the `tl.get_c_niche` function work? #4

Open atharva-bhagwat opened 3 months ago

atharva-bhagwat commented 3 months ago

Can you please provide some insights on how tl.get_c_niche works? Thank you!

wheat-whq commented 2 months ago

tl.get_c_niche calculates the proportion of cell types in the neighborhood of each cell through the spatial network, and then clusters them. There is a bug in the version installed by pip. It has been fixed in github and will be updated in pip later.

atharva-bhagwat commented 2 months ago

One bug i found is that there is a mismatch between C_niche values in adata.uns['SOAPy'] and adata.obs. Is it fixed now?