Comments (2)
Hi @Mari123i, I am not quite sure I understand the subsetting steps correctly, could you share the exact code you are running? Ideally on a dataset on which I can also reproduce e.g. the vignette example data.
I suspect this error might come from subsetting the cell-level adata, but not the nhood-level anndata stored in adata.uns['nhood_adata']
. Do you re-run milopy.core.make_nhoods
and milopy.core.count_cells
after subsetting?
from milopy.
Hi @Mari123i, I am not quite sure I understand the subsetting steps correctly, could you share the exact code you are running? Ideally on a dataset on which I can also reproduce e.g. the vignette example data.
I suspect this error might come from subsetting the cell-level adata, but not the nhood-level anndata stored in
adata.uns['nhood_adata']
. Do you re-runmilopy.core.make_nhoods
andmilopy.core.count_cells
after subsetting?
Thank you for your reply! I do recalculate the KNN and neighbors for each subset. But no worries, the issue resolved itself. Thank you a lot for your time!
from milopy.
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