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pheno_jaccard_ig to be a csr matrix #2295

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Merged
Zethson merged 3 commits into from
Apr 19, 2023
Merged

pheno_jaccard_ig to be a csr matrix #2295

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1f7fc46
pheno_jaccard fix
Jul 15, 2022
6369a0b
Simpler tocsr
Zethson Apr 19, 2023
63142f7
Merge branch 'master' into master
Zethson Apr 19, 2023
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3 changes: 2 additions & 1 deletion scanpy/external/tl/_phenograph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import numpy as np
import pandas as pd
from anndata import AnnData
import scipy as sp
from scipy.sparse import spmatrix

from ...tools._leiden import MutableVertexPartition
Expand Down Expand Up @@ -242,7 +243,7 @@ def phenograph(
if copy:
return communities, graph, Q
else:
adata.obsp[ig_key] = graph
adata.obsp[ig_key] = graph.tocsr()
if comm_key:
adata.obs[comm_key] = pd.Categorical(communities)
if Q:
Expand Down