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Update velocity.py #1310

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5 changes: 4 additions & 1 deletion scvelo/tools/velocity.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import warnings

import numpy as np
import scanpy as sc

from scvelo import logging as logg
from scvelo import settings
Expand Down Expand Up @@ -323,7 +324,9 @@ def velocity(
perc = [5, 95]
adata = data.copy() if copy else data
if not use_raw and "Ms" not in adata.layers.keys():
moments(adata)
sc.pp.pca(adata)
sc.pp.neighbors(adata, n_pcs=30, n_neighbors=30)
moments(adata, n_neighbors=None, n_pcs=None,)

logg.info("computing velocities", r=True)

Expand Down