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fix bug for partial_fit when the number of batch samples is less than n_comp #3313

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fix bug for partial_fit when the number of batch samples is less than n_comp #3313

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8d1cb04
fix bug for partial_fit when the number of batch samples is less than…
DingWB Sep 12, 2024
9550f8f
fix bug for partial_fit
DingWB Oct 23, 2024
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5 changes: 4 additions & 1 deletion src/scanpy/preprocessing/_pca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -263,7 +263,10 @@ def pca(

for chunk, _, _ in adata_comp.chunked_X(chunk_size):
chunk = chunk.toarray() if issparse(chunk) else chunk
pca_.partial_fit(chunk)
if n_comps <= chunk.shape[0]:
pca_.partial_fit(chunk)
else:
continue

for chunk, start, end in adata_comp.chunked_X(chunk_size):
chunk = chunk.toarray() if issparse(chunk) else chunk
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