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pre-commit-ci[bot]Reovirus
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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src/scanpy/tools/_score_genes.py

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -37,16 +37,18 @@ def _sparse_nanmean(X: CSBase, axis: Literal[0, 1]) -> NDArray[np.float64]:
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Z = X.copy()
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# count the number of nonzero elements (include nans) per row/column (dep. on axis)
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nonzeros_and_nones=Z.count_nonzero(axis=axis)
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nonzeros_and_nones = Z.count_nonzero(axis=axis)
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# just sum the data withput nan
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Z.data[np.isnan(Z.data)] = 0
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Z.eliminate_zeros()
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s = Z.sum(axis, dtype="float64")
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# Z.count_nonzero(axis=axis) is now non-zero not-nan elements in X
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#diff between nonzeros_and_nones and curr nonzero is nans
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n_elements=(Z.shape[axis] - (nonzeros_and_nones - Z.count_nonzero(axis=axis))).reshape(s.shape, copy=False)
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# diff between nonzeros_and_nones and curr nonzero is nans
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n_elements = (
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Z.shape[axis] - (nonzeros_and_nones - Z.count_nonzero(axis=axis))
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).reshape(s.shape, copy=False)
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m = s / n_elements
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return m

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