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Backport PR #4090 on branch 1.12.x (perf: hoist _tiecorrect out of per-group loop in vs-rest Wilcoxon) (#4094)
Co-authored-by: Zach Boldyga <zboldyga@users.noreply.github.com>
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src/scanpy/tools/_rank_genes_groups.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -363,11 +363,11 @@ def wilcoxon(
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tc_coef = np.zeros((n_groups, n_genes))
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for ranks, left, right in _ranks(self.X):
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if tie_correct:
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tc_coef[:, left:right] = _tiecorrect(ranks)
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# sum up adjusted_ranks to calculate W_m,n
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for group_index, mask_obs in enumerate(self.groups_masks_obs):
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scores[group_index, left:right] = ranks[mask_obs, :].sum(axis=0)
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if tie_correct:
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tc_coef[group_index, left:right] = _tiecorrect(ranks)
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for group_index, mask_obs in enumerate(self.groups_masks_obs):
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n_active = np.count_nonzero(mask_obs)

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