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Bug fix for scanpy.tl.score_genes #3167

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Bug fix for scanpy.tl.score_genes #3167

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fix_score_genes.py
gmvaccaro Jul 24, 2024
9aa2f83
Merge branch 'main' into patch-1
flying-sheep Jul 26, 2024
51f2f5f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 26, 2024
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6 changes: 4 additions & 2 deletions src/scanpy/tools/_score_genes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -237,8 +237,10 @@ def _score_genes_bins(
# Sometimes (and I don’t know how) missing data may be there, with NaNs for missing entries
obs_avg = obs_avg[np.isfinite(obs_avg)]

n_items = int(np.round(len(obs_avg) / (n_bins - 1)))
obs_cut = obs_avg.rank(method="min") // n_items
obs_avg.sort_values(ascending=True, inplace=True)
n_items = int(np.ceil(len(obs_avg) / (n_bins)))
rank = np.repeat(np.arange(n_bins), n_items)[: len(obs_avg)]
obs_cut = pd.Series(rank, index=obs_avg.index)
keep_ctrl_in_obs_cut = False if ctrl_as_ref else obs_cut.index.isin(gene_list)

# now pick `ctrl_size` genes from every cut
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