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feat: add layer argument for sc.tl.score_genes_cell_cycle #3138

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feat: add layer argument for sc.tl.score_genes_cell_cycle #3138

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fcd3399
add the layer argument for sc.tl.score_genes_cell_cycle
shinthor Jul 2, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 5, 2024
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shinthor Jul 8, 2024
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flying-sheep Jul 25, 2024
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shinthor Aug 31, 2025
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shinthor Aug 31, 2025
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flying-sheep Sep 9, 2025
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5 changes: 4 additions & 1 deletion src/scanpy/tools/_score_genes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -207,6 +207,7 @@ def score_genes_cell_cycle(
s_genes: Sequence[str],
g2m_genes: Sequence[str],
copy: bool = False,
layer: str | None = None,
**kwargs,
) -> AnnData | None:
"""\
Expand All @@ -226,6 +227,8 @@ def score_genes_cell_cycle(
List of genes associated with G2M phase.
copy
Copy `adata` or modify it inplace.
layer
Key from `adata.layers` whose value will be used to perform tests on.
**kwargs
Are passed to :func:`~scanpy.tl.score_genes`. `ctrl_size` is not
possible, as it's set as `min(len(s_genes), len(g2m_genes))`.
Expand Down Expand Up @@ -254,7 +257,7 @@ def score_genes_cell_cycle(
adata = adata.copy() if copy else adata
ctrl_size = min(len(s_genes), len(g2m_genes))
for genes, name in [(s_genes, "S_score"), (g2m_genes, "G2M_score")]:
score_genes(adata, genes, score_name=name, ctrl_size=ctrl_size, **kwargs)
score_genes(adata, genes, score_name=name, ctrl_size=ctrl_size, layer=layer, **kwargs)
scores = adata.obs[["S_score", "G2M_score"]]

# default phase is S
Expand Down