Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add layer argument for sc.tl.score_genes_cell_cycle #3138

Draft
wants to merge 4 commits into
base: main
Choose a base branch
from
Draft

add layer argument for sc.tl.score_genes_cell_cycle #3138

Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
fcd3399
add the layer argument for sc.tl.score_genes_cell_cycle
shinthor Jul 2, 2024
a00fd76
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 5, 2024
66b52dc
Merge branch 'main' into main
shinthor Jul 8, 2024
4ed4477
Merge branch 'main' into main
flying-sheep Jul 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion src/scanpy/tools/_score_genes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -207,6 +207,7 @@
s_genes: Sequence[str],
g2m_genes: Sequence[str],
copy: bool = False,
layer: str | None = None,
**kwargs,
) -> AnnData | None:
"""\
Expand All @@ -226,6 +227,8 @@
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 @@
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)

Check warning on line 260 in src/scanpy/tools/_score_genes.py

View check run for this annotation

Codecov / codecov/patch

src/scanpy/tools/_score_genes.py#L260 

Added line #L260 was not covered by tests
scores = adata.obs[["S_score", "G2M_score"]]

# default phase is S
Expand Down
Loading