Skip to content

fillna(1) spatialfdr #913

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

Merged
Zethson merged 2 commits into from
Feb 9, 2026
Merged

fillna(1) spatialfdr #913

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
5c1d7c9
fillna(1) spatialfdr
ktpolanski Feb 5, 2026
b392304
link issue
ktpolanski Feb 5, 2026
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
4 changes: 4 additions & 0 deletions pertpy/tools/_milo.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -789,6 +789,10 @@ def _graph_spatial_fdr(
sample_adata.var["SpatialFDR"] = np.nan
sample_adata.var.loc[keep_nhoods, "SpatialFDR"] = adjp

# Fill missing values with 1 to avoid downstream NaN complications
# e.g. https://github.com/scverse/pertpy/issues/912
sample_adata.var["SpatialFDR"] = sample_adata.var["SpatialFDR"].fillna(1)

@_doc_params(common_plot_args=doc_common_plot_args)
def plot_nhood_graph( # pragma: no cover # noqa: D417
self,
Expand Down
Loading