From 5c1d7c98dcf919f27a685d37a942a214a57efd47 Mon Sep 17 00:00:00 2001 From: ktpolanski Date: Thu, 5 Feb 2026 14:07:46 +0000 Subject: [PATCH 1/2] fillna(1) spatialfdr --- pertpy/tools/_milo.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pertpy/tools/_milo.py b/pertpy/tools/_milo.py index c545e3c3..2c4c626d 100644 --- a/pertpy/tools/_milo.py +++ b/pertpy/tools/_milo.py @@ -789,6 +789,9 @@ 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 + 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, From b392304cafb0026ea10641b5dcb427dd396e5337 Mon Sep 17 00:00:00 2001 From: ktpolanski Date: Thu, 5 Feb 2026 14:17:59 +0000 Subject: [PATCH 2/2] link issue --- pertpy/tools/_milo.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pertpy/tools/_milo.py b/pertpy/tools/_milo.py index 2c4c626d..13ddd64e 100644 --- a/pertpy/tools/_milo.py +++ b/pertpy/tools/_milo.py @@ -790,6 +790,7 @@ def _graph_spatial_fdr( 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)