From fbff5cb4fc0b9c41df2ed1b2df3f88cba2732980 Mon Sep 17 00:00:00 2001 From: FrancescaDr Date: Mon, 10 Feb 2025 15:36:33 +0100 Subject: [PATCH 1/2] missing var_names in BasePlot --- src/scanpy/plotting/_baseplot_class.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/scanpy/plotting/_baseplot_class.py b/src/scanpy/plotting/_baseplot_class.py index e14d387f84..8e7499c44e 100644 --- a/src/scanpy/plotting/_baseplot_class.py +++ b/src/scanpy/plotting/_baseplot_class.py @@ -140,6 +140,18 @@ def __init__( ) self._update_var_groups() + + # exlude var_names not present in adata.var_names + missing_var_names = set(self.var_names).difference(adata.var_names) + if missing_var_names: + logg.warning( + f"The following var_names are not present in adata.var_names: {missing_var_names}" + ) + self.var_names = [ + var_name + for var_name in self.var_names + if var_name not in missing_var_names + ] self.categories, self.obs_tidy = _prepare_dataframe( adata, From 73f6c0bf14b757597b2dfbe191bdb37ad3faa2a5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 10 Feb 2025 15:01:34 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/scanpy/plotting/_baseplot_class.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/scanpy/plotting/_baseplot_class.py b/src/scanpy/plotting/_baseplot_class.py index 8e7499c44e..4b31c0eef5 100644 --- a/src/scanpy/plotting/_baseplot_class.py +++ b/src/scanpy/plotting/_baseplot_class.py @@ -140,7 +140,7 @@ def __init__( ) self._update_var_groups() - + # exlude var_names not present in adata.var_names missing_var_names = set(self.var_names).difference(adata.var_names) if missing_var_names: