Fix stacked_violin’s standard_scale parameter (#3243)

scverse · Sep 20, 2024 · dbabafa · dbabafa
1 parent bd75839
commit dbabafa
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Showing 12 changed files with 15 additions and 7 deletions.
diff --git a/docs/release-notes/3243.bugfix.md b/docs/release-notes/3243.bugfix.md
@@ -0,0 +1 @@
+Accept `'group'` instead of `'obs'` for `standard_scale` parameter in {func}`~scanpy.pl.stacked_violin` {smaller}`P Angerer`
diff --git a/src/scanpy/plotting/_stacked_violin.py b/src/scanpy/plotting/_stacked_violin.py
@@ -222,6 +222,10 @@ def __init__(
         )
 
         if standard_scale == "obs":
+            standard_scale = "group"
+            msg = "`standard_scale='obs'` is deprecated, use `standard_scale='group'` instead"
+            warnings.warn(msg, FutureWarning)
+        if standard_scale == "group":
             self.obs_tidy = self.obs_tidy.sub(self.obs_tidy.min(1), axis=0)
             self.obs_tidy = self.obs_tidy.div(self.obs_tidy.max(1), axis=0).fillna(0)
         elif standard_scale == "var":
@@ -680,7 +684,7 @@ def stacked_violin(
     gene_symbols: str | None = None,
     var_group_positions: Sequence[tuple[int, int]] | None = None,
     var_group_labels: Sequence[str] | None = None,
-    standard_scale: Literal["var", "obs"] | None = None,
+    standard_scale: Literal["var", "group"] | None = None,
     var_group_rotation: float | None = None,
     layer: str | None = None,
     stripplot: bool = StackedViolin.DEFAULT_STRIPPLOT,

diff --git a/tests/_images/dotplot/expected.png b/tests/_images/dotplot/expected.png
diff --git a/tests/_images/dotplot_dict/expected.png b/tests/_images/dotplot_dict/expected.png
diff --git a/tests/_images/matrixplot/expected.png b/tests/_images/matrixplot/expected.png
diff --git a/tests/_images/matrixplot2/expected.png b/tests/_images/matrixplot2/expected.png
diff --git a/tests/_images/matrixplot_std_scale_group/expected.png b/tests/_images/matrixplot_std_scale_group/expected.png
diff --git a/tests/_images/stacked_violin/expected.png b/tests/_images/stacked_violin/expected.png
diff --git a/tests/_images/stacked_violin_no_cat_obs/expected.png b/tests/_images/stacked_violin_no_cat_obs/expected.png
diff --git a/tests/_images/stacked_violin_std_scale_group/expected.png b/tests/_images/stacked_violin_std_scale_group/expected.png
diff --git a/tests/_images/stacked_violin_std_scale_var_dict/expected.png b/tests/_images/stacked_violin_std_scale_var_dict/expected.png
diff --git a/tests/test_plotting.py b/tests/test_plotting.py
@@ -167,9 +167,9 @@ def test_clustermap(image_comparer, obs_keys, name):
     save_and_compare_images(name)
 
 
-@pytest.mark.parametrize(
-    ("id", "fn"),
-    [
+params_dotplot_matrixplot_stacked_violin = [
+    pytest.param(id, fn, id=id)
+    for id, fn in [
         (
             "dotplot",
             partial(
@@ -317,10 +317,13 @@ def test_clustermap(image_comparer, obs_keys, name):
                 figsize=(8, 2.5),
             ),
         ),
-    ],
-)
+    ]
+]
+
+
+@pytest.mark.parametrize(("id", "fn"), params_dotplot_matrixplot_stacked_violin)
 def test_dotplot_matrixplot_stacked_violin(image_comparer, id, fn):
-    save_and_compare_images = partial(image_comparer, ROOT, tol=15)
+    save_and_compare_images = partial(image_comparer, ROOT, tol=5)
 
     adata = krumsiek11()
     adata.obs["numeric_column"] = adata.X[:, 0]