fix: copy size array before reorder in multi-color scatter plots

src/scanpy/plotting/_tools/scatterplots.py

@@ -295,8 +295,9 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
             # Null points go on bottom
             order = np.argsort(~pd.isnull(color_source_vector), kind="stable")
         # Set orders
-        if isinstance(size, np.ndarray):
-            size = np.array(size)[order]
+        # Copy size before reordering so the original array is preserved
+        # across loop iterations (fixes #4024)
+        _size = size[order] if isinstance(size, np.ndarray) else size
         color_source_vector = color_source_vector[order]
         color_vector = color_vector[order]
         coords = basis_values[:, dims][order, :]
@@ -348,10 +349,10 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
             )
         else:
             scatter = (
-                partial(ax.scatter, s=size, plotnonfinite=True)
+                partial(ax.scatter, s=_size, plotnonfinite=True)
                 if scale_factor is None
                 else partial(
-                    circles, s=size, ax=ax, scale_factor=scale_factor
+                    circles, s=_size, ax=ax, scale_factor=scale_factor
                 )  # size in circles is radius
             )
 
@@ -366,7 +367,7 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
                 # with some transparency.
 
                 bg_width, gap_width = outline_width
-                point = np.sqrt(size)
+                point = np.sqrt(_size)
                 gap_size = (point + (point * gap_width) * 2) ** 2
                 bg_size = (np.sqrt(gap_size) + (point * bg_width) * 2) ** 2
                 # the default black and white colors can be changes using

tests/test_plotting.py

@@ -1875,6 +1875,23 @@ def test_umap_mask_no_modification():
     pd.testing.assert_series_equal(pbmc.obs["louvain"], data_copy)
 
 
+def test_scatter_size_not_mutated_across_panels():
+    """Per-point size array must not be cumulatively reordered across subplots.
+
+    Regression test for https://github.com/scverse/scanpy/issues/4024
+    """
+    pbmc = pbmc3k_processed()
+    rng = np.random.default_rng(0)
+    sizes = rng.uniform(10, 200, size=pbmc.n_obs)
+    sizes_original = sizes.copy()
+
+    axes = sc.pl.umap(pbmc, color=["louvain", "n_genes"], size=sizes, show=False)
+    plt.close()
+
+    # The input array must not be modified
+    np.testing.assert_array_equal(sizes, sizes_original)
+
+
 def test_string_mask(tmp_path, check_same_image):
     """Check that the same mask given as string or bool array provides the same result."""
     pbmc = pbmc3k_processed()