fix(color): honour palette for outline-only columns and over .uns colors

src/spatialdata_plot/pl/_color.py

@@ -662,9 +662,11 @@ def _set_color_source_vec(
         table_to_use = _resolve_color_table(value_from_element, table_name, sdata)
         adata_for_mapping = sdata[table_to_use] if table_to_use is not None else None
 
-        # Check if custom colors exist in the resolved table's .uns slot
+        # Check if custom colors exist in the resolved table's .uns slot; an explicit
+        # category->color dict palette takes precedence over them.
         if (
             value_to_plot is not None
+            and not isinstance(palette, dict)
             and table_to_use is not None
             and _has_colors_in_uns(sdata, table_to_use, value_to_plot)
         ):

src/spatialdata_plot/pl/_validate.py

@@ -72,9 +72,10 @@ def _gate_palette_and_groups(
     element_params: dict[str, Any],
     param_dict: dict[str, Any],
 ) -> None:
-    """Set palette/groups on element_params only when col_for_color is present, else warn."""
+    """Keep palette when a fill or outline column is present; groups only with a fill column, else warn."""
     has_col = element_params.get("col_for_color") is not None
-    element_params["palette"] = param_dict["palette"] if has_col else None
+    has_outline_col = element_params.get("col_for_outline_color") is not None
+    element_params["palette"] = param_dict["palette"] if has_col or has_outline_col else None
     if not has_col and param_dict["groups"] is not None:
         logger.warning(_GROUPS_IGNORED_WARNING)
     element_params["groups"] = param_dict["groups"] if has_col else None

tests/pl/test_render_labels.py

@@ -6,7 +6,7 @@
 import pytest
 import scanpy as sc
 from anndata import AnnData
-from matplotlib.colors import Normalize
+from matplotlib.colors import Normalize, to_hex
 from matplotlib.legend import Legend
 from spatial_image import to_spatial_image
 from spatialdata import SpatialData, deepcopy, get_element_instances
@@ -852,6 +852,17 @@ def test_labels_outline_color_groups_filter_aligns(sdata_blobs: SpatialData):
     plt.close(fig)
 
 
+def test_render_labels_respects_dict_palette(sdata_blobs: SpatialData):
+    # Regression test: default colors materialized in `.uns` used to override an explicit dict palette.
+    sdata_blobs = _annotate_labels_with_outline_columns(sdata_blobs)
+    palette = {"c1": "#ff00ff", "c2": "#00ff00"}
+    fig, ax = plt.subplots()
+    sdata_blobs.pl.render_labels("blobs_labels", color="cluster", palette=palette).pl.show(ax=ax)
+    pixels = np.asarray(ax.images[0].get_array())[..., :3].reshape(-1, 3)
+    plt.close(fig)
+    assert set(palette.values()) <= {to_hex(p) for p in np.unique(pixels, axis=0)}
+
+
 def test_render_labels_color_list_creates_one_panel_per_key(sdata_blobs: SpatialData):
     """A list of color keys produces one panel per key, titled by the key (#611)."""
     # the default blobs table annotates blobs_labels with channel_*_sum vars

tests/pl/test_render_shapes.py

@@ -9,7 +9,7 @@
 import pytest
 import scanpy as sc
 from anndata import AnnData
-from matplotlib.colors import Normalize
+from matplotlib.colors import Normalize, to_hex
 from shapely.geometry import MultiPolygon, Point, Polygon
 from spatialdata import SpatialData, deepcopy
 from spatialdata.models import ShapesModel, TableModel
@@ -1688,6 +1688,19 @@ def test_outline_color_column_groups_filter_aligns(sdata_blobs: SpatialData):
     plt.close(fig)
 
 
+def test_outline_color_column_respects_palette_without_fill_column(sdata_blobs: SpatialData):
+    # Regression test for #777: palette was dropped when only `outline_color` named a column.
+    sdata_blobs = _annotate_polygons_with_outline_columns(sdata_blobs)
+    palette = {"c1": "#ff00ff", "c2": "#00ff00"}
+    fig, ax = plt.subplots()
+    sdata_blobs.pl.render_shapes(
+        "blobs_polygons", outline_color="cluster", palette=palette, fill_alpha=0, outline_width=1.5
+    ).pl.show(ax=ax)
+    edge_colors = {to_hex(c) for c in ax.collections[0].get_edgecolor()}
+    plt.close(fig)
+    assert set(palette.values()) <= edge_colors
+
+
 def test_outline_color_column_collision_raises(sdata_blobs: SpatialData):
     """If `outline_color` is a string that is both a matplotlib color and an obs column, raise."""
     sdata_blobs["table"].obs["region"] = pd.Categorical(["blobs_polygons"] * sdata_blobs["table"].n_obs)