Warn when groups values don't match color categories (#556)

Author: timtreis

src/spatialdata_plot/pl/render.py

@@ -108,6 +108,37 @@ def _reparse_points(
     )
 
 
+def _warn_missing_groups(
+    groups: str | list[str],
+    color_source_vector: pd.Categorical,
+    col_for_color: str | None = None,
+) -> None:
+    """Warn when ``groups`` contains values absent from the color column's categories."""
+    groups_set = {groups} if isinstance(groups, str) else set(groups)
+    missing = groups_set - set(color_source_vector.categories)
+    if not missing:
+        return
+    col_label = f" '{col_for_color}'" if col_for_color else " the color column"
+    try:
+        missing_str = str(sorted(missing))
+    except TypeError:
+        missing_str = str(list(missing))
+    if missing == groups_set:
+        logger.warning(
+            f"None of the requested groups {missing_str} were found in{col_label}. "
+            "This usually means `groups` refers to values from a different column than `color`. "
+            "The `groups` parameter selects categories of the column specified via `color`."
+        )
+    else:
+        try:
+            cats_str = str(sorted(color_source_vector.categories))
+        except TypeError:
+            cats_str = str(list(color_source_vector.categories))
+        logger.warning(
+            f"Groups {missing_str} were not found in{col_label} and will be ignored. Available categories: {cats_str}."
+        )
+
+
 def _filter_groups_transparent_na(
     groups: str | list[str],
     color_source_vector: pd.Categorical,
@@ -298,10 +329,13 @@ def _render_shapes(
 
     values_are_categorical = color_source_vector is not None
 
+    if groups is not None and color_source_vector is not None:
+        _warn_missing_groups(groups, color_source_vector, col_for_color)
+
     # When groups are specified, filter out non-matching elements by default.
     # Only show non-matching elements if the user explicitly sets na_color.
     _na = render_params.cmap_params.na_color
-    if groups is not None and values_are_categorical and (_na.default_color_set or _na.alpha == "00"):
+    if groups is not None and color_source_vector is not None and (_na.default_color_set or _na.alpha == "00"):
         keep, color_source_vector, color_vector = _filter_groups_transparent_na(
             groups, color_source_vector, color_vector
         )
@@ -750,6 +784,9 @@ def _render_points(
     if added_color_from_table and col_for_color is not None:
         _reparse_points(sdata_filt, element, points_pd_with_color, transformation_in_cs, coordinate_system)
 
+    if groups is not None and color_source_vector is not None:
+        _warn_missing_groups(groups, color_source_vector, col_for_color)
+
     # When groups are specified, filter out non-matching elements by default.
     # Only show non-matching elements if the user explicitly sets na_color.
     _na = render_params.cmap_params.na_color
@@ -1298,6 +1335,9 @@ def _render_labels(
         else:
             assert color_source_vector is None
 
+    if groups is not None and color_source_vector is not None:
+        _warn_missing_groups(groups, color_source_vector, col_for_color)
+
     # When groups are specified, zero out non-matching label IDs so they render as background.
     # Only show non-matching labels if the user explicitly sets na_color.
     _na = render_params.cmap_params.na_color

src/spatialdata_plot/pl/utils.py

@@ -553,6 +553,9 @@ def _create_patches(
         shapes_df, fill_c.tolist(), outline_c.tolist() if hasattr(outline_c, "tolist") else outline_c, s
     )
 
+    if patches.empty:
+        return PatchCollection([])
+
     return PatchCollection(
         patches["geometry"].values.tolist(),
         snap=False,

tests/pl/test_render_labels.py

@@ -12,6 +12,7 @@
 from spatialdata.models import Labels2DModel, TableModel
 
 import spatialdata_plot  # noqa: F401
+from spatialdata_plot._logging import logger, logger_warns
 from tests.conftest import DPI, PlotTester, PlotTesterMeta, _viridis_with_under_over, get_standard_RNG
 
 sc.pl.set_rcParams_defaults()
@@ -428,3 +429,21 @@ def test_raises_when_table_does_not_annotate_element(sdata_blobs: SpatialData):
             color="channel_0_sum",
             table_name="other_table",
         ).pl.show()
+
+
+def test_groups_warns_when_no_groups_match_labels(sdata_blobs: SpatialData, caplog):
+    """Warning fires when no groups match label color categories."""
+    labels_name = "blobs_labels"
+    instances = get_element_instances(sdata_blobs[labels_name])
+    n_obs = len(instances)
+    adata = AnnData(np.zeros((n_obs, 1)))
+    adata.obs["instance_id"] = instances.values
+    adata.obs["cat"] = pd.Categorical(["a", "b"] * (n_obs // 2) + ["a"] * (n_obs % 2))
+    adata.obs["region"] = labels_name
+    sdata_blobs["label_table"] = TableModel.parse(
+        adata=adata, region_key="region", instance_key="instance_id", region=labels_name
+    )
+    with logger_warns(caplog, logger, match="None of the requested groups"):
+        sdata_blobs.pl.render_labels(
+            labels_name, color="cat", groups=["nonexistent"], table_name="label_table", na_color=None
+        ).pl.show()

tests/pl/test_render_points.py

@@ -22,6 +22,7 @@
 from spatialdata.transformations._utils import _set_transformations
 
 import spatialdata_plot  # noqa: F401
+from spatialdata_plot._logging import logger, logger_warns
 from tests.conftest import DPI, PlotTester, PlotTesterMeta, _viridis_with_under_over, get_standard_RNG
 
 sc.pl.set_rcParams_defaults()
@@ -607,6 +608,26 @@ def test_groups_na_color_none_no_match_points(sdata_blobs: SpatialData):
     ).pl.show()
 
 
+@pytest.mark.parametrize("na_color", [None, "red"])
+def test_groups_warns_when_no_groups_match_points(sdata_blobs: SpatialData, caplog, na_color):
+    """Warning fires regardless of na_color when no groups match."""
+    sdata_blobs["blobs_points"]["cat_color"] = pd.Series(["a", "b", "c", "a"] * 50, dtype="category")
+    with logger_warns(caplog, logger, match="None of the requested groups"):
+        sdata_blobs.pl.render_points(
+            "blobs_points", color="cat_color", groups=["nonexistent"], na_color=na_color, size=30
+        ).pl.show()
+
+
+@pytest.mark.parametrize("na_color", [None, "red"])
+def test_groups_warns_when_some_groups_missing_points(sdata_blobs: SpatialData, caplog, na_color):
+    """Warning fires regardless of na_color when some groups are missing."""
+    sdata_blobs["blobs_points"]["cat_color"] = pd.Series(["a", "b", "c", "a"] * 50, dtype="category")
+    with logger_warns(caplog, logger, match="were not found in"):
+        sdata_blobs.pl.render_points(
+            "blobs_points", color="cat_color", groups=["a", "nonexistent"], na_color=na_color, size=30
+        ).pl.show()
+
+
 def test_raises_when_table_does_not_annotate_element(sdata_blobs: SpatialData):
     # Work on an independent copy since we mutate tables
     sdata_blobs_local = deepcopy(sdata_blobs)

tests/pl/test_render_shapes.py

@@ -1016,6 +1016,26 @@ def test_groups_na_color_none_no_match_shapes(sdata_blobs: SpatialData):
     sdata_blobs.pl.render_shapes("blobs_polygons", color="cat_color", groups=["nonexistent"], na_color=None).pl.show()
 
 
+@pytest.mark.parametrize("na_color", [None, "red"])
+def test_groups_warns_when_no_groups_match(sdata_blobs: SpatialData, caplog, na_color):
+    """Warning fires regardless of na_color when no groups match."""
+    sdata_blobs["blobs_polygons"]["cat_color"] = pd.Series(["a", "b", "a", "b", "a"], dtype="category")
+    with logger_warns(caplog, logger, match="None of the requested groups"):
+        sdata_blobs.pl.render_shapes(
+            "blobs_polygons", color="cat_color", groups=["nonexistent"], na_color=na_color
+        ).pl.show()
+
+
+@pytest.mark.parametrize("na_color", [None, "red"])
+def test_groups_warns_when_some_groups_missing(sdata_blobs: SpatialData, caplog, na_color):
+    """Warning fires regardless of na_color when some groups are missing."""
+    sdata_blobs["blobs_polygons"]["cat_color"] = pd.Series(["a", "b", "a", "b", "a"], dtype="category")
+    with logger_warns(caplog, logger, match="were not found in"):
+        sdata_blobs.pl.render_shapes(
+            "blobs_polygons", color="cat_color", groups=["a", "nonexistent"], na_color=na_color
+        ).pl.show()
+
+
 def test_plot_can_handle_nan_values_in_color_data(sdata_blobs: SpatialData, caplog):
     """Test that NaN values in color data are handled gracefully and logged."""
     sdata_blobs["table"].obs["region"] = pd.Categorical(["blobs_circles"] * sdata_blobs["table"].n_obs)