Add warning if table_name and color are specified but the table doesn't annotate the element (#490)

Author: timtreis

src/spatialdata_plot/pl/utils.py

@@ -1834,7 +1834,8 @@ def _validate_label_render_params(
 
         element_params[el]["table_name"] = None
         element_params[el]["color"] = None
-        if (color := param_dict["color"]) is not None:
+        color = param_dict["color"]
+        if color is not None:
             color, table_name = _validate_col_for_column_table(sdata, el, color, param_dict["table_name"], labels=True)
             element_params[el]["table_name"] = table_name
             element_params[el]["color"] = color
@@ -1996,6 +1997,11 @@ def _validate_col_for_column_table(
         if table_name not in tables or (
             col_for_color not in sdata[table_name].obs.columns and col_for_color not in sdata[table_name].var_names
         ):
+            warnings.warn(
+                f"Table '{table_name}' does not annotate element '{element_name}'.",
+                UserWarning,
+                stacklevel=2,
+            )
             table_name = None
             col_for_color = None
     else:

tests/pl/test_render_labels.py

@@ -299,3 +299,25 @@ def test_plot_can_handle_dropping_small_labels_after_rasterize_categorical(self,
         sdata_blobs = self._prepare_small_labels(sdata_blobs)
 
         sdata_blobs.pl.render_labels("blobs_labels_large", color="category", table_name="table").pl.show()
+
+
+def test_warns_when_table_does_not_annotate_element(sdata_blobs: SpatialData):
+    # Work on an independent copy since we mutate tables
+    sdata_blobs_local = deepcopy(sdata_blobs)
+
+    # Create a table that annotates a DIFFERENT element than the one we will render
+    other_table = sdata_blobs_local["table"].copy()
+    other_table.obs["region"] = "blobs_multiscale_labels"
+    other_table.uns["spatialdata_attrs"]["region"] = "blobs_multiscale_labels"
+    sdata_blobs_local["other_table"] = other_table
+
+    # Rendering "blobs_labels" with a table that annotates "blobs_multiscale_labels"
+    # should raise a warning and fall back to using no table.
+    with pytest.warns(UserWarning, match="does not annotate element"):
+        (
+            sdata_blobs_local.pl.render_labels(
+                "blobs_labels",
+                color="channel_0_sum",
+                table_name="other_table",
+            ).pl.show()
+        )

tests/pl/test_render_points.py

@@ -5,6 +5,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+import pytest
 import scanpy as sc
 from anndata import AnnData
 from matplotlib.colors import Normalize
@@ -350,3 +351,25 @@ def test_plot_can_annotate_points_with_table_layer(self, sdata_blobs: SpatialDat
         sdata_blobs["points_table"].layers["normalized"] = RNG.random((nrows, ncols))
 
         sdata_blobs.pl.render_points("blobs_points", color="feature0", size=10, table_layer="normalized").pl.show()
+
+
+def test_warns_when_table_does_not_annotate_element(sdata_blobs: SpatialData):
+    # Work on an independent copy since we mutate tables
+    sdata_blobs_local = deepcopy(sdata_blobs)
+
+    # Create a table that annotates a DIFFERENT element than the one we will render
+    other_table = sdata_blobs_local["table"].copy()
+    other_table.obs["region"] = "blobs_labels"  # Different from blobs_points
+    other_table.uns["spatialdata_attrs"]["region"] = "blobs_labels"
+    sdata_blobs_local["other_table"] = other_table
+
+    # Rendering "blobs_points" with a table that annotates "blobs_labels"
+    # should raise a warning and fall back to using no table.
+    with pytest.warns(UserWarning, match="does not annotate element"):
+        (
+            sdata_blobs_local.pl.render_points(
+                "blobs_points",
+                color="channel_0_sum",
+                table_name="other_table",
+            ).pl.show()
+        )

tests/pl/test_render_shapes.py

@@ -6,6 +6,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+import pytest
 import scanpy as sc
 from anndata import AnnData
 from matplotlib.colors import Normalize
@@ -564,3 +565,25 @@ def test_plot_can_annotate_shapes_with_table_layer(self, sdata_blobs: SpatialDat
         sdata_blobs["circle_table"].layers["normalized"] = RNG.random((nrows, ncols))
 
         sdata_blobs.pl.render_shapes("blobs_circles", color="feature0", table_layer="normalized").pl.show()
+
+
+def test_warns_when_table_does_not_annotate_element(sdata_blobs: SpatialData):
+    # Work on an independent copy since we mutate tables
+    sdata_blobs_local = deepcopy(sdata_blobs)
+
+    # Create a table that annotates a DIFFERENT element than the one we will render
+    other_table = sdata_blobs_local["table"].copy()
+    other_table.obs["region"] = "blobs_points"  # Different from blobs_circles
+    other_table.uns["spatialdata_attrs"]["region"] = "blobs_points"
+    sdata_blobs_local["other_table"] = other_table
+
+    # Rendering "blobs_circles" with a table that annotates "blobs_points"
+    # should raise a warning and fall back to using no table.
+    with pytest.warns(UserWarning, match="does not annotate element"):
+        (
+            sdata_blobs_local.pl.render_shapes(
+                "blobs_circles",
+                color="channel_0_sum",
+                table_name="other_table",
+            ).pl.show()
+        )