fix: render shapes unannotated by the table with na_color instead of dropping them (#710)

render_shapes joined the element to its table with how="inner", silently dropping shapes whose
instance had no table row. Points (how="left" merge) and labels (raster + na_color) keep unannotated
elements, so shapes were the inconsistent outlier (and it broke the labels<->shapes interchangeability).

Switch _join_table_for_element to how="left": all shapes survive, and the per-shape color lookup
(_extract_color_column, reindexed to the element) yields NaN -> na_color for the unannotated ones, via
the existing NaN-handling path. Fully-annotated data is unaffected (verified pixel-identical: inner == left
when nothing is dropped), so only partial-annotation output changes.

Adds a visual regression test: coloring blobs_polygons by a table column now renders the one unannotated
polygon (instance 0 has no table row) with na_color instead of dropping it.

Author: timtreis

src/spatialdata_plot/pl/render.py

@@ -646,7 +646,7 @@ def _render_shapes(
     outline_color_vector: Any = None
     if col_for_outline_color is not None:
         # When the outline column lives in a table that hasn't been joined yet
-        # (no fill table, or a different table than fill's), inner-join it onto
+        # (no fill table, or a different table than fill's), left-join it onto
         # the element so the lookup is aligned and the element row count matches
         # the outline vector length.
         if outline_table_name is not None and outline_table_name != table_name:

src/spatialdata_plot/pl/utils.py

@@ -444,7 +444,11 @@ def _join_table_for_element(
     element: str,
     table_name: str,
 ) -> tuple[Any, AnnData]:
-    """Inner-join ``element`` with its annotating ``table_name``.
+    """Left-join ``element`` with its annotating ``table_name``.
+
+    A left join keeps every shape, including those without a table row (they get no color value and
+    are rendered with ``na_color``), matching the points/labels behaviour instead of silently dropping
+    unannotated shapes.
 
     Wraps the workaround for scverse/spatialdata#1099: ``join_spatialelement_table``
     calls ``table.obs.reset_index()`` which fails when the obs index name matches
@@ -470,7 +474,7 @@ def _join_table_for_element(
 
     try:
         element_dict, joined_table = join_spatialelement_table(
-            sdata, spatial_element_names=element, table_name=table_name, how="inner"
+            sdata, spatial_element_names=element, table_name=table_name, how="left"
         )
     finally:
         if _saved_index is not None:

tests/pl/test_render_shapes.py

@@ -439,6 +439,13 @@ def test_render_shapes_raises_for_missing_column_in_table(self, sdata_blobs_shap
                 element="blobs_polygons", color="not_a_column", table_name="table"
             )
 
+    def test_plot_shapes_unannotated_by_table_render_with_na_color(self, sdata_blobs_shapes_annotated: SpatialData):
+        # Regression for #710: blobs_polygons instance 0 has no row in the table (instance_id starts
+        # at 1), so coloring by a table column must render it with na_color, not drop it.
+        sdata_blobs_shapes_annotated.pl.render_shapes(
+            "blobs_polygons", color="channel_0_sum", na_color="red"
+        ).pl.show()
+
     def test_plot_can_plot_shapes_after_spatial_query(self, sdata_blobs: SpatialData):
         # subset to only shapes, should be unnecessary after rasterizeation of multiscale images is included
         blob = SpatialData.init_from_elements(