Fix render_points(color="z") silently dropping data column

src/spatialdata_plot/pl/render.py

@@ -117,10 +117,19 @@ def _reparse_points(
     df: pd.DataFrame,
     transformation: Any,
     coordinate_system: str,
+    color_column: str | None = None,
 ) -> None:
-    """Re-register a points DataFrame in *sdata_filt* with its transformation."""
+    """Re-register a points DataFrame in *sdata_filt* with its transformation.
+
+    ``PointsModel.parse`` silently drops columns whose names collide with
+    reserved coordinate axes (currently only ``"z"``). When ``color_column``
+    names such a column, re-attach it so downstream color lookup can find it.
+    """
     dd_frame = dask.dataframe.from_pandas(df, npartitions=1)
-    sdata_filt.points[element] = PointsModel.parse(dd_frame, coordinates={"x": "x", "y": "y"})
+    parsed = PointsModel.parse(dd_frame, coordinates={"x": "x", "y": "y"})
+    if color_column is not None and color_column in df.columns and color_column not in parsed.columns:
+        parsed[color_column] = dd_frame[color_column]
+    sdata_filt.points[element] = parsed
     set_transformation(
         element=sdata_filt.points[element],
         transformation=transformation,
@@ -820,7 +829,7 @@ def _render_points(
 
     # Convert back to dask dataframe to modify sdata
     transformation_in_cs = sdata_filt.points[element].attrs["transform"][coordinate_system]
-    _reparse_points(sdata_filt, element, points_for_model, transformation_in_cs, coordinate_system)
+    _reparse_points(sdata_filt, element, points_for_model, transformation_in_cs, coordinate_system, col_for_color)
 
     if col_for_color is not None:
         assert isinstance(col_for_color, str)
@@ -877,6 +886,7 @@ def _render_points(
             points_pd_with_color,
             transformation_in_cs,
             coordinate_system,
+            col_for_color,
         )
 
     _warn_groups_ignored_continuous(groups, color_source_vector, col_for_color)
@@ -897,7 +907,7 @@ def _render_points(
         # filter the materialized points, adata, and re-register in sdata_filt
         points = points[keep].reset_index(drop=True)
         adata = adata[keep]
-        _reparse_points(sdata_filt, element, points, transformation_in_cs, coordinate_system)
+        _reparse_points(sdata_filt, element, points, transformation_in_cs, coordinate_system, col_for_color)
 
     # color_source_vector is None when the values aren't categorical
     if color_source_vector is None and render_params.transfunc is not None:

tests/pl/test_render_points.py

@@ -1006,6 +1006,40 @@ def test_no_table_fallback_warning_for_element_column(caplog):
     plt.close("all")
 
 
+def test_render_points_color_by_z_data_column():
+    # regression test for #615
+    pts = PointsModel.parse(
+        pd.DataFrame({"x": [1.0, 2.0, 3.0], "y": [1.0, 2.0, 3.0], "z": [0.1, 0.5, 0.9]}),
+    )
+    assert "z" in pts.columns
+    sdata = SpatialData(points={"p": pts})
+    fig, ax = plt.subplots()
+    try:
+        sdata.pl.render_points("p", color="z").pl.show(ax=ax)
+    finally:
+        plt.close(fig)
+
+
+def test_render_points_color_by_z_with_extra_columns():
+    # regression test for #615
+    pts = PointsModel.parse(
+        pd.DataFrame(
+            {
+                "x": [1.0, 2.0, 3.0],
+                "y": [1.0, 2.0, 3.0],
+                "z": [0.1, 0.5, 0.9],
+                "score": [0.0, 0.5, 1.0],
+            }
+        ),
+    )
+    sdata = SpatialData(points={"p": pts})
+    fig, ax = plt.subplots()
+    try:
+        sdata.pl.render_points("p", color="score").pl.show(ax=ax)
+    finally:
+        plt.close(fig)
+
+
 def test_render_points_disjoint_instance_ids_clear_error():
     # regression test for #603: disjoint instance_id values must raise a clear ValueError
     points = PointsModel.parse(pd.DataFrame({"x": [1.0, 2.0, 3.0], "y": [1.0, 2.0, 3.0]}))