render_points for categorical columns assumes there is always a table #486
Description
from spatialdata.datasets import blobs
import spatialdata_plot
sdata = blobs()
del sdata['table']
sdata.pl.render_points('blobs_points', color='genes').pl.show()The table is not annotating the point, yet if there is no table we get an exception because of a sdata['table'] in the code.
Full traceback
[/opt/miniconda3/envs/ome/lib/python3.12/site-packages/legacy_api_wrap/__init__.py:82](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.12/site-packages/legacy_api_wrap/__init__.py#line=81): FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
return fn(*args_all, **kw)
[/opt/miniconda3/envs/ome/lib/python3.12/functools.py:909](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.12/functools.py#line=908): ImplicitModificationWarning: Transforming to str index.
return dispatch(args[0].__class__)(*args, **kw)
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[20], line 6
4 sdata = blobs()
5 del sdata['table']
----> 6 sdata.pl.render_points('blobs_points', color='genes').pl.show()
File [~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata-plot/src/spatialdata_plot/pl/basic.py:953](http://localhost:8888/lab/tree/dependencies/spatialdata-notebooks/notebooks/examples/~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata-plot/src/spatialdata_plot/pl/basic.py#line=952), in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save)
948 wanted_elements, wanted_points_on_this_cs, wants_points = _get_wanted_render_elements(
949 sdata, wanted_elements, params_copy, cs, "points"
950 )
952 if wanted_points_on_this_cs:
--> 953 _render_points(
954 sdata=sdata,
955 render_params=params_copy,
956 coordinate_system=cs,
957 ax=ax,
958 fig_params=fig_params,
959 scalebar_params=scalebar_params,
960 legend_params=legend_params,
961 )
963 elif cmd == "render_labels" and has_labels:
964 wanted_elements, wanted_labels_on_this_cs, wants_labels = _get_wanted_render_elements(
965 sdata, wanted_elements, params_copy, cs, "labels"
966 )
File [~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata-plot/src/spatialdata_plot/pl/render.py:538](http://localhost:8888/lab/tree/dependencies/spatialdata-notebooks/notebooks/examples/~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata-plot/src/spatialdata_plot/pl/render.py#line=537), in _render_points(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
535 # when user specified a single color, we emulate the form of `na_color` and use it
536 default_color = color if col_for_color is None and color is not None else render_params.cmap_params.na_color
--> 538 color_source_vector, color_vector, _ = _set_color_source_vec(
539 sdata=sdata_filt,
540 element=points,
541 element_name=element,
542 value_to_plot=col_for_color,
543 groups=groups,
544 palette=palette,
545 na_color=default_color,
546 cmap_params=render_params.cmap_params,
547 alpha=render_params.alpha,
548 table_name=table_name,
549 render_type="points",
550 )
552 # color_source_vector is None when the values aren't categorical
553 if color_source_vector is None and render_params.transfunc is not None:
File [~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata-plot/src/spatialdata_plot/pl/utils.py:785](http://localhost:8888/lab/tree/dependencies/spatialdata-notebooks/notebooks/examples/~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata-plot/src/spatialdata_plot/pl/utils.py#line=784), in _set_color_source_vec(sdata, element, value_to_plot, na_color, element_name, groups, palette, cmap_params, alpha, table_name, table_layer, render_type)
781 color_source_vector = pd.Categorical(color_source_vector) # convert, e.g., `pd.Series`
783 # TODO check why table_name is not passed here.
784 color_mapping = _get_categorical_color_mapping(
--> 785 adata=sdata["table"],
786 cluster_key=value_to_plot,
787 color_source_vector=color_source_vector,
788 cmap_params=cmap_params,
789 alpha=alpha,
790 groups=groups,
791 palette=palette,
792 na_color=na_color,
793 render_type=render_type,
794 )
796 color_source_vector = color_source_vector.set_categories(color_mapping.keys())
797 if color_mapping is None:
File [~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py:2290](http://localhost:8888/lab/tree/dependencies/spatialdata-notebooks/notebooks/examples/~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py#line=2289), in SpatialData.__getitem__(self, item)
2277 def __getitem__(self, item: str) -> SpatialElement | AnnData:
2278 """
2279 Return the element with the given name.
2280
(...) 2288 The element.
2289 """
-> 2290 _, _, element = self._find_element(item)
2291 return element
File [~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py:2191](http://localhost:8888/lab/tree/dependencies/spatialdata-notebooks/notebooks/examples/~/embl/projects/basel/spatialdata-data-converter/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py#line=2190), in SpatialData._find_element(self, element_name)
2188 found.append((element_type, element_name_, element))
2190 if len(found) == 0:
-> 2191 raise KeyError(f"Could not find element with name {element_name!r}")
2193 if len(found) > 1:
2194 raise ValueError(f"Found multiple elements with name {element_name!r}")
KeyError: "Could not find element with name 'table'"