Key error in render_points with method=datashader when coloring by table.obs #479
Description
When attempting to plot points colored by an annotation column from table.obs, it works as expected with the matplotlib backend, but fails with a KeyError when using the datashader backend.
Steps to reproduce
import spatialdata as sd
import spatialdata_plot
import pandas as pd
import anndata as ad
sdata = sd.datasets.blobs()
adata = sd.models.TableModel.parse(
ad.AnnData(
obs = pd.DataFrame().assign(
region=pd.Categorical(["blobs_points"] * 200),
foo = pd.Categorical(["a", "b"] * 100),
instance = range(200)
)
)
)
adata.uns["spatialdata_attrs"] = {
"region": "blobs_points",
"region_key": "region",
"instance_key": "instance"
}
sd.models.TableModel().validate(adata)
sdata.tables["table_for_points"] = adata
# works
sdata.pl.render_points("blobs_points", method="matplotlib", color="foo", table_name="table_for_points").pl.show()
# doesn't work
sdata.pl.render_points("blobs_points", method="datashader", color="foo", table_name="table_for_points").pl.show()Stacktrace
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File /scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/pandas/core/indexes/base.py:3812, in Index.get_loc(self, key)
3811 try:
-> [3812](https://vscode-remote+ssh-002dremote-002binh.vscode-resource.vscode-cdn.net/scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/pandas/core/indexes/base.py:3812) return self._engine.get_loc(casted_key)
3813 except KeyError as err:
File pandas/_libs/index.pyx:167, in pandas._libs.index.IndexEngine.get_loc()
File pandas/_libs/index.pyx:196, in pandas._libs.index.IndexEngine.get_loc()
File pandas/_libs/hashtable_class_helper.pxi:7088, in pandas._libs.hashtable.PyObjectHashTable.get_item()
File pandas/_libs/hashtable_class_helper.pxi:7096, in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 'foo'
The above exception was the direct cause of the following exception:
KeyError Traceback (most recent call last)
Cell In[33], [line 1](vscode-notebook-cell:?execution_count=33&line=1)
----> [1](vscode-notebook-cell:?execution_count=33&line=1) sdata.pl.render_points("blobs_points", method="datashader", color="foo", table_name="table_for_points").pl.show()
File /cfs/sturmgre/projects/scverse/spatialdata-plot/src/spatialdata_plot/pl/basic.py:953, 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](https://vscode-remote+ssh-002dremote-002binh.vscode-resource.vscode-cdn.net/cfs/sturmgre/projects/scverse/spatialdata-plot/src/spatialdata_plot/pl/basic.py: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 /cfs/sturmgre/projects/scverse/spatialdata-plot/src/spatialdata_plot/pl/render.py:593, in _render_points(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
590 # use datashader for the visualization of points
591 cvs = ds.Canvas(plot_width=plot_width, plot_height=plot_height, x_range=x_ext, y_range=y_ext)
--> [593](https://vscode-remote+ssh-002dremote-002binh.vscode-resource.vscode-cdn.net/cfs/sturmgre/projects/scverse/spatialdata-plot/src/spatialdata_plot/pl/render.py:593) color_by_categorical = col_for_color is not None and transformed_element[col_for_color].values.dtype in (
594 object,
595 "categorical",
596 )
597 if color_by_categorical and transformed_element[col_for_color].values.dtype == object:
598 transformed_element[col_for_color] = transformed_element[col_for_color].astype("category")
File /scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/dask/dataframe/core.py:4955, in DataFrame.__getitem__(self, key)
4952 return self.loc[key]
4954 # error is raised from pandas
-> [4955](https://vscode-remote+ssh-002dremote-002binh.vscode-resource.vscode-cdn.net/scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/dask/dataframe/core.py:4955) meta = self._meta[_extract_meta(key)]
4956 dsk = partitionwise_graph(operator.getitem, name, self, key)
4957 graph = HighLevelGraph.from_collections(name, dsk, dependencies=[self])
File /scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/pandas/core/frame.py:4107, in DataFrame.__getitem__(self, key)
4105 if self.columns.nlevels > 1:
4106 return self._getitem_multilevel(key)
-> [4107](https://vscode-remote+ssh-002dremote-002binh.vscode-resource.vscode-cdn.net/scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/pandas/core/frame.py:4107) indexer = self.columns.get_loc(key)
4108 if is_integer(indexer):
4109 indexer = [indexer]
File /scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/pandas/core/indexes/base.py:3819, in Index.get_loc(self, key)
3814 if isinstance(casted_key, slice) or (
3815 isinstance(casted_key, abc.Iterable)
3816 and any(isinstance(x, slice) for x in casted_key)
3817 ):
3818 raise InvalidIndexError(key)
-> [3819](https://vscode-remote+ssh-002dremote-002binh.vscode-resource.vscode-cdn.net/scratch/sturmgre/projects/scverse/spatialdata-plot/.venv/lib/python3.13/site-packages/pandas/core/indexes/base.py:3819) raise KeyError(key) from err
3820 except TypeError:
3821 # If we have a listlike key, _check_indexing_error will raise
3822 # InvalidIndexError. Otherwise we fall through and re-raise
3823 # the TypeError.
3824 self._check_indexing_error(key)
KeyError: 'foo'
Session Info
| Package | Version |
|---|---|
| spatialdata | 0.5.0 |
| spatialdata-plot | 0.2.12.dev0+g788eb2206.d20250827 |
| pandas | 2.3.2 |
| anndata | 0.12.2 |
| dask | 2024.11.2 |
| Dependency | Version |
|---|---|
| scikit-image | 0.25.2 |
| MarkupSafe | 3.0.2 |
| spatial_image | 1.2.3 |
| setuptools | 80.9.0 |
| executing | 2.2.0 |
| defusedxml | 0.7.1 |
| jaraco.functools | 4.0.1 |
| charset-normalizer | 3.4.3 |
| urllib3 | 2.5.0 |
| Pygments | 2.19.2 |
| jaraco.text | 3.12.1 |
| pyct | 0.5.0 |
| toolz | 1.0.0 |
| matplotlib | 3.10.5 |
| jupyter_client | 8.6.3 |
| kiwisolver | 1.4.9 |
| platformdirs | 4.4.0 |
| pyarrow | 21.0.0 |
| typing_extensions | 4.15.0 |
| natsort | 8.4.0 |
| parso | 0.8.5 |
| psutil | 7.0.0 |
| ipywidgets | 8.1.7 |
| multiscale_spatial_image | 2.0.3 |
| multipledispatch | 1.0.0 (0.6.0) |
| threadpoolctl | 3.6.0 |
| jedi | 0.19.2 |
| cycler | 0.12.1 |
| pure_eval | 0.2.3 |
| legacy-api-wrap | 1.4.1 |
| scanpy | 1.11.4 |
| pyparsing | 3.2.3 |
| pytz | 2025.2 |
| Jinja2 | 3.1.6 |
| asciitree | 0.3.3 |
| ome-zarr | 0.11.1 |
| pyzmq | 27.0.2 |
| jaraco.collections | 5.1.0 |
| traitlets | 5.14.3 |
| param | 2.2.1 |
| rich | 14.1.0 |
| scikit-learn | 1.7.1 |
| requests | 2.32.5 |
| matplotlib-scalebar | 0.9.0 |
| idna | 3.10 |
| xarray | 2025.8.0 |
| numcodecs | 0.15.1 |
| dask-image | 2024.5.3 |
| cloudpickle | 3.1.1 |
| numpy | 2.2.6 |
| joblib | 1.5.2 |
| datashader | 0.18.2 |
| session-info2 | 0.2.1 |
| cffi | 1.17.1 |
| wcwidth | 0.2.13 |
| wrapt | 1.17.3 |
| jupyter_core | 5.8.1 |
| pyproj | 3.7.2 |
| jaraco.context | 5.3.0 |
| asttokens | 3.0.0 |
| numba | 0.61.2 |
| scipy | 1.16.1 |
| comm | 0.2.3 |
| tornado | 6.5.2 |
| decorator | 5.2.1 |
| prompt_toolkit | 3.0.51 |
| Deprecated | 1.2.18 |
| h5py | 3.14.0 |
| xarray-dataclass | 3.0.0 |
| xarray-schema | 0.0.3 |
| geopandas | 1.1.1 |
| zarr | 2.18.7 |
| PyYAML | 6.0.2 |
| more-itertools | 10.3.0 |
| stack-data | 0.6.3 |
| pillow | 11.3.0 |
| matplotlib-inline | 0.1.7 |
| xarray-spatial | 0.4.0 |
| lazy_loader | 0.4 |
| python-dateutil | 2.9.0.post0 |
| debugpy | 1.8.16 |
| certifi | 2025.8.3 (2025.08.03) |
| networkx | 3.5 |
| packaging | 25.0 |
| ipykernel | 6.30.1 |
| six | 1.17.0 |
| attrs | 25.3.0 |
| fsspec | 2025.7.0 |
| llvmlite | 0.44.0 |
| pycparser | 2.22 |
| ipython | 9.4.0 |
| shapely | 2.1.1 |
| Component | Info |
|---|---|
| Python | 3.13.1 (main, Jan 14 2025, 22:47:38) [Clang 19.1.6 ] |
| OS | Linux-5.14.0-427.31.1.el9_4.x86_64-x86_64-with-glibc2.34 |
| Updated | 2025-08-27 13:59 |