sdata.pl.render_shapes/render_labels how to define the cell color based on cell type annotation #374
Description
Hi,
I am trying to assign different color to different cell type annotation in 'leiden' field of my Scanpy Object, however, the plotting function below always not working:
Script
sdata.pl.render_shapes(
"cell_circles", color='leiden'
).pl.show(title=f"cell types", coordinate_systems="global", figsize=(6, 6))
Error message:
[/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/spatialdata_plot/pl/utils.py:772](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/spatialdata_plot/pl/utils.py#line=771): FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
color_vector = color_source_vector.map(color_mapping)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[60], line 1
----> 1 sdata.pl.render_shapes(
2 "cell_circles", color='leiden'
3 ).pl.show(title=f"cell types", coordinate_systems="global", figsize=(6, 6))
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/spatialdata_plot/pl/basic.py:903](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/spatialdata_plot/pl/basic.py#line=902), 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)
898 wanted_elements, wanted_shapes_on_this_cs, wants_shapes = _get_wanted_render_elements(
899 sdata, wanted_elements, params_copy, cs, "shapes"
900 )
902 if wanted_shapes_on_this_cs:
--> 903 _render_shapes(
904 sdata=sdata,
905 render_params=params_copy,
906 coordinate_system=cs,
907 ax=ax,
908 fig_params=fig_params,
909 scalebar_params=scalebar_params,
910 legend_params=legend_params,
911 )
913 elif cmd == "render_points" and has_points:
914 wanted_elements, wanted_points_on_this_cs, wants_points = _get_wanted_render_elements(
915 sdata, wanted_elements, params_copy, cs, "points"
916 )
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/spatialdata_plot/pl/render.py:191](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/spatialdata_plot/pl/render.py#line=190), in _render_shapes(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
189 # in case we are coloring by a column in table
190 if col_for_color is not None and col_for_color not in sdata_filt.shapes[element].columns:
--> 191 sdata_filt.shapes[element][col_for_color] = (
192 color_vector if color_source_vector is None else color_source_vector
193 )
194 # Render shapes with datashader
195 color_by_categorical = col_for_color is not None and color_source_vector is not None
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/geopandas/geodataframe.py:1819](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/geopandas/geodataframe.py#line=1818), in GeoDataFrame.__setitem__(self, key, value)
1814 except TypeError:
1815 warnings.warn(
1816 "Geometry column does not contain geometry.",
1817 stacklevel=2,
1818 )
-> 1819 super().__setitem__(key, value)
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/frame.py:4299](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/frame.py#line=4298), in DataFrame.__setitem__(self, key, value)
4296 self._setitem_array([key], value)
4297 else:
4298 # set column
-> 4299 self._set_item(key, value)
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/frame.py:4512](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/frame.py#line=4511), in DataFrame._set_item(self, key, value)
4502 def _set_item(self, key, value) -> None:
4503 """
4504 Add series to DataFrame in specified column.
4505
(...)
4510 ensure homogeneity.
4511 """
-> 4512 value, refs = self._sanitize_column(value)
4514 if (
4515 key in self.columns
4516 and value.ndim == 1
4517 and not isinstance(value.dtype, ExtensionDtype)
4518 ):
4519 # broadcast across multiple columns if necessary
4520 if not self.columns.is_unique or isinstance(self.columns, MultiIndex):
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/frame.py:5253](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/frame.py#line=5252), in DataFrame._sanitize_column(self, value)
5250 return _reindex_for_setitem(value, self.index)
5252 if is_list_like(value):
-> 5253 com.require_length_match(value, self.index)
5254 arr = sanitize_array(value, self.index, copy=True, allow_2d=True)
5255 if (
5256 isinstance(value, Index)
5257 and value.dtype == "object"
(...)
5260 # TODO: Remove kludge in sanitize_array for string mode when enforcing
5261 # this deprecation
File [/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/common.py:571](https://ondemand.carc.usc.edu/project/sli68423_1316/users/yang/conda/envs/py39/lib/python3.9/site-packages/pandas/core/common.py#line=570), in require_length_match(data, index)
567 """
568 Check the length of data matches the length of the index.
569 """
570 if len(data) != len(index):
--> 571 raise ValueError(
572 "Length of values "
573 f"({len(data)}) "
574 "does not match length of index "
575 f"({len(index)})"
576 )
ValueError: Length of values (154472) does not match length of index (162254)
Thank you!
Best,
Yang