Bug when trying to plot Visium HD bins as points

[LucaMarconato]

While updating the Visium HD notebook I have tried converting the bins to points and plotting them, and I found that this leads to an error in spatialdata-plot.

Here is how to reproduce (I also copy-paste some markdown text as a note to myself; I am removing it from the notebook now and I'll restore it when the bug is fixed).

from spatialdata.models import points_geopandas_to_dask_dataframe

sdata["points_016um"] = points_geopandas_to_dask_dataframe(sdata["Visium_HD_Mouse_Small_Intestine_square_016um"])
# gives the error:
sdata.pl.render_points("points_016um").pl.show()

Traceback:

[/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:430](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py#line=429): FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
[/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py#line=66): ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:106](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=105): UserWarning: Key `points_016um` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
[/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:430](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py#line=429): FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
[/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py#line=66): ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:106](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=105): UserWarning: Key `points_016um` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
[/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:430](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py#line=429): FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
[/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py#line=66): ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
[/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py:106](http://localhost:8888/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/_elements.py#line=105): UserWarning: Key `points_016um` already exists. Overwriting it in-memory.
  self._check_key(key, self.keys(), self._shared_keys)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[28], line 1
----> 1 sdata.pl.render_points("points_016um").pl.show()

File [~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/basic.py:906](http://localhost:8888/~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/basic.py#line=905), 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)
    901     wanted_elements, wanted_points_on_this_cs, wants_points = _get_wanted_render_elements(
    902         sdata, wanted_elements, params_copy, cs, "points"
    903     )
    905     if wanted_points_on_this_cs:
--> 906         _render_points(
    907             sdata=sdata,
    908             render_params=params_copy,
    909             coordinate_system=cs,
    910             ax=ax,
    911             fig_params=fig_params,
    912             scalebar_params=scalebar_params,
    913             legend_params=legend_params,
    914         )
    916 elif cmd == "render_labels" and has_labels:
    917     wanted_elements, wanted_labels_on_this_cs, wants_labels = _get_wanted_render_elements(
    918         sdata, wanted_elements, params_copy, cs, "labels"
    919     )

File [~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/render.py:459](http://localhost:8888/~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/render.py#line=458), in _render_points(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
    452 else:
    453     ds_result = ds.tf.shade(
    454         ds.tf.spread(agg, px=px),
    455         rescale_discrete_levels=True,
    456         cmap=render_params.cmap_params.cmap,
    457     )
--> 459 rbga_image = np.transpose(ds_result.to_numpy().base, (0, 1, 2))
    460 cax = ax.imshow(rbga_image, zorder=render_params.zorder, alpha=render_params.alpha)
    461 if aggregate_with_sum is not None:

File [/opt/miniconda3/envs/ome/lib/python3.10/site-packages/numpy/core/fromnumeric.py:655](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/numpy/core/fromnumeric.py#line=654), in transpose(a, axes)
    588 @array_function_dispatch(_transpose_dispatcher)
    589 def transpose(a, axes=None):
    590     """
    591     Returns an array with axes transposed.
    592 
   (...)
    653 
    654     """
--> 655     return _wrapfunc(a, 'transpose', axes)

File [/opt/miniconda3/envs/ome/lib/python3.10/site-packages/numpy/core/fromnumeric.py:56](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/numpy/core/fromnumeric.py#line=55), in _wrapfunc(obj, method, *args, **kwds)
     54 bound = getattr(obj, method, None)
     55 if bound is None:
---> 56     return _wrapit(obj, method, *args, **kwds)
     58 try:
     59     return bound(*args, **kwds)

File [/opt/miniconda3/envs/ome/lib/python3.10/site-packages/numpy/core/fromnumeric.py:45](http://localhost:8888/opt/miniconda3/envs/ome/lib/python3.10/site-packages/numpy/core/fromnumeric.py#line=44), in _wrapit(obj, method, *args, **kwds)
     43 except AttributeError:
     44     wrap = None
---> 45 result = getattr(asarray(obj), method)(*args, **kwds)
     46 if wrap:
     47     if not isinstance(result, mu.ndarray):

ValueError: axes don't match array