InvalidIndexError: (slice(None, None, None), (0, 1)) when using sc.pl.spatial

[Flyingcattle]

Hi there,
Thanks for the powerful tool.
When reproducing the tutorial, I got an error when using

with mplscience.style_context():
sc.pl.spatial(
adata,
color=genes,
cmap=cmap,
frameon=False,
vmin='p0',
vmax='p95',
spot_size=30,
)

The error looks like this:

TypeError Traceback (most recent call last)
File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/pandas/core/indexes/base.py:3621, in Index.get_loc(self, key, method, tolerance)
3620 try:
-> 3621 return self._engine.get_loc(casted_key)
3622 except KeyError as err:

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/pandas/_libs/index.pyx:136, in pandas._libs.index.IndexEngine.get_loc()

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/pandas/_libs/index.pyx:142, in pandas._libs.index.IndexEngine.get_loc()

TypeError: '(slice(None, None, None), (0, 1))' is an invalid key

During handling of the above exception, another exception occurred:

InvalidIndexError Traceback (most recent call last)
Input In [22], in <cell line: 1>()
1 with mplscience.style_context():
----> 2 sc.pl.spatial(
3 adata,
4 color=genes,
5 cmap=cmap,
6 frameon=False,
7 vmin='p0',
8 vmax='p95',
9 spot_size=30,
10 )

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/scanpy/plotting/_tools/scatterplots.py:1003, in spatial(adata, basis, img, img_key, library_id, crop_coord, alpha_img, bw, size, scale_factor, spot_size, na_color, show, return_fig, save, **kwargs)
1000 cmap_img = None
1001 circle_radius = size * scale_factor * spot_size * 0.5
-> 1003 axs = embedding(
1004 adata,
1005 basis=basis,
1006 scale_factor=scale_factor,
1007 size=circle_radius,
1008 na_color=na_color,
1009 show=False,
1010 save=False,
1011 **kwargs,
1012 )
1013 if not isinstance(axs, list):
1014 axs = [axs]

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/scanpy/plotting/_tools/scatterplots.py:286, in embedding(adata, basis, color, gene_symbols, use_raw, sort_order, edges, edges_width, edges_color, neighbors_key, arrows, arrows_kwds, groups, components, dimensions, layer, projection, scale_factor, color_map, cmap, palette, na_color, na_in_legend, size, frameon, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, colorbar_loc, vmax, vmin, vcenter, norm, add_outline, outline_width, outline_color, ncols, hspace, wspace, title, show, save, ax, return_fig, **kwargs)
284 color_source_vector = color_source_vector[order]
285 color_vector = color_vector[order]
--> 286 coords = basis_values[:, dims][order, :]
288 # if plotting multiple panels, get the ax from the grid spec
289 # else use the ax value (either user given or created previously)
290 if grid:

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/pandas/core/frame.py:3505, in DataFrame.getitem(self, key)
3503 if self.columns.nlevels > 1:
3504 return self._getitem_multilevel(key)
-> 3505 indexer = self.columns.get_loc(key)
3506 if is_integer(indexer):
3507 indexer = [indexer]

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/pandas/core/indexes/base.py:3628, in Index.get_loc(self, key, method, tolerance)
3623 raise KeyError(key) from err
3624 except TypeError:
3625 # If we have a listlike key, _check_indexing_error will raise
3626 # InvalidIndexError. Otherwise we fall through and re-raise
3627 # the TypeError.
-> 3628 self._check_indexing_error(key)
3629 raise
3631 # GH#42269

File ~/anaconda3/envs/hotspotsc2/lib/python3.8/site-packages/pandas/core/indexes/base.py:5637, in Index._check_indexing_error(self, key)
5633 def _check_indexing_error(self, key):
5634 if not is_scalar(key):
5635 # if key is not a scalar, directly raise an error (the code below
5636 # would convert to numpy arrays and raise later any way) - GH29926
-> 5637 raise InvalidIndexError(key)

InvalidIndexError: (slice(None, None, None), (0, 1))

Be grateful if you could give some help
Thank you for your time!

[chuangzhao0601]

encountered the same error, did you figure out how to resolve it?