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

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!

YosefLab / Hotspot

InvalidIndexError: (slice(None, None, None), (0, 1)) when using sc.pl.spatial #29