error plotting velocity_embedding

[johnjeang]

Hello, I am using the scvelo package to analyze my RNAseq data. I think this is a great tool, but I'm just running into a few errors when trying to follow the tutorial here: https://scvelo.readthedocs.io/en/stable/getting_started/

...

To simplify the reproducibility I am using the pancreas dataset provided by scvelo.

import scvelo as scv
adata = scv.datasets.pancreas()
scv.pp.filter_and_normalize(adata)
scv.pp.moments(adata)
scv.tl.velocity(adata, mode='stochastic')
scv.tl.velocity_graph(adata)

The above code appears to work fine and creates what I think are the correct fields in the adata.uns and adata.layers attributes of the anndata object. However I run into the following error when plotting.

# All of these produce the same error
# scv.pl.velocity_embedding(adata, basis='umap', color = ['clusters'])
# scv.pl.velocity_embedding_grid(adata, basis='umap', color = ['clusters'])
# scv.pl.velocity_embedding_stream(adata, basis='velocity_umap', color = ['clusters'])
# scv.pl.velocity(adata, var_names=['Sox17','Xkr4'], color = ['clusters'])

Error output

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[25], line 3
      1 # scv.pl.velocity_embedding(adata, basis='umap')
      2 # scv.pl.velocity_embedding_grid(adata, basis='umap')
----> 3 scv.pl.velocity_embedding_stream(adata, basis='velocity_umap')
      4 # scv.pl.velocity(adata, var_names=['Sox17','Xkr4'])

File ~/opt/anaconda3/envs/cellrank/lib/python3.9/site-packages/scvelo/plotting/velocity_embedding_stream.py:252, in velocity_embedding_stream(adata, basis, vkey, density, smooth, min_mass, cutoff_perc, arrow_color, arrow_size, arrow_style, max_length, integration_direction, linewidth, n_neighbors, recompute, color, use_raw, layer, color_map, colorbar, palette, size, alpha, perc, X, V, X_grid, V_grid, sort_order, groups, components, legend_loc, legend_fontsize, legend_fontweight, xlabel, ylabel, title, fontsize, figsize, dpi, frameon, show, save, ax, ncols, **kwargs)
    249 ax.streamplot(X_grid[0], X_grid[1], V_grid[0], V_grid[1], **stream_kwargs)
    251 size = 8 * default_size(adata) if size is None else size
--> 252 ax = scatter(
    253     adata,
    254     layer=layer,
    255     color=color,
    256     size=size,
    257     title=title,
    258     ax=ax,
    259     zorder=0,
    260     **scatter_kwargs,
    261 )
    262 if save is True:
    263     save = "embedding_stream"

File ~/opt/anaconda3/envs/cellrank/lib/python3.9/site-packages/scvelo/plotting/scatter.py:668, in scatter(adata, basis, x, y, vkey, color, use_raw, layer, color_map, colorbar, palette, size, alpha, linewidth, linecolor, perc, groups, sort_order, components, projection, legend_loc, legend_loc_lines, legend_fontsize, legend_fontweight, legend_fontoutline, legend_align_text, xlabel, ylabel, title, fontsize, figsize, xlim, ylim, add_density, add_assignments, add_linfit, add_polyfit, add_rug, add_text, add_text_pos, add_margin, add_outline, outline_width, outline_color, n_convolve, smooth, normalize_data, rescale_color, color_gradients, dpi, frameon, zorder, ncols, nrows, wspace, hspace, show, save, ax, **kwargs)
    666     if not (add_outline is None or g_bool is None):
    667         groups = add_outline
--> 668     set_legend(
    669         adata,
    670         ax,
    671         color,
    672         legend_loc,
    673         scatter_array,
    674         legend_fontweight,
    675         legend_fontsize,
    676         legend_fontoutline,
    677         legend_align_text,
    678         groups,
    679     )
    680 if add_density:
    681     plot_density(x, y, add_density, ax=ax)

File ~/opt/anaconda3/envs/cellrank/lib/python3.9/site-packages/scvelo/plotting/utils.py:555, in set_legend(adata, ax, value_to_plot, legend_loc, scatter_array, legend_fontweight, legend_fontsize, legend_fontoutline, legend_align_text, groups)
    553     legend_fontoutline = 1
    554 obs_vals = adata.obs[value_to_plot]
--> 555 obs_vals.cat.categories = obs_vals.cat.categories.astype(str)
    556 color_keys = adata.uns[f"{value_to_plot}_colors"]
    557 if isinstance(color_keys, dict):

File ~/opt/anaconda3/envs/cellrank/lib/python3.9/site-packages/pandas/core/base.py:178, in NoNewAttributesMixin.__setattr__(self, key, value)
    172 if getattr(self, "__frozen", False) and not (
    173     key == "_cache"
    174     or key in type(self).__dict__
    175     or getattr(self, key, None) is not None
    176 ):
    177     raise AttributeError(f"You cannot add any new attribute '{key}'")
--> 178 object.__setattr__(self, key, value)

File ~/opt/anaconda3/envs/cellrank/lib/python3.9/site-packages/pandas/core/accessor.py:99, in PandasDelegate._add_delegate_accessors.<locals>._create_delegator_property.<locals>._setter(self, new_values)
     98 def _setter(self, new_values):
---> 99     return self._delegate_property_set(name, new_values)

File ~/opt/anaconda3/envs/cellrank/lib/python3.9/site-packages/pandas/core/arrays/categorical.py:2460, in CategoricalAccessor._delegate_property_set(self, name, new_values)
   2459 def _delegate_property_set(self, name, new_values):
-> 2460     return setattr(self._parent, name, new_values)

AttributeError: can't set attribute

To be fair, plots actually are produced, but I wondered whether I should be worried about this error -- like if the plots have incomplete calculations? The plots also seem to be missing their legend.

Versions

Here are the package versions I am using. Originally I had numpy==1.24.4, but I was having some compatibility issues so I downgraded to 1.21.5.

scvelo==0.2.5  scanpy==1.9.3  anndata==0.9.1  loompy==3.0.7  numpy==1.21.5  scipy==1.11.1  matplotlib==3.7.2  sklearn==1.1.3  pandas==2.0.3 

Thanks so much!

[anemartinezlarrinaga2898]

Hello,

I'm having the same issue how did you solved it?