Plotting with using scanpy.pl gives attribute error. #2680
Comments
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I also have encountered this same error when trying to use sc.pl.violin |
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I have the same error on scanpy 1.9.5, seaborn 0.13.0, the error seems to be specific to 'multi_panel = True' and produces 3 empty graphs that all inherit the "n_genes_by_counts" x-label instead of the proper one.
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We're also hitting this. I didnt test this yet, but from our CI history it seems like this worked with seaborn-0.12.2, but broke when that updated to seaborn-0.13.0 |
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Hey, I'll look into this, for the moment it appears that for the violin plot
For urgent violin plots, either of these two options should produce them. Will get back to this asap. |
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Hey, indeed there seems to be an issue with our current usage of For users running into this issue now
this makes sure you are using the working version of seaborn. Hope this helps! |
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Thank you so much! |
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Hey @victorlga are you still interested in fixing this? :) |
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Hi, Thanks! |
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We sped up our release process, which means it’s not a huge deal to make one. But it’s still more than just clicking a button, so since we just made a release, maybe in 1-2 weeks? |
Please make sure these conditions are met
What happened?
Plotting with scanpy.pl gives attribute error.
Minimal code sample
Error output
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Cell In[47], line 1 ----> 1 sc.pl.violin(adata, ["n_genes_by_counts", "total_counts", "pct_counts_mt"], jitter=0.4, multi_panel=True) File ~/anaconda3/lib/python3.11/site-packages/scanpy/plotting/_anndata.py:795, in violin(adata, keys, groupby, log, use_raw, stripplot, jitter, size, layer, scale, order, multi_panel, xlabel, ylabel, rotation, show, save, ax, **kwds) 790 if multi_panel and groupby is None and len(ys) == 1: 791 # This is a quick and dirty way for adapting scales across several 792 # keys if groupby is None. 793 y = ys[0] --> 795 g = sns.catplot( 796 y=y, 797 data=obs_tidy, 798 kind="violin", 799 scale=scale, 800 col=x, 801 col_order=keys, 802 sharey=False, 803 order=keys, 804 cut=0, 805 inner=None, 806 **kwds, 807 ) 809 if stripplot: 810 grouped_df = obs_tidy.groupby(x) File ~/anaconda3/lib/python3.11/site-packages/seaborn/categorical.py:2932, in catplot(data, x, y, hue, row, col, kind, estimator, errorbar, n_boot, units, seed, order, hue_order, row_order, col_order, col_wrap, height, aspect, log_scale, native_scale, formatter, orient, color, palette, hue_norm, legend, legend_out, sharex, sharey, margin_titles, facet_kws, ci, **kwargs) 2929 linecolor = plot_kws.pop("linecolor", "auto") 2930 linecolor = p._complement_color(linecolor, color, p._hue_map) -> 2932 p.plot_violins( 2933 width=width, 2934 dodge=dodge, 2935 gap=gap, 2936 split=split, 2937 color=color, 2938 fill=fill, 2939 linecolor=linecolor, 2940 linewidth=linewidth, 2941 inner=inner, 2942 density_norm=density_norm, 2943 common_norm=common_norm, 2944 kde_kws=kde_kws, 2945 inner_kws=inner_kws, 2946 plot_kws=plot_kws, 2947 ) 2949 elif kind == "boxen": 2951 plot_kws = kwargs.copy() File ~/anaconda3/lib/python3.11/site-packages/seaborn/categorical.py:1153, in _CategoricalPlotter.plot_violins(self, width, dodge, gap, split, color, fill, linecolor, linewidth, inner, density_norm, common_norm, kde_kws, inner_kws, plot_kws) 1151 legend_artist = _get_patch_legend_artist(fill) 1152 common_kws = {**plot_kws, "linewidth": linewidth, "edgecolor": linecolor} -> 1153 self._configure_legend(ax, legend_artist, common_kws) File ~/anaconda3/lib/python3.11/site-packages/seaborn/categorical.py:420, in _CategoricalPlotter._configure_legend(self, ax, func, common_kws, semantic_kws) 418 if show_legend: 419 self.add_legend_data(ax, func, common_kws, semantic_kws=semantic_kws) --> 420 handles, _ = ax.get_legend_handles_labels() 421 if handles: 422 ax.legend(title=self.legend_title) AttributeError: 'NoneType' object has no attribute 'get_legend_handles_labels'Versions
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