scverse / scverse/scanpy

sc.pl.paga_compare fails when color is different than groups parameter of sc.tl.paga

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Description

When I run the following code:

import scanpy as sc

sc.set_figure_params(dpi=70)
adata = sc.datasets.paul15()
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata)
sc.tl.paga(adata, groups='paul15_clusters')
print(adata.uns['paga'].keys())
sc.pl.paga_compare(adata, color='leiden')

It fails with the following exception:

KeyError                                  Traceback (most recent call last)
<ipython-input-1-5ec08bc29df7> in <module>
      7 sc.tl.leiden(adata)
      8 sc.tl.paga(adata, groups='paul15_clusters')
----> 9 sc.pl.paga_compare(adata, color='leiden')
     10 adata.uns['paga'].keys()

~/.anaconda3/lib/python3.7/site-packages/scanpy/plotting/_tools/paga.py in paga_compare(adata, basis, edges, color, alpha, groups, components, projection, legend_loc, legend_fontsize, legend_fontweight, color_map, palette, frameon, size, title, right_margin, left_margin, show, save, title_graph, groups_graph, **paga_graph_params)
    108             paga_graph_params['pos'] = utils._tmp_cluster_pos
    109         else:
--> 110             paga_graph_params['pos'] = adata.uns['paga']['pos']
    111     xlim, ylim = axs[0].get_xlim(), axs[0].get_ylim()
    112     axs[1].set_xlim(xlim)

KeyError: 'pos'

and it prints:

dict_keys(['connectivities', 'connectivities_tree', 'groups'])

@falexwolf might have broken this with https://github.com/theislab/scanpy/commit/504b87e57327be8824d0697b92bac30fd86f0a82 :) but I didn't fully debug.

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Research direction

Start in scanpy/plotting/_tools/paga.py at paga_compare and compare its handling of the groups passed to sc.tl.paga with the color passed to sc.pl.paga_compare. Reproduce the example using the paul15 dataset and inspect how the PAGA position is generated; done means the example no longer raises KeyError when color differs from groups.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, data-visualization
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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