Remove `paga_compare` groups argument?

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Example of potentially bad groups argument (copied from PR):

For example, on current master passing any value for groups to sc.pl.paga_compare causes an error (since the "wrong" number of medians is calculated). Now it works, but it's a bit unclear if it's doing the right thing:

import scanpy as sc

adata = sc.datasets.pbmc3k_processed()
sc.tl.paga(adata, "louvain")
sc.pl.paga_compare(adata, groups=list(adata.obs["louvain"].cat.categories[:4])

On master:

traceback

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-13-e5188d753713> in <module>
      1 adata = sc.datasets.pbmc3k_processed()
      2 sc.tl.paga(adata, "louvain")
----> 3 sc.pl.paga_compare(adata, groups=list(adata.obs["louvain"].cat.categories[:4]))

~/github/scanpy/scanpy/plotting/_tools/paga.py in paga_compare(adata, basis, edges, color, alpha, groups, components, projection, legend_loc, legend_fontsize, legend_fontweight, legend_fontoutline, color_map, palette, frameon, size, title, right_margin, left_margin, show, save, title_graph, groups_graph, **paga_graph_params)
    135     if legend_fontoutline is not None:
    136         paga_graph_params['fontoutline'] = legend_fontoutline
--> 137     paga(
    138         adata,
    139         ax=axs[1],

~/github/scanpy/scanpy/plotting/_tools/paga.py in paga(adata, threshold, color, layout, layout_kwds, init_pos, root, labels, single_component, solid_edges, dashed_edges, transitions, fontsize, fontweight, fontoutline, text_kwds, node_size_scale, node_size_power, edge_width_scale, min_edge_width, max_edge_width, arrowsize, title, left_margin, random_state, pos, normalize_to_color, cmap, cax, colorbar, cb_kwds, frameon, add_pos, export_to_gexf, use_raw, colors, groups, plot, show, save, ax)
    552             if title[icolor] is not None:
    553                 axs[icolor].set_title(title[icolor])
--> 554             sct = _paga_graph(
    555                 adata,
    556                 axs[icolor],

~/github/scanpy/scanpy/plotting/_tools/paga.py in _paga_graph(adata, ax, solid_edges, dashed_edges, adjacency_solid, adjacency_dashed, transitions, threshold, root, colors, labels, fontsize, fontweight, fontoutline, text_kwds, node_size_scale, node_size_power, edge_width_scale, normalize_to_color, title, pos, cmap, frameon, min_edge_width, max_edge_width, export_to_gexf, colorbar, use_raw, cb_kwds, single_component, arrowsize)
    820         with warnings.catch_warnings():
    821             warnings.simplefilter("ignore")
--> 822             nx.draw_networkx_edges(
    823                 nx_g_solid, pos, ax=ax, width=widths, edge_color='black'
    824             )

/usr/local/lib/python3.8/site-packages/networkx/drawing/nx_pylab.py in draw_networkx_edges(G, pos, edgelist, width, edge_color, style, alpha, arrowstyle, arrowsize, edge_cmap, edge_vmin, edge_vmax, ax, arrows, label, node_size, nodelist, node_shape, connectionstyle, min_source_margin, min_target_margin)
    654 
    655     # set edge positions
--> 656     edge_pos = np.asarray([(pos[e[0]], pos[e[1]]) for e in edgelist])
    657 
    658     # Check if edge_color is an array of floats and map to edge_cmap.

/usr/local/lib/python3.8/site-packages/networkx/drawing/nx_pylab.py in <listcomp>(.0)
    654 
    655     # set edge positions
--> 656     edge_pos = np.asarray([(pos[e[0]], pos[e[1]]) for e in edgelist])
    657 
    658     # Check if edge_color is an array of floats and map to edge_cmap.

KeyError: 5

In this PR:

Why is groups a handled argument if it doesn't do anything with the paga representation? Should it be an available argument at all? What was the intent of the argument when it was added?

Start in scanpy/plotting/_tools/paga.py at paga_compare, paga, and _paga_graph, then reproduce the supplied PBMC example with a groups value. Determine the intended behavior of groups and resolve the resulting KeyError by either clarifying supported behavior or removing the argument; the example should complete without the reported failure.

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Example of potentially bad groups argument (copied from PR):

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Remove `paga_compare` groups argument?

Description

Example of potentially bad groups argument (copied from PR):

Contributor guide

First steps

Research direction

Assessment

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