key Error - paga_path

[xlw1207]

I am getting an error with sc.pl.paga_path. It doesnt plot genes that my data has - i doubled checked my gene, it is in adata.var_names... if i use a gene that is not in adata.var_names, then it can plot... any idea about why the code is wrong?

_, axs = pl.subplots(ncols=3, figsize=(6, 2.5), gridspec_kw={'wspace': 0.05, 'left': 0.12})
pl.subplots_adjust(left=0.05, right=0.98, top=0.82, bottom=0.2)
for ipath, (descr, path) in enumerate(paths):
    _, data = sc.pl.paga_path(
        adata, path, gene_names,
        show_node_names=False,
        ax=axs[ipath],
        ytick_fontsize=12,
        left_margin=0.15,
        n_avg=50,
        annotations=['distance'],
        show_yticks=True if ipath==0 else False,
        show_colorbar=False,
        color_map='Greys',
        groups_key='clusters',
        color_maps_annotations={'distance': 'viridis'},
        title='{} path'.format(descr),
        return_data=True,
        show=False)
pl.savefig('./figures/paga_path_paul15.pdf')
pl.show()

Errors:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/opt/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   2645             try:
-> 2646                 return self._engine.get_loc(key)
   2647             except KeyError:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'Ascl1'

During handling of the above exception, another exception occurred:

KeyError                                  Traceback (most recent call last)
<ipython-input-522-a191d9b34213> in <module>
     17         title='{} path'.format(descr),
     18         return_data=True,
---> 19         show=False)
     20     data.to_csv('./write/paga_path_{}.csv'.format(descr))
     21 pl.savefig('./figures/paga_path_paul15.pdf')

~/opt/anaconda3/lib/python3.7/site-packages/scanpy/plotting/_tools/paga.py in paga_path(adata, nodes, keys, use_raw, annotations, color_map, color_maps_annotations, palette_groups, n_avg, groups_key, xlim, title, left_margin, ytick_fontsize, title_fontsize, show_node_names, show_yticks, show_colorbar, legend_fontsize, legend_fontweight, normalize_to_zero_one, as_heatmap, return_data, show, save, ax)
   1090                 x += list(adata.obs[key].values[idcs])
   1091             else:
-> 1092                 x += list(adata_X[:, key].X[idcs])
   1093             if ikey == 0:
   1094                 groups += [group for i in range(len(idcs))]

~/opt/anaconda3/lib/python3.7/site-packages/anndata/_core/raw.py in __getitem__(self, index)
     99 
    100     def __getitem__(self, index):
--> 101         oidx, vidx = self._normalize_indices(index)
    102 
    103         # To preserve two dimensional shape

~/opt/anaconda3/lib/python3.7/site-packages/anndata/_core/raw.py in _normalize_indices(self, packed_index)
    159         obs, var = unpack_index(packed_index)
    160         obs = _normalize_index(obs, self._adata.obs_names)
--> 161         var = _normalize_index(var, self.var_names)
    162         return obs, var
    163 

~/opt/anaconda3/lib/python3.7/site-packages/anndata/_core/index.py in _normalize_index(indexer, index)
     72         return indexer
     73     elif isinstance(indexer, str):
---> 74         return index.get_loc(indexer)  # int
     75     elif isinstance(indexer, (Sequence, np.ndarray, pd.Index, spmatrix, np.matrix)):
     76         if hasattr(indexer, "shape") and (

~/opt/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   2646                 return self._engine.get_loc(key)
   2647             except KeyError:
-> 2648                 return self._engine.get_loc(self._maybe_cast_indexer(key))
   2649         indexer = self.get_indexer([key], method=method, tolerance=tolerance)
   2650         if indexer.ndim > 1 or indexer.size > 1:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'Ascl1'