subsetting isn't working after updating scanpy

subsetting doesn’t work: I’ve this object

>>> tiss

AnnData object with n_obs × n_vars = 29322 × 19860

>>> tiss[tiss.obs['cell_ontology_class']=='B cell']

IndexError                                Traceback (most recent call last)
<ipython-input-269-28b4524131cb> in <module>()
----> 1 tiss[tiss.obs['cell_ontology_class']=='B cell']

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in __getitem__(self, index)
   1299     def __getitem__(self, index):
   1300         """Returns a sliced view of the object."""
-> 1301         return self._getitem_view(index)
   1302 
   1303     def _getitem_view(self, index):

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in _getitem_view(self, index)
   1303     def _getitem_view(self, index):
   1304         oidx, vidx = self._normalize_indices(index)
-> 1305         return AnnData(self, oidx=oidx, vidx=vidx, asview=True)
   1306 
   1307     def _remove_unused_categories(self, df_full, df_sub, uns):

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, oidx, vidx)
    662             if not isinstance(X, AnnData):
    663                 raise ValueError('`X` has to be an AnnData object.')
--> 664             self._init_as_view(X, oidx, vidx)
    665         else:
    666             self._init_as_actual(

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in _init_as_view(self, adata_ref, oidx, vidx)
    713             raise KeyError('Unknown Index type')
    714         # fix categories
--> 715         self._remove_unused_categories(adata_ref.obs, obs_sub, uns_new)
    716         self._remove_unused_categories(adata_ref.var, var_sub, uns_new)
    717         # set attributes

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in _remove_unused_categories(self, df_full, df_sub, uns)
   1318                     uns[k + '_colors'] = np.array(uns[k + '_colors'])[
   1319                         np.where(np.in1d(
-> 1320                             all_categories, df_sub[k].cat.categories))[0]]
   1321 
   1322     def rename_categories(self, key, categories):

IndexError: index 7 is out of bounds for axis 1 with size 7

even though it’s part of the set:

>>> set(tiss.obs['cell_ontology_class'])
{'B cell',
 'NA',
 'T cell',
 'dendritic cell',
 'macrophage',
 'natural killer cell'}

it does work for louvain though:

>>> tiss[tiss.obs['louvain']=='0']`

View of AnnData object with n_obs × n_vars = 5862 × 19860`

[HYsxe]

Hi @aopisco ! @falexwolf I ran into the same problem but got everything to work by deleting all the unnecessary items in adata.uns.

keep = ['neighbors', ]
keys = list(adata.uns.keys())
for key in keys:
    if key not in keep:
        del adata.uns[key]

I don’t get errors anymore but I fear that this might cause other problems I’m currently unaware of.

[simonewebb]

I do get this issue from time to time and @HYsxe 's solution works for me (thanks!). Any idea why this is? Thanks!