sc.pl.stacked_violin: issue using imported adata

Hi,

I am testing sc.pl.stacked_violin and I had an issue with running it on an AnnData variable that is imported from a h5ad file. I explain.

If I run:

>>> import scanpy.api as sc
>>> adata = sc.datasets.krumsiek11()
>>> sc.pl.stacked_violin(adata, adata.var_names, 'cell_type', use_raw=False, color='blue', show=False)

No problem, but if I run:

>>> import scanpy.api as sc
>>> adata = sc.datasets.krumsiek11()
>>> adata.write('anndata.h5ad')
>>> adata = sc.read_h5ad('anndata.h5ad')
>>> sc.pl.stacked_violin(adata, adata.var_names, 'cell_type', use_raw=False, color='blue', show=False)

then I got the error:

Traceback (most recent call last):
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/miniconda3/envs/scanpy/lib/python3.6/site-packages/scanpy/plotting/anndata.py", line 896, in stacked_violin
    orient='vertical', scale=scale, ax=ax, **kwds)
  File "/miniconda3/envs/scanpy/lib/python3.6/site-packages/seaborn/categorical.py", line 2387, in violinplot
    color, palette, saturation)
  File "/miniconda3/envs/scanpy/lib/python3.6/site-packages/seaborn/categorical.py", line 562, in __init__
    self.establish_variables(x, y, hue, data, orient, order, hue_order)
  File "/miniconda3/envs/scanpy/lib/python3.6/site-packages/seaborn/categorical.py", line 155, in establish_variables
    raise ValueError(err)
ValueError: Could not interpret input 'variable'

I tested it with versions 1.3.1 and 1.3.2, installed with bioconda.

Any idea?

Bérénice

Reproduce the two examples, especially the h5ad round-trip, then inspect scanpy/plotting/anndata.py around stacked_violin and line 896 where seaborn receives its data. Done means the imported AnnData case completes without the “Could not interpret input 'variable'” error while the in-memory example still works.