Error with scanpy.api.pl.highest_expr_genes()

I have an error when trying this function for my data:

sc.pl.highest_expr_genes(adata)

results in

filtered out 14139 cells that have less than 1 counts
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-11-1f5b130b9d4e> in <module>()
----> 1 sc.pl.highest_expr_genes(adata)

/usr/local/lib/python3.6/site-packages/scanpy-1.2.2+90.g47c579f-py3.6.egg/scanpy/plotting/qc.py in highest_expr_genes(adata, n_top, save, show, ax, **kwargs)
     41 
     42     # identify the genes with the highest mean
---> 43     dat.var['mean_percent'] = dat.X.mean(axis=0).A1
     44 
     45     top = dat.var.sort_values('mean_percent', ascending=False).index[:n_top]

AttributeError: 'numpy.ndarray' object has no attribute 'A1'

It is not critical, but I wonder why this error happens. I have the most recent version from github. Maybe I’m not transforming my data to a certain format properly? Didn’t find this documented anyway. However, a lot of other analysis that I do via Scanpy works for me, so generally the data is read and processed correctly.

[falexwolf]

Thank you, @LuckyMD!

[pritykin]

Works for me now, thank you!