scv.pp.moment error

Hello,

First try with this testing release. I cloned the git repo, and installed with pip install . on python 3.6.5 I loaded an annotated dataframe I am using to work on (created/pp with scanpy), then:

>>> scv.pp.moments(adata)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path/to/scvelo/scvelo/preprocessing/moments.py", line 42, in moments
    adata.layers['Ms'] = csr_matrix.dot(connectivities, adata.layers['spliced']).toarray()
  File "/path/to/local/python/python-dev/lib/python3.6/site-packages/anndata/layers.py", line 41, in __getitem__
    return self._layers[key]
KeyError: 'spliced'

Many thanks for your work, Best.

[VolkerBergen]

.X contains the logarithmized normalized spliced counts used e.g. for computing neighbor graphs and embeddings, while .layers['spliced'] contains the non-logarithmized normalized spliced counts (keeping it comparable to unspliced counts). Indeed, we might be better off just applying np.log1p whenever needed instead of storing another count table. However, since batch correction and other preprocessing procedures should only affect .X as well, it is probably best to keep it as is.

The initially raised plotting issue (seemed to have been lost in the course of conversation) is still on my to-do list.

[juugii]

Hi @VolkerBergen, Sorry for my late answer. I have been able to use the plotting functions, yet I have to use plt.show() as explained. But it is functional, and gives expected results. I have been able to work with loom files after upgrading to the latest scanpy. I’m also building on creating an AnnData according to your recommendations, but it is outside the scope of this OP, I can close it. Thanks for your help.