Which version of scanpy and anndata should i use?

[kunwang34]

I've read the PROSSTT paper with great interest and find its amazing! I'm trying to run examples you provided but theres some error when import scanpy and anndata. I think I didn't choose their version right. Could you please tell me which version should I use? Thanks a lot.

[galicae]

Hi @kunwang34, happy to hear that :) Would you mind posting the full error message here? Otherwise I'm afraid I can't help too much with debugging :(

[kunwang34]

Thanks for your reply @galicae. I'm trying to run the example with scanpy 1.7.2 and anndata 0.7.6. Here's error:

ImportError Traceback (most recent call last)

in 1 import anndata as ad ----> 2 from scanpy.api import pp 3 from scanpy.api.tl import diffmap 4 5 # data = ad.AnnData(np.log(X+1)) c:\users\wangkun\miniconda3\envs\prosstt\lib\site-packages\scanpy\api\__init__.py in 25 26 from . import tl ---> 27 from . import pl 28 from . import pp 29 from ..readwrite import ( c:\users\wangkun\miniconda3\envs\prosstt\lib\site-packages\scanpy\api\pl.py in ----> 1 from ..plotting._anndata import ( 2 scatter, 3 violin, 4 ranking, 5 clustermap, ImportError: cannot import name 'stacked_violin' Thanks again.

[galicae]

you are right - these are relics of a previous scanpy version. For the examples to run normally, please remove the api from the scanpy imports: instead of from scanpy.api import pp just do from scanpy import pp. I will amend the notebooks and push again :)

[kunwang34]

Thank you very much @galicae . It works.