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Teichlab / covid19_MS1

Analysis notebooks for "SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes".
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AttributeError: module 'scanpy_scripts.lib' has no attribute 'expression_colormap' #1

Open rahulbhadani opened 4 years ago

rahulbhadani commented 4 years ago

With reference to reproducing the output of the notebook: https://github.com/Teichlab/covid19_MS1/blob/master/reprocess_dataset/baron16.ipynb

I tried to install https://github.com/ebi-gene-expression-group/scanpy-scripts/tree/nh3 and also tried by git cloning, switching to branch nh3 and and doing python setup.py install, but in both cases, executing

import scanpy_scripts as ss
expr_cmap = ss.lib.expression_colormap()

gives error

AttributeError: module 'scanpy_scripts.lib' has no attribute 'expression_colormap'

and executing 

ss.lib.calculate_qc(raw_ad)

gives

AttributeError: module 'scanpy_scripts.lib' has no attribute 'calculate_qc'

What's going on?

nh3 commented 3 years ago

Hello, sorry for extremely late reply. But the functions do exist and are exported as you can see from https://github.com/ebi-gene-expression-group/scanpy-scripts/blob/nh3/scanpy_scripts/lib/__init__.py and https://github.com/ebi-gene-expression-group/scanpy-scripts/blob/nh3/scanpy_scripts/lib/_plot.py . If you installed by python setup.py install, please check your installation location whether the installed code there are as expected. What's also worth checking is if the python called by your jupyter notebook is the expected one.

rahulbhadani commented 3 years ago

Okay, I will give it another try and let you know asap.