A problem about batch correction in single-cell-tutorial's code
Closed this issue · 4 comments
Describe the bug
It is a KeyError when I use this code.
To Reproduce
simba_object.gen_graph()
simba_object.train(num_workers=6)
adata2=simba_object.batch_correction() # This code can not run and say that KeyError
adata.obsm['X_simba']=adata2.obsm['X_simba'].copy()
out put
out put.txt
Expected behavior
Batch correction
Desktop (please complete the following information):
omicverse 1.5.7
WSL2 ubuntu20.04
windows10
Additional context
The tutorial is
https://single-cell-tutorial.readthedocs.io/zh/latest/preprocess/2-5/
Could you provide your input obj or with the similar structure?
Could you provide your input obj or with the similar structure?
I am following this tutorial to run the code, all the data and code is there
https://single-cell-tutorial.readthedocs.io/zh/latest/preprocess/2-5/
data:
s1d3: https://figshare.com/ndownloader/files/41932005
s2d1: https://figshare.com/ndownloader/files/41932011
s3d7: https://figshare.com/ndownloader/files/41932008
The error is occurring in the part "基于细胞与特征共嵌入图".
Please check #57 @Starlitnightly