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jianhuupenn / SpaGCN

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network
MIT License
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Error at the steps with louvain algorithm #43

Closed avsarg closed 2 years ago

avsarg commented 2 years ago

Hi! First of all, thanks for this nice method, SpaGCN. I want to run it for my own data and follow the given tutorial (https://github.com/jianhuupenn/SpaGCN/blob/master/tutorial/tutorial.ipynb). However, I got error which says “BaseException: Could not construct partition: vector too long” at the steps which use Louvain algorithm.

Can you please help me to solve this problem?

Thanks,

avsarg commented 2 years ago

It is solved, thanks.

huimin230 commented 2 years ago

It is solved, thanks.

Hi, I have the similar problem, "BaseException: Could not construct partition: vector", could you please let me know how did you solve this problem?

Big thanks!

avsarg commented 2 years ago

Hi, in my situation, the problem occurred bcz of version mismatch between anndata, scipy, h5py, louvain and so. I just created a new environment which is similar to the tested "Enviroment 3" in Readme file, and the problem solved.