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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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Reproduction issue on tutorial: error at the steps with louvain algorithm #45

Closed huimin230 closed 11 months ago

huimin230 commented 2 years ago

Hi Dr. Hu,

I want to reproduce results via SpaGCN in the given tutorial (https://github.com/jianhuupenn/SpaGCN/blob/master/tutorial/tutorial.ipynb). However, I got error “BaseException: Could not construct partition: vector” which seems in the steps using Louvain algorithm.

Can you please provide any help to solve this problem?

Thanks,

jianhuupenn commented 2 years ago

Thanks for your interest in SpaGCN. If you are running on the toy data and got this error, I believe it is because of the support package versions. Could you check the package version, especially for louvain and scanpy? A list of tested environments can be found here: https://github.com/jianhuupenn/SpaGCN#versions-the-software-has-been-tested-on

huimin230 commented 2 years ago

Hi Dr.Hu,

Thanks for your reply. I checked all packages version as below, the error still exists. BTW: my computer system is macOS Monterey Apple M1 Pro

System: Anaconda Python: 3.10.4 Python packages: pandas = 1.5.0, numpy = 1.23.3, python-igraph=0.10.1, torch=1.12.1, louvain=0.7.1, scipy = 1.9.2, scanpy = 1.9.1, anndata = 0.8.0, natsort = 8.2.0, scikit-learn = 1.1.2