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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Compatibility of hdWGCNA with Visium HD Data #286

Open wnddl111 opened 1 week ago

wnddl111 commented 1 week ago

Hello,

I am interested in using the hdWGCNA package with Visium HD data. Firstly, I would like to confirm if this is possible.

While attempting to proceed on my own, I encountered an issue due to the absence of the required metadata in my dataframe. Specifically, the package requires 'row', 'col', 'imagerow', and 'imagecol' columns.

Could you please clarify what is meant by the 'row' and 'col' columns in this context?

Regarding 'imagerow' and 'imagecol', I am considering using the 'x.coordinates' and 'y.coordinates' obtained from the Loupe Browser export CSV. Would this approach be acceptable?

Your guidance on how to properly prepare my dataframe for hdWGCNA would be greatly appreciated.

Thank you for your assistance.

Best regards, juyoung lee

smorabit commented 1 week ago

Hi,

I have not tested hdWGCNA with Visium HD, but I think it could work in theory. Since I have not tried it, I currently have no recommendation on how to handle Visium HD data.

To clarify, your issue is very similar to #278. It seems like when Visium HD was released, Seurat changed how their data structure handles the images and coordinates, making it incompatible with hdWGCNA. I am planning to fix this but I am currently busy with other obligations and I won't have time to fix it for a few weeks.