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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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spatial location file #58

Closed YyLu5 closed 6 months ago

YyLu5 commented 1 year ago

Hello,

Thank you so much for this useful tool for domain detection. I'm trying to use it on my own data, but I only have pixel coordinates. I followed your tutorial with your example data, everything works fine. I'm wondering if I don't have x_array/y_array, how can I proceed? Especially x/y_array are needed in spg.calculate_adj_matrix function.

Or if I only have x/y array, can I replace the x/y pixel in the tutorial with them?

Thank you.

zji90 commented 6 months ago

I have the same question. Data other than Visium (e.g., MERFISH) does not have x/y array. Only x/y coordinates are available.

jianhuupenn commented 6 months ago

Please use the same x/y coordinates as x/y array.