error' single positional indexer is out-of-bounds' when using 'ct.tl.spatial_communication'

[yao50985098]

Hello, thank you for your nice work for quantifying spatial signaling.
I got an error when calculating customized pathway using ct.tl.spatial_communication.
I followed the steps in your uploaded code in the breast slide.

Then :


I think I generated the right form, since some pathways were successfully calculated,but more pathways got the error' single positional indexer is out-of-bounds' .
Looking forward to your kind help, thank you!

[izabellaleahz]

I also had this issue and it turned out to be the fact that there was no overlap between the gene list in the adata and df_ligrec[0] genes. In my case it was the gene names in adata were lowercase instead of uppercase.