New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Issues displaying pathways in spatial context #309

Open

alipirani88 opened this issue Feb 6, 2025 · 0 comments

alipirani88 commented Feb 6, 2025 •

edited

Loading

Hi,

I am experiencing errors while displaying pathway contribution in spatial context. Here is the code snippet that gives me an error:


netVisual_aggregate(cellchat, signaling = pathways.show, layout = "spatial", edge.width.max = 2, vertex.size.max = 1, alpha.image = 0.2, vertex.label.cex = 3.5)


Error in if (ncol(coordinates) == 2) { : argument is of length zero

I can see that cellchat contains spatial image data as well:

> cellchat@images
$fov
Spatial coordinates for 321020 cells and 541 molecules
 First 10 molecules: ABI3BP, ACAN, ADAM10, ADAMTS16, ADAMTS3, ADIPOQ
Default segmentation boundary: centroids 
Associated assay: Xenium 
Key: Xenium_

The text was updated successfully, but these errors were encountered:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment