Spatial plots

[SaskiaFreytag]

Great paper and thanks for sharing the code!

Do you also have code on how to create the spatial plots in Figure 5 and Supplementary Figure 5? I am after the overlay of the different tumour states on the Visium slide.

Cheers,

Saskia

[ccruizm]

Hello @SaskiaFreytag,

Glad you liked it :)

I was cleaning up the code to reproduce/generate the figures in the paper but had to stop uploading the missing figures/sections since we got the comments from the reviewers. The ST section will likely change, but I can share the code on how I generated that figure.

What section of figure 5/supp 5 were you referring to (from your comment, I assume they are Fig5b,c, and Supp5 a,c)? Do you know if you only need the figures' code or how to deconvolve the data with cell2location?

[SaskiaFreytag]

Totally understandable that you are trying to get the revisions out first. I would indeed like Fig 5b,c and Supp 5 a,c. And if you could get me the cell2location code as well I would be most grateful.

[ccruizm]

Sorry for the delay! Please find attached the file that includes the code and an example of how I generated the figures. I hope this helps (and it is what you are looking for 😉)!
cell2location_extended_gbmap.zip