RankNet for several samples

[mboisvert1]

Hi,

I am wondering if it is possible to run the rankNet function on a cellchat object that has multiple (~5) different samples?

When I run compareInteractions on the cellchat object, it shows the # of interactions across all 5 samples. However, when I run rankNet, it only shows the comparison of signaling molecules between the first two samples.

gg1 <- rankNet(cellchat, mode = "comparison", measure = "weight", sources.use = NULL, targets.use = NULL, stacked = T, do.stat = TRUE) gg2 <- rankNet(cellchat, mode = "comparison", measure = "weight", sources.use = NULL, targets.use = NULL, stacked = F, do.stat = TRUE)

gg1 + gg2