Identify the up-regulated and down-regulated signaling ligand-receptor pairs

[tumorscholar]

Hello Jin,
I have calculated the up-regulated L-R pairs using netVisual_bubble, but the p-value in the data (gg1$data) doesn't match the p-value in the figure. The p-value in gg1$data is 3, not sure what went wrong. Help please

netVisual_bubble(cellchat, sources.use = 4, targets.use = c(5:29),  comparison = c(1, 2), angle.x = 45)
gg1 <- netVisual_bubble(cellchat, sources.use = 3, targets.use = c(4:25),  comparison = c(1, 2), max.dataset = 2, title.name = "Increased signaling in Fibrosis", angle.x = 45, remove.isolate = T)
data <- gg1$data
write.csv(data, "/data/home/hdx044/files/cellchat/LIVER/InteractionsProbabilityInLIVERfibrosis.csv")