Error of netVisual_bubble in "Identify dysfunctional signaling by using differential expression analysis"

[hjames1]

Hello, thank you for providing such an excellent R package.

In the section “Identify dysfunctional signaling by using differential expression analysis”, I used netVisual_bubble to plot pathways upregulated in the BM group, but I noticed that some downregulated pathways were also included.

The code I used is as follows:

gg1 <- netVisual_bubble(cellchat, pairLR.use = pairLR.use.up, 
                        sources.use = grep(pattern = source_celltypes,group.new), color.text = c('blue','red'),
                        targets.use = grep(pattern = target_celltypes,group.new), 
                        comparison = c(1, 2),  
                        # max.dataset = 2,
                        angle.x = 45, remove.isolate = T,title.name = paste0("Up-regulated signaling in ", names(object.list)[2]))
gg1

gg2 <- netVisual_bubble(cellchat, pairLR.use = pairLR.use.up, 
                        sources.use = grep(pattern = source_celltypes,group.new), color.text = c('blue','red'),
                        targets.use = grep(pattern = target_celltypes,group.new), 
                        comparison = c(1, 2),  
                        max.dataset = 2,
                        angle.x = 45, remove.isolate = T,title.name = paste0("Up-regulated signaling in ", names(object.list)[2]))
gg2

gg1+gg2

In your tutorial (A Bubble plot) under the (A) Bubble plot section, the code is:

pairLR.use.up = net.up[, "interaction_name", drop = F]
gg1 <- netVisual_bubble(cellchat, pairLR.use = pairLR.use.up, sources.use = 4, targets.use = c(5:11), comparison = c(1, 2),  angle.x = 90, remove.isolate = T,title.name = paste0("Up-regulated signaling in ", names(object.list)[2]))
#> Comparing communications on a merged object
pairLR.use.down = net.down[, "interaction_name", drop = F]
gg2 <- netVisual_bubble(cellchat, pairLR.use = pairLR.use.down, sources.use = 4, targets.use = c(5:11), comparison = c(1, 2),  angle.x = 90, remove.isolate = T,title.name = paste0("Down-regulated signaling in ", names(object.list)[2]))
#> Comparing communications on a merged object
gg1 + gg2

However, the comparison condition parameter max.dataset = 2 or max.dataset = 1 is missing in this code.