1. 合并多组数据

library(CellChat)
cellchat.1 <- readRDS("group1.cellchat.rds")
cellchat.2 <- readRDS("group2.cellchat.rds")
object.list <- list(Group1 = cellchat.1, Group2 = cellchat.2)
cellchat <- mergeCellChat(object.list, add.names = names(object.list))
saveRDS(cellchat,"cellchat.merged.rds")

2.绘制两组circle图

weight.max <- getMaxWeight(object.list, attribute = c("idents","count"))
par(mfrow = c(1,2), xpd=TRUE)
for (i in 1:length(object.list)) {
  netVisual_circle(object.list[[i]]@net$count, weight.scale = T, remove.isolate = T,
                   label.edge= T, #在线上标记相互作用强度
                   edge.weight.max = weight.max[2],
                   sources.use = "Epithelial cells", #选择source细胞类型
                   targets.use = c("CD8 Teff","CD8 Tem","CD8 Tex","CD8 Tn"),
                   edge.width.max = 30, vertex.weight.max = 10,title.name = paste0(names(object.list)[i]))
}

3.绘制两组bubble图

# 将选择的lrpair以dataframe形式传递给参数
lr <- data.frame(interaction_name=c("SPP1_CD44","CDH1_KLRG1","CLEC2B_KLRB1"))
# pairLR.use <- extractEnrichedLR(cellchat, signaling = c("CCL","CXCL","FGF"))
bubble1 <- netVisual_bubble(cellchat,  
                 pairLR.use = lr,
                 sources.use = "Epithelial cells",
                 targets.use = c("CD8 Teff","CD8 Tem","CD8 Tex","CD8 Tn"),
                 return.data = TRUE,
                 comparison = c(1, 2),
                 angle.x = 90)
print(bubble1$gg.obj)

更多详情，可查看官方说明Comparison_analysis_of_multiple_datasets