单细胞 | CellChat（一） · 单样本细胞互作

一.生成cellchat文件，选择数据库

library(CellChat)
library(ggplot2)
library(ggalluvial)
library(svglite)
library(Seurat)
library(SeuratData)

#创建CellChat文件
cellchat <- createCellChat(object = sc, meta = sc@meta.data, group.by = "celltype")

#设置配体-受体相互作用数据库
CellChatDB <- CellChatDB.mouse #use CellChatDB.human if running on human data
showDatabaseCategory(CellChatDB)
cellchat@DB <- CellChatDB
#CellChatDB.use <- subsetDB(CellChatDB, 
                            search = "Secreted Signaling", 
                            key = "annotation") #也可选择指定数据库
cellchat <- subsetData(cellchat) 

二.处理表达数据

cellchat <- subsetData(cellchat)
#识别过表达基因
cellchat <- identifyOverExpressedGenes(cellchat)
#识别过表达配体受体对
cellchat <- identifyOverExpressedInteractions(cellchat)
cellchat <- projectData(cellchat,PPI.mouse)
#推断cell-cell communication network
cellchat <- computeCommunProb(cellchat,raw.use = F,population.size = TRUE)
cellchat <- filterCommunication(cellchat,min.cells = 10)
#计算每个信号通路相关的所有配体-受体相互作用的通信结果
cellchat <- computeCommunProbPathway(cellchat)
#计算整合的细胞类型之间通信结果
cellchat <- aggregateNet(cellchat)

三.可视化1：celltype之间通讯结果

groupSize <- as.numeric(table(cellchat@idents))
par(mfrow = c(1,2), xpd=TRUE)
netVisual_circle(cellchat@net$count, vertex.weight = groupSize, 
                 weight.scale = T, label.edge= F, 
                 title.name = "Number of interactions")
netVisual_circle(cellchat@net$weight, vertex.weight = groupSize, 
                 weight.scale = T, label.edge= F, 
                 title.name = "Interaction weights/strength")

mat <- cellchat@net$weight
par(mfrow = c(3,4), xpd=TRUE)
for (i in 1:nrow(mat)) {
  mat2 <- matrix(0, nrow = nrow(mat), ncol = ncol(mat), 
                 dimnames = dimnames(mat))
  mat2[i, ] <- mat[i, ]
  netVisual_circle(mat2, vertex.weight = groupSize, 
                   weight.scale = T, edge.weight.max = max(mat), 
                   title.name = rownames(mat)[i])
}

可视化2：特定信号通路的互作情况

pathways.show <- c("CXCL") 
netVisual_heatmap(cellchat, signaling = pathways.show, color.heatmap = "Reds")

可视化3：计算并可视化网络中心性分数

cellchat <- netAnalysis_computeCentrality(cellchat, slot.name = "netP") 
netAnalysis_signalingRole_network(cellchat, 
                     signaling = pathways.show, 
                     width = 8, height = 2.5, font.size = 10)

可视化4：根据结构相似性和功能相似性识别信号组 

#功能相似性
cellchat <- computeNetSimilarity(cellchat, type = "functional")
cellchat <- netEmbedding(cellchat, type = "functional")
cellchat <- netClustering(cellchat, type = "functional")
netVisual_embedding(cellchat, type = "functional", label.size = 3.5)

#结构相似性
cellchat <- computeNetSimilarity(cellchat, type = "structural")
cellchat <- netEmbedding(cellchat, type = "structural")
cellchat <- netClustering(cellchat, type = "structural")
netVisual_embedding(cellchat, type = "structural", label.size = 3.5)

netVisual_embeddingZoomIn(cellchat, type = "structural", nCol = 2)

参考：Inference and analysis of cell-cell communication using CellChat (htmlpreview.github.io)