学习 CellChat 细胞间通讯分析
[第一部分：CellChat对象的数据输入&处理及初始化] (2022-05-22 - 简书 (jianshu.com)
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第二部分：细胞间通信网络的推断
[Reference] (https://github.com/sqjin/CellChat/blob/master/tutorial/CellChat-vignette.html)
1. 计算通信概率并推断通信网络
cellchat <- computeCommunProb(cellchat) #笔记本运行比较耗时
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2. 过滤细胞
cellchat <- filterCommunication(cellchat, min.cells = 10)
3. 在信号通路水平上推断细胞间通讯
cellchat <- computeCommunProbPathway(cellchat)
4. 在信号通路水平上推断细胞间通讯
cellchat <- aggregateNet(cellchat)
5. 展示细胞间通讯
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")
展示细胞间通讯
