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8 months ago 单细胞cellchat细胞通讯-完整代码分享 by 生信小博士
关于cellchat通讯的文章已经有很多了。但是没有看到完整版的代码分享。今天分享一下完整代码，并且提醒大家此代码对数据input的要求。
1 首先加载必要r包
library(CellChat)library(patchwork)library(ggplot2)library(ggalluvial)library(svglite)library(Seurat)library(openxlsx)
2 读取rds文件
load('subset_data.rds')3.我们来看看rds文件的内容，这一步非常重要，是成功运行代码的关键
rds对象里一定要有stim列，表示组别
cell.type 列，表示细胞类型
> head(subset_data@meta.data)orig.ident nCount_RNA nFeature_RNA percent.mt stim RNA_snn_res.0.6 seurat_clusters RNA_snn_res.1 cluster.sort cell.type legend_labels groupsAAACCTGAGCTCCTCT.1 silicosis 3630 1428 1.460055 SiO2_7 2 2 2 1 Macrophage-1 1 Macrophage-1 <NA>AAACCTGCACAACTGT.1 silicosis 2559 945 2.032044 SiO2_7 2 2 2 1 Macrophage-1 1 Macrophage-1 <NA>AAACCTGCACGTAAGG.1 silicosis 4055 1538 1.602959 SiO2_7 2 2 2 1 Macrophage-1 1 Macrophage-1 <NA>AAACCTGCATGCGCAC.1 silicosis 917 556 1.308615 SiO2_7 2 2 2 1 Macrophage-1 1 Macrophage-1 <NA>AAACCTGGTACGCTGC.1 silicosis 2398 1192 1.542952 SiO2_7 2 2 2 1 Macrophage-1 1 Macrophage-1 <NA>AAACCTGGTAGGCTGA.1 silicosis 1993 1066 4.264927 SiO2_7 1 1 1 1 Macrophage-1 1 Macrophage-1 <NA>
组别和细胞类型：
> table(subset_data$stim)NS_56 NS_7 SiO2_56 SiO2_73123 2842 4524 1790> table(subset_data$cell.type)Endothelial cell-1 Endothelial cell-2 Fibroblast Macrophage-1 Macrophage-2 nc rTEM tr unknown456 287 1185 4588 377
4 接下来直接运行下面的代码即可得到 不同组别内 所有细胞互作的结果
for(stim in c('NS_56' , 'NS_7' ,'SiO2_56', 'SiO2_7' )){#stim="NS_56"#stim="SiO2_7","NS_7"path="/home/data/t040413/mmm_/20231009_cellchat_mmm_silicosis/cellchat"dir.create(paste(path, "cellchat", stim, sep = "/"),recursive = TRUE)setwd( paste(path, "cellchat", stim, sep = "/") )getwd()data.input = subset_data$RNA@data[, subset_data$stim==stim]head(data.input)meta = data.frame(labels = Idents(subset_data)[subset_data$stim==stim], row.names = colnames(subset_data)[subset_data$stim==stim])head(meta)cellchat <- createCellChat(object = data.input, meta = meta, group.by = "labels")CellChatDB <- CellChatDB.mousecellchat@DB <- CellChatDBcellchat <- subsetData(cellchat)#future::plan("multiprocess", workers = 4)cellchat <- identifyOverExpressedGenes(cellchat)cellchat <- identifyOverExpressedInteractions(cellchat)cellchat <- projectData(cellchat, PPI.mouse)cellchat <- computeCommunProb(cellchat) #不可有有为0的细胞数的组cellchat <- filterCommunication(cellchat, min.cells = 10) #设置最低细胞数cellchat <- computeCommunProbPathway(cellchat)cellchat <- aggregateNet(cellchat)df.net <- subsetCommunication(cellchat)write.xlsx(df.net,file='0.Cell-Cell_Communications_At_L-R.xlsx', rowNames=F, colNames=T)df.net <- subsetCommunication(cellchat, slot.name = "netP")write.xlsx(df.net,file='0.Cell-Cell_Communications_At_Pathway.xlsx', rowNames=F, colNames=T)groupSize <- as.numeric(table(cellchat@idents))## NumberOfInteractionsmat <- cellchat@net$countwrite.xlsx(mat, file='1.NumberOfInteractions.xlsx', rowNames=T, colNames=T)pdf("1.NumberOfInteractions.pdf")netVisual_circle(mat, vertex.weight = groupSize, weight.scale = T, label.edge= F, title.name = "Number of interactions")dev.off()pdf("1.NumberOfInteractions_Split.pdf")for (i in 1:nrow(mat)) {mat2 <- matrix(0, nrow = nrow(mat), ncol = ncol(mat), dimnames = dimnames(mat))mat2[i, ] <- mat[i, ]p = netVisual_circle(mat2, vertex.weight = groupSize, weight.scale = T, edge.weight.max = max(mat), title.name = rownames(mat)[i])print(p)}dev.off()## InteractionWeightsmat <- cellchat@net$weightwrite.xlsx(mat, file='2.InteractionWeights.xlsx', rowNames=T, colNames=T)pdf("2.InteractionWeights.pdf")netVisual_circle(mat, vertex.weight = groupSize, weight.scale = T, label.edge= F, title.name = "Interaction weights/strength")dev.off()pdf("2.InteractionWeights_Split.pdf")for (i in 1:nrow(mat)) {mat2 <- matrix(0, nrow = nrow(mat), ncol = ncol(mat), dimnames = dimnames(mat))mat2[i, ] <- mat[i, ]p = netVisual_circle(mat2, vertex.weight = groupSize, weight.scale = T, edge.weight.max = max(mat), title.name = rownames(mat)[i])print(p)}dev.off()## cellchat@netP$pathways: the signaling pathways showing significant communicationspathways = cellchat@netP$pathways## the left portion shows autocrine and paracrine signaling to certain cell groups of interest (i.e, the defined vertex.receiver)## the right portion shows autocrine and paracrine signaling to the remaining cell groups in the datasetvertex.receiver = seq(1,5)pdf("3.Sig_Pathway_Hierarchy_Plot.pdf")for(i in pathways){print(i)p = netVisual_aggregate(cellchat, signaling = i,vertex.receiver = vertex.receiver, vertex.label.cex = 0.4)print(p)}dev.off()pdf("3.Sig_Pathway_Circle_Plot.pdf")for(i in pathways){print(i)p = netVisual_aggregate(cellchat, signaling = i,vertex.receiver = vertex.receiver, layout = "circle")print(p)}dev.off()pdf("4.Sig_Pathway_L-R_pair_Contribution.pdf")for(i in pathways){print(i)p = netAnalysis_contribution(cellchat, signaling = i, title = paste0(i, " signaling pathway", " Contribution of each L-R pair"))print(p)}dev.off()pdf("4.Sig_Pathway_L-R_pair_bubbleplot.pdf", width=25, height=20)p = netVisual_bubble(cellchat, remove.isolate = FALSE)print(p)dev.off()cellchat <- netAnalysis_computeCentrality(cellchat, slot.name = "netP")pdf("5.Signaling_Roles_Of_Cell_Groups_Heatmap.pdf")for(i in pathways){print(i)p = netAnalysis_signalingRole_network(cellchat, signaling = i, width = 8, height = 2.5, font.size = 10)print(p)}dev.off()pdf("4.Sig_Pathway_L-R_pair_bubbleplot.pdf", width=25, height=20)p = netVisual_bubble(cellchat, remove.isolate = FALSE)print(p)dev.off()pdf("5.Signaling_Roles_Of_Cell_Groups_2D.pdf")p = netAnalysis_signalingRole_scatter(cellchat)print(p)dev.off()pdf("5.signals_Contribution_Of_Cell_Groups_Heatmap.pdf", width=10)ht1 <- netAnalysis_signalingRole_heatmap(cellchat, pattern = "outgoing", font.size = 5)ht2 <- netAnalysis_signalingRole_heatmap(cellchat, pattern = "incoming", font.size = 5)print(ht1 + ht2)dev.off()save(cellchat, file = paste0("cellchat_",stim,"_.RData"))}
5 输出的文件如下：
$ tree.├── NS_56│ ├── 0.Cell-Cell_Communications_At_L-R.xlsx│ ├── 0.Cell-Cell_Communications_At_Pathway.xlsx│ ├── 1.NumberOfInteractions.pdf│ ├── 1.NumberOfInteractions_Split.pdf│ ├── 1.NumberOfInteractions.xlsx│ ├── 2.InteractionWeights.pdf│ ├── 2.InteractionWeights_Split.pdf│ ├── 2.InteractionWeights.xlsx│ ├── 3.Sig_Pathway_Circle_Plot.pdf│ ├── 3.Sig_Pathway_Hierarchy_Plot.pdf│ ├── 4.Sig_Pathway_L-R_pair_bubbleplot.pdf│ ├── 4.Sig_Pathway_L-R_pair_Contribution.pdf│ ├── 5.Signaling_Roles_Of_Cell_Groups_2D.pdf│ ├── 5.Signaling_Roles_Of_Cell_Groups_Heatmap.pdf│ ├── 5.signals_Contribution_Of_Cell_Groups_Heatmap.pdf│ └── cellchat_NS_56_.RData├── NS_7│ ├── 0.Cell-Cell_Communications_At_L-R.xlsx│ ├── 0.Cell-Cell_Communications_At_Pathway.xlsx│ ├── 1.NumberOfInteractions.pdf│ ├── 1.NumberOfInteractions_Split.pdf│ ├── 1.NumberOfInteractions.xlsx│ ├── 2.InteractionWeights.pdf│ ├── 2.InteractionWeights_Split.pdf│ ├── 2.InteractionWeights.xlsx│ ├── 3.Sig_Pathway_Circle_Plot.pdf│ ├── 3.Sig_Pathway_Hierarchy_Plot.pdf│ ├── 4.Sig_Pathway_L-R_pair_bubbleplot.pdf│ ├── 4.Sig_Pathway_L-R_pair_Contribution.pdf│ ├── 5.Signaling_Roles_Of_Cell_Groups_2D.pdf│ ├── 5.Signaling_Roles_Of_Cell_Groups_Heatmap.pdf│ ├── 5.signals_Contribution_Of_Cell_Groups_Heatmap.pdf│ └── cellchat_NS_7_.RData├── SiO2_56│ ├── 0.Cell-Cell_Communications_At_L-R.xlsx│ ├── 0.Cell-Cell_Communications_At_Pathway.xlsx│ ├── 1.NumberOfInteractions.pdf│ ├── 1.NumberOfInteractions_Split.pdf│ ├── 1.NumberOfInteractions.xlsx│ ├── 2.InteractionWeights.pdf│ ├── 2.InteractionWeights_Split.pdf│ ├── 2.InteractionWeights.xlsx│ ├── 3.Sig_Pathway_Circle_Plot.pdf│ ├── 3.Sig_Pathway_Hierarchy_Plot.pdf│ ├── 4.Sig_Pathway_L-R_pair_bubbleplot.pdf│ ├── 4.Sig_Pathway_L-R_pair_Contribution.pdf│ ├── 5.Signaling_Roles_Of_Cell_Groups_2D.pdf│ ├── 5.Signaling_Roles_Of_Cell_Groups_Heatmap.pdf│ ├── 5.signals_Contribution_Of_Cell_Groups_Heatmap.pdf│ └── cellchat_SiO2_56_.RData└── SiO2_7├── 0.Cell-Cell_Communications_At_L-R.xlsx├── 0.Cell-Cell_Communications_At_Pathway.xlsx├── 1.NumberOfInteractions.pdf├── 1.NumberOfInteractions_Split.pdf├── 1.NumberOfInteractions.xlsx├── 2.InteractionWeights.pdf├── 2.InteractionWeights_Split.pdf├── 2.InteractionWeights.xlsx├── 3.Sig_Pathway_Circle_Plot.pdf├── 3.Sig_Pathway_Hierarchy_Plot.pdf├── 4.Sig_Pathway_L-R_pair_bubbleplot.pdf├── 4.Sig_Pathway_L-R_pair_Contribution.pdf├── 5.Signaling_Roles_Of_Cell_Groups_2D.pdf├── 5.Signaling_Roles_Of_Cell_Groups_Heatmap.pdf├── 5.signals_Contribution_Of_Cell_Groups_Heatmap.pdf└── cellchat_SiO2_7_.RData4 directories, 64 files
图形设计隐私，这里仅放出部分
output节选：
https://mp.weixin.qq.com/s/NBkQpp7XFY_5jJW0HIOVKQ