wgcna_3

knitr::opts_chunk$set(echo = TRUE)

library(WGCNA)
load(file = "wgcna-network.Rdata")
load(file = "trait_analysis.RData")
nGenes = ncol(datExpr)
nSamples = nrow(datExpr)

7.基因共表达网络可视化

7.1.使用所有基因绘制

#计算dissTOM, dissTOM = 1 - TOM
dissTOM = 1-TOMsimilarityFromExpr(datExpr, power = 6);
  
#取7次方，仅为展示更显著
plotTOM =1 - dissTOM^7
  
#绘图
diag(plotTOM) = NA;
sizeGrWindow(9,9)
geneTree = net$dendrograms[[1]]
TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot,allgenes")

7.2随机选择 400 条绘图

nSelect = 400
set.seed(10)
select = sample(nGenes, size = nSelect)
selectTOM = dissTOM[select, select]
#重新聚类
selectTree = hclust(as.dist(selectTOM), method = "average")
selectColors = moduleColors[select]
#Open a graphical window
sizeGrWindow(9,9)
plotDiss =1 - selectTOM^7
#绘图
diag(plotDiss) = NA;
TOMplot(plotDiss, selectTree, selectColors, main = "Network heatmap plot, selected genes")

8.模块特征向量网络可视化

#重新计算MEs
MEs = moduleEigengenes(datExpr, moduleColors)$eigengenes
#Plot the relationships among the eigengenes and the trait
sizeGrWindow(5,7.5)
par(cex = 0.9)
plotEigengeneNetworks(MEs, "", marDendro = c(0,4,1,2), marHeatmap = c(3,4,1,2), 
                      cex.lab = 0.8, xLabelsAngle = 90)

#Plot the dendrogram
sizeGrWindow(6,6)
par(cex = 1.0)
plotEigengeneNetworks(MEs, "Eigengene dendrogram", marDendro = c(0,4,2,0),
                      plotHeatmaps = FALSE)

#Plot the heatmap matrix (note: this plot will overwrite the dendrogram plot)
par(cex = 1.0)
plotEigengeneNetworks(MEs, "Eigengene adjacency heatmap", marHeatmap = c(3,4,2,2),
                      plotDendrograms = FALSE, xLabelsAngle = 90)

9.生成 Cytoscape 的输入文件

#重新计算 TOM
TOM = TOMsimilarityFromExpr(datExpr, power = sft$powerEstimate);
#要可视化的模块
modules = c("blue")
#要可视化的基因
probes = colnames(datExpr)
inModule = is.finite(match(moduleColors, modules));
 modProbes = probes[inModule]
#候选基因的 TOM
modTOM = TOM[inModule, inModule]
  
dimnames(modTOM) = list(modProbes, modProbes)
#Export the network into edge and node list files Cytoscape can read
cyt = exportNetworkToCytoscape(modTOM,
                               edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""),
                               nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""),
                               weighted = TRUE,
                               threshold = 0.02,
                               nodeNames = modProbes,
                               nodeAttr = moduleColors[inModule])