pheatmap热图

#install.packages("pheatmap")

library(pheatmap)        #引用包

expFile="uniSigGeneExp.txt"        #32 表达数据文件

geneCluFile="geneCluster.txt"      #32 基因分型的结果文件：样本名称 基因分型结果

prgCluFile="PRGcluster.txt"        #24 细胞焦亡分型的结果文件：样本名称 细胞焦亡分型结果

cliFile="clinical.txt"            #24 临床数据文件 ID AGE GENDER T N

#设置工作目录

setwd("D:/※zixue/dead/140prgTME/34.geneHeatmap")

#读取输入文件

exp=read.table(expFile, header=T, sep="\t", check.names=F, row.names=1)

prgClu=read.table(prgCluFile, header=T, sep="\t", check.names=F, row.names=1)

geneClu=read.table(geneCluFile, header=T, sep="\t", check.names=F, row.names=1)

#三个文件取交集，合并数据

exp=as.data.frame(t(exp))

sameSample=intersect(row.names(exp), row.names(prgClu))

exp=exp[sameSample,,drop=F]

#三个文件cbind，列名为geneClu，PRGcluster

expData=cbind(exp, geneCluster=geneClu[sameSample,], PRGcluster=prgClu[sameSample,])

#Project为TCGA GSE

Project=gsub("(.*?)\\_.*", "\\1", rownames(expData))#TCGA GSE

rownames(expData)=gsub("(.*?)\\_(.*?)", "\\2", rownames(expData))

expData=cbind(expData, Project)

#合并临床数据

cli=read.table(cliFile, header=T, sep="\t", check.names=F, row.names=1)

cli[,"Age"]=ifelse(cli[,"Age"]=="unknow", "unknow", ifelse(cli[,"Age"]>65,">65","<=65"))

sameSample=intersect(row.names(expData), row.names(cli))

expData=expData[sameSample,,drop=F]

cli=cli[sameSample,,drop=F]

data=cbind(expData, cli)

#提取热图数据

data=data[order(data$geneCluster),]

Type=data[,((ncol(data)-2-ncol(cli)):ncol(data))]

data=t(data[,1:(ncol(expData)-3)])

#聚类颜色

bioCol=c("#0066FF","#FF9900","#FF0000","#6E568C","#7CC767","#223D6C","#D20A13","#FFD121","#088247","#11AA4D")

ann_colors=list()

#PRGcol

PRGcol=bioCol[1:length(levels(factor(Type$PRGcluster)))]

names(PRGcol)=levels(factor(Type$PRGcluster))

ann_colors[["PRGcluster"]]=PRGcol

#GENEcol

GENEcol=bioCol[1:length(levels(factor(Type$geneCluster)))]

names(GENEcol)=levels(factor(Type$geneCluster))

ann_colors[["geneCluster"]]=GENEcol

#热图可视化

pdf("heatmap.pdf", height=6, width=8)

pheatmap(data,

        #注释文件

        annotation=Type,

        annotation_colors = ann_colors,#注释颜色

        #热图颜色，低表达蓝色，高表达红色 c(rep("blue",5), "white", rep("red",5))

        color = colorRampPalette(c(rep("#56B1F7",5), "white", rep("pink",5)))(50),

        cluster_cols =F,#对列不聚类

        cluster_rows =F,#对行不聚类

        scale="row",#对行校正

        show_colnames=F,#显示列名称

        show_rownames=F,#显示行名称

        #字体大小

        fontsize=6,

        fontsize_row=2,

        fontsize_col=6)

dev.off()