绘制森林图

#install.packages("survival")
#install.packages("forestplot")
rm(list = ls())
library(survival)
library(forestplot)

setwd("H:\\BaiduNetdiskDownload\\pan-cancer\\panCancer\\09.cox")                       #设置工作目录
rt=read.table("expTime.txt",header=T,sep="\t",check.names=F,row.names=1)    #读取输入文件
rt$futime=rt$futime/365
gene=colnames(rt)[3]

#对肿瘤类型进行循环
outTab=data.frame()
for(i in levels(rt[,"CancerType"])){
	rt1=rt[(rt[,"CancerType"]==i),]
	cox=coxph(Surv(futime, fustat) ~ rt1[,gene], data = rt1)
	coxSummary = summary(cox)
    coxP=coxSummary$coefficients[,"Pr(>|z|)"]
	outTab=rbind(outTab,
	             cbind(cancer=i,
	                   HR=coxSummary$conf.int[,"exp(coef)"],
	                   HR.95L=coxSummary$conf.int[,"lower .95"],
	                   HR.95H=coxSummary$conf.int[,"upper .95"],
			           pvalue=coxP) )
}
write.table(outTab,file="cox.result.txt",sep="\t",row.names=F,quote=F)    #输出基因和p值表格文件


############绘制森林图函数############
bioForest=function(coxFile=null,forestFile=null,forestCol=null){
    #读取输入文件
	rt=read.table("cox.result.txt",header=T,sep="\t",row.names=1,check.names=F)
	data=(rt)
	HR=data[,1:3]
	hr=sprintf("%.3f",HR[,"HR"])
	hrLow=sprintf("%.3f",HR[,"HR.95L"])
	hrHigh=sprintf("%.3f",HR[,"HR.95H"])
	pVal=data[,"pvalue"]
	pVal=ifelse(pVal<0.001, "<0.001", sprintf("%.3f", pVal))
#	clrs <- fpColors(box=forestCol,line="darkblue", summary="royalblue")      #定义颜色
	clrs <- fpColors(box="red",line="darkblue", summary="royalblue")    
	tabletext <- 
	  list(c(NA, rownames(HR)),
	       append("pvalue", pVal),
	       append("Hazard ratio",paste0(hr,"(",hrLow,"-",hrHigh,")")) )   #定义图片文字
	pdf(file="forest1.pdf",width = 9,height = 6,onefile = FALSE)
	forestplot(tabletext, 
	           rbind(rep(NA, 3), HR),
	           col=clrs,
	           graphwidth=unit(50, "mm"),
	           xlog=T,
	           lwd.ci=4,
	           boxsize=0.6,
	           xlab="Hazard ratio",
	           txt_gp=fpTxtGp(ticks=gpar(cex=1.1),xlab=gpar(cex = 1.25))
	           )
	dev.off()
}
############绘制森林图函数############