森林图绘制

输入文件input.txt.png

inputFile="input.txt"        
outFile="forest.pdf"         
setwd("D:\\biowolf")    

rt=read.table(inputFile,header=T,sep="\t",row.names=1,check.names=F)
gene=rownames(rt)
hr=sprintf("%.3f",rt$"HR")
hrLow=sprintf("%.3f",rt$"HR.95L")
hrHigh=sprintf("%.3f",rt$"HR.95H")
Hazard.ratio=paste0(hr,"(",hrLow,"-",hrHigh,")")
pVal=ifelse(rt$pvalue<0.001, "<0.001", sprintf("%.3f", rt$pvalue))

#出图格式
pdf(file=outFile, width = 6, height =4.5)
n=nrow(rt)
nRow=n+1
ylim=c(1,nRow)
layout(matrix(c(1,2),nc=2),width=c(3,2))

#森林图左边的基因信息
xlim = c(0,3)
par(mar=c(4,2,1.5,1.5))
plot(1,xlim=xlim,ylim=ylim,type="n",axes=F,xlab="",ylab="")
text.cex=0.8
text(0,n:1,gene,adj=0,cex=text.cex)
text(1.5-0.5*0.2,n:1,pVal,adj=1,cex=text.cex);text(1.5-0.5*0.2,n+1,'pvalue',cex=text.cex,font=2,adj=1)
text(3,n:1,Hazard.ratio,adj=1,cex=text.cex);text(3,n+1,'Hazard ratio',cex=text.cex,font=2,adj=1,)

#绘制森林图
par(mar=c(4,1,1.5,1),mgp=c(2,0.5,0))
xlim = c(0,max(as.numeric(hrLow),as.numeric(hrHigh)))
plot(1,xlim=xlim,ylim=ylim,type="n",axes=F,ylab="",xaxs="i",xlab="Hazard ratio")
arrows(as.numeric(hrLow),n:1,as.numeric(hrHigh),n:1,angle=90,code=3,length=0.03,col="darkblue",lwd=2.5)
abline(v=1,col="black",lty=2,lwd=2)
boxcolor = ifelse(as.numeric(hr) > 1, 'red', 'blue')
points(as.numeric(hr), n:1, pch = 15, col = boxcolor, cex=1.3)
axis(1)
dev.off()