（生物信息学）R语言绘图初-中-高级——3-10分文章必备——森林图（初级）

 setwd("D:\ 自噬临床模型预测\ 自噬相关基因临床模型预测\ 取交集，做Venn图")

    
 dir()
    
 data <- read.csv("uniCox.csv",header = T,sep = ",")
    
 gene <- read.csv("Genes.csv",header = T,sep = ",")
    
 head(data)
    
 head(gene)
    
 dim(data)
    
 dim(gene)
    
  
    
 #> head(data)
    
 #     id        HR    HR.95L    HR.95H      pvalue
    
 #1  ARNT 0.6351214 0.4632206 0.8708145 0.004817746
    
 #2  ARSA 1.3420299 1.0574458 1.7032024 0.015549633
    
 #3  ARSB 0.8044525 0.6854727 0.9440839 0.007708357
    
 #4  ATF4 1.2992683 0.9911638 1.7031474 0.058000088
    
 #5  ATF6 0.5463545 0.4204763 0.7099168 0.000006060
    
 #6 ATG10 0.5813549 0.4138701 0.8166173 0.001757369
    
 #> head(gene)
    
 #  X   gene
    
 #1 1   MTOR
    
 #2 2 CDKN2A
    
 #3 3  ERBB2
    
 #4 4  LAMP1
    
 #5 5  HSPA8
    
 #6 6   BAG1
    
 #> dim(data)
    
 #[1] 213   5
    
 #> dim(gene)
    
 #[1] 41  2
    
    
    
    
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 rownames(data) <- data$id

    
 data <- data[,-1]
    
 head(data)
    
  
    
 #> head(data)
    
 #              HR    HR.95L    HR.95H       pvalue
    
 #MTOR   0.6400590 0.4651810 0.8806799 0.0061381040
    
 #CDKN2A 1.2660554 1.0990494 1.4584388 0.0010810870
    
 #ERBB2  0.6362310 0.5311304 0.7621290 0.0000009170
    
 #LAMP1  0.6604439 0.4853477 0.8987087 0.0083037820
    
 #HSPA8  0.6870117 0.5782518 0.8162275 0.0000196000
    
 #BAG1   0.5103609 0.4004077 0.6505076 0.0000000553
    
    
    
    
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 rt <- data

    
 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))
    
  
    
 gene <- rownames(rt)
    
  
    
 n <- nrow(rt)
    
 nRow <- n+1
    
 ylim <- c(1,nRow)
    
 layout(matrix(c(1,2),nc=2),width=c(3,2.5))
    
 xlim = c(0,3)
    
 par(mar=c(4,2.5,2,1))
    
 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,)
    
  
    
 par(mar=c(4,1,2,1),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=0.05,col="darkblue",lwd=2.5)
    
 abline(v=1,col="black",lty=2,lwd=2)
    
 boxcolor = ifelse((as.numeric(hr)>1)&(pVal<0.05),'red3',"green3")
    
 points(as.numeric(hr), n:1, pch = 15, col = boxcolor, cex=1.3)
    
 axis(1)
    
    
    
    
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