When I run the R language, the following error occurs, how do I fix it?
#install.packages("survival")
>
> library(survival) #引用包
> inputFile="expTime.txt" #输入文件
> pFilter=0.001 #显著性过滤条件
> setwd("C:\\Users\\ASUS\\Desktop\\tmeimmune\\22.cox") #设置共工作目录
>
> #读取输入文件
> rt=read.table(inputFile,header=T,sep="\t",check.names=F,row.names=1)
> rt$futime=rt$futime/365 #以年为单位，除以365
>
> outTab=data.frame()
> for(gene in colnames(rt[,3:ncol(rt)])){
+ #单因素cox分析
+ cox=coxph(Surv(futime, fustat) ~ rt[,gene], data = rt)
+ coxSummary = summary(cox)
+ coxP=coxSummary$coefficients[,"Pr(>|z|)"]
+
+ #KM检验，后续需要可视乎，要和生存相关
+ group=ifelse(rt[,gene]<=median(rt[,gene]),"Low","High")
+ diff=survdiff(Surv(futime, fustat) ~ group,data = rt)
+ pValue=1-pchisq(diff$chisq,df=1)
+
+ #保存满足条件的基因
+ if((pValue<pFilter) & (coxP<pFilter)){
+ outTab=rbind(outTab,
+ cbind(gene=gene,
+ KM=pValue,
+ HR=coxSummary$conf.int[,"exp(coef)"],
+ HR.95L=coxSummary$conf.int[,"lower .95"],
+ HR.95H=coxSummary$conf.int[,"upper .95"],
+ pvalue=coxP) )
+ }
+ }
*There were 50 or more warnings (use warnings() to see the first 50)*
> #输出基因和P值表格文件
> write.table(outTab,file="cox.result.txt",sep="\t",row.names=F,quote=F)
>
> #绘制森林图
> #读取输入文件
> rt <- read.table("cox.result.txt",header=T,sep="\t",row.names=1,check.names=F)
Error in read.table("cox.result.txt", header = T, sep = "\t", row.names = 1, :
no lines available in input
> gene <- rownames(rt)
> hr <- sprintf("%.3f",rt$"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))
>
> #输出图形
> pdf(file="forest.pdf", width = 7,height = 6)
> n <- nrow(rt)
> nRow <- n+1
> ylim <- c(1,nRow)
> layout(matrix(c(1,2),nc=2),width=c(3,2))
>
> #绘制森林图左边的基因信息
> 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)
Error in text.default(1.5 - 0.5 * 0.2, n:1, pVal, adj = 1, cex = text.cex) :
'labels'长度不能设成零
> 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(4,1,2,1),mgp=c(2,0.5,0))
> xlim = c(0,max(as.numeric(hrLow),as.numeric(hrHigh)))
Warning message:
In max(as.numeric(hrLow), as.numeric(hrHigh)) :
no non-missing arguments to max; returning -Inf
> plot(1,xlim=xlim,ylim=ylim,type="n",axes=F,ylab="",xaxs="i",xlab="Hazard ratio")
Error in plot.window(...) : 'xlim'值不能是无限的
> arrows(as.numeric(hrLow),n:1,as.numeric(hrHigh),n:1,angle=90,code=3,length=0.05,col="darkblue",lwd=2.5)
Error in arrows(as.numeric(hrLow), n:1, as.numeric(hrHigh), n:1, angle = 90, :
不能将零长度的座标同其它长度的座标混合在一起
> abline(v=1,col="black",lty=2,lwd=2)
> boxcolor = ifelse(as.numeric(hr) > 1, 'red', 'green')
> points(as.numeric(hr), n:1, pch = 15, col = boxcolor, cex=1.3)
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
> axis(1)
> dev.off()
null device
1