1

setwd('D:\\prrc\\TCGA\\GDC\\mutation\\lnc\\survival')
library(survival)
library(caret)
library(glmnet)
library(survminer)
library(tidyverse)
library(ggplot2)

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
rt<-rt[,-c(3:10)]
rt<-na.omit(rt)
sigGenes=c("futime","fustat")

for(i in colnames(rt[,3:ncol(rt)])){
  
  case_when(rt[,i]<=unname(quantile(rt[,i],0.25))~ 'low',  
            rt[,i]>unname(quantile(rt[,i],0.25))&rt[,i]<unname(quantile(rt[,i],0.75))~'median',
            rt[,i]>=unname(quantile(rt[,i],0.75))~'high')->rt[,i]
            rt[,i]<-as.factor(rt[,i])
}

data=rt

dd<-list()
for(i in 3:ncol(data)){
  
  k=colnames(data[i])
  
 dd[[k]]<-subset(data,data[,k]=='low'|data[,k]=='high',select = c("futime","fustat",k))
 dd[[k]][,3]<-as.factor(as.character(dd[[k]][,3]))
}

#
fit=list()
for(i in 1:length(dd)){
  

 diff=survdiff(Surv(dd[[i]]$futime,dd[[i]]$fustat) ~ dd[[i]][,3],data =dd[[i]])

 pValue=1-pchisq(diff$chisq,df=1)
 

  if(pValue<0.05){
    
    sigGenes=c(sigGenes,names(dd)[i])
    
   print(i)
    
    fit[[i]]=survfit(Surv(dd[[i]]$futime,dd[[i]]$fustat)~ as.factor(dd[[i]][,3]),data =dd[[i]])
  ggsurvplot(fit[[i]])
  }
       }




#
splots <- list()
splots[[1]]<-ggsurvplot(fit,
                        xlab = "Time_years",
                        ylab="survival probability",##根据需要调整
                        pval = T,
                        conf.int= F,
                        risk.table = T,
                        legend.title = names(dd)[i],
                        #surv.median.line = "hv",# 中位生存
                        palette="lancet")

res<-arrange_ggsurvplots(splots, print = F,
                         ncol = 1, nrow = 1, risk.table.height = 0.25)
ggsave(paste(names(dd)[i],"All_surv.pdf",sep = "_"), res,width=7,height = 6)





setwd('D:\\prrc\\TCGA\\GDC\\mutation\\lnc\\survival')
library(DESeq2)
library(tidyverse)

 rt=read.table("symbol.txt",header=T,sep="\t",check.names=F)  
 rt2<-rt[,!grepl("-11A-", colnames(rt))]
 rt2<-rt2[,!grepl("-11B-", colnames(rt2))]
 clus<-read.table('cluster.txt',sep = '\t')
 colnames(rt2)<-substr(colnames(rt2),1,12)
 clus$V1<-substr(clus$V1,1,12)
 r3<-intersect(clus$V1,colnames(rt2))
 clus1<-filter(clus,V1 %in% r3)
 View(clus1)
 rt3<-select(rt2,c(1,r3))