rm(list = ls())
 
library(limma)
library(ggpubr)


expFile="merge.txt"                 
scoreFile="score.group.txt"     


 
load("merge.RDATA")
rt=outTab
data=outTab
colnames(data)=gsub("(.*?)\\_(.*?)", "\\2", colnames(data))
data2=data



gene="CTLA4"            
 
data=rbind(data2, gene=data2[gene,])
exp=t(data[c("gene",gene),])
exp=avereps(exp)

 
score=read.table(scoreFile, header=T, sep="\t", check.names=F, row.names=1)

 
sameSample=intersect(row.names(exp), row.names(score))
exp=exp[sameSample,]

score=score[sameSample,]
data=cbind(as.data.frame(exp), as.data.frame(score))

 
data$group=factor(data$group, levels=c("Low", "High"))
group=levels(factor(data$group))
comp=combn(group,2)
my_comparisons=list()
for(i in 1:ncol(comp)){my_comparisons[[i]]<-comp[,i]}

 
boxplot=ggboxplot(data, x="group", y="gene", fill="group",
                  xlab="score",
                  ylab=paste(gene, "expression"),
                  legend.title="score",
                  palette=c("#00AFBB", "#E7B800"))+ 
  stat_compare_means(comparisons = my_comparisons)

 
pdf(file=paste0(gene, ".pdf"), width=5, height=4.5)
print(boxplot)
dev.off()