library(ggpubr)

setwd("/Users/Desktop/生物信息学/测试")                #数据要整齐 不能有空缺数值或na

rt=read.table("cl.txt",sep="\t",header=T,check.names=F,row.names=1)         

rt

gene=colnames(rt)[3]      #获取基因名字

#临床相关分析

for(clinical in colnames(rt[,4:ncol(rt)])){

  data=rt[c(gene,clinical)]

  colnames(data)=c("gene","clinical")

  #设置比较组

  group=levels(factor(data$clinical))

  comp=combn(group,2)

  my_comparisons=list()

  for(i in 1:ncol(comp)){my_comparisons[[i]]<-comp[,i]}

  #绘制boxplot

  boxplot=ggboxplot(data, x="clinical", y="gene", color="clinical",

                    xlab=clinical,

                    ylab=paste(gene,"expression"),

                    legend.title=clinical,

                    add = "jitter")+

    stat_compare_means(comparisons = my_comparisons)

  pdf(file=paste0(clinical,".pdf"),width=5.5,height=5)

  print(boxplot)

  dev.off()

}