inputFile="M singleGeneClinical.txt" 

setwd("/Users/zhongyue/Desktop/生物信息学/13.mergeclinical") 

rt=read.table(inputFile,sep="\t",header=T,check.names=F)

head(rt)

compared<-list(c("M0","M1"))

clinical="M"                                                      

gene="MAL2"

library(ggplot2)

library(ggsignif)

library(ggpubr)

outPdf=paste0(gene,".",clinical,".pdf")

pdf(file=outPdf,

    width=9,

    height=6,)

p<-ggplot(data=rt,aes(M,MAL2))+geom_boxplot(aes(fill=M),width=0.5)+theme_classic()+scale_fill_discrete(name="M classificaition")#修改图例的名字

p+theme(legend.title=element_text(size=14,face="bold"),axis.title=element_text(size=12,face="bold"),axis.text.y=element_text(size=12,face="bold"),axis.text.x=element_text(size=12,face="bold"),legend.position="top",plot.title = element_text(size = 16,hjust=0.5))+ggtitle("MAL2 expression group by M classificaition")+stat_compare_means(method = "kruskal.test",label = "p.format",label.y = 500,size=6,face="bold")+xlab("M classificaition")+ylab("MAL2 expression")+ylim(0,500)#要放同一行，两组用wilcox.test

dev.off()#axis.text是xy轴的刻度和字体，axis.title是xy轴下面的文本标题