可视化结果：

图片.png

数据输入

画图数据需要两个文件，一个是表达量数据，列为样本，行为基因。另外一个是注释信息，是关于样本分组的。

表达数据：

图片.png

样本信息：

图片.png

代码

library(RColorBrewer)
library(ggpubr)
library(ggplot2)
library(cowplot)


setwd("D:/生物信息学")
Exp <- read.csv("Exp.csv",header=T,row.names=1)#读入源文件
gene <- c("CD28","CD3D","CD8A","LCK",
          "GATA3","EOMES","IL23A","CXCL8",
          "IL1R2","IL1R1","MMP8","MMP9")#这里我们只选择这几个基因做数据
gene <- as.vector(gene)
Exp <- log2(Exp+1) #因为是FPKM数据，标准化一下
Exp_plot <- Exp[,gene]#提取需要作图得基因表达信息

info <- read.csv("info.csv",header=T)
Exp_plot<- Exp_plot[info$Sample,]
Exp_plot$sam=info$Type
Exp_plot$sam <- factor(Exp_plot$sam,levels=c("Asymptomatic","Mild","Severe","Critical"))

col <-c("#5CB85C","#337AB7","#F0AD4E","#D9534F")

plist2<-list()
for (i in 1:length(gene)){
  bar_tmp<-Exp_plot[,c(gene[i],"sam")]
  colnames(bar_tmp)<-c("Expression","sam")
  my_comparisons1 <- list(c("Asymptomatic", "Mild")) 
  my_comparisons2 <- list(c("Asymptomatic", "Severe"))
  my_comparisons3 <- list(c("Asymptomatic", "Critical"))
  my_comparisons4 <- list(c("Mild", "Severe"))
  my_comparisons5 <- list(c("Mild", "Critical"))
  my_comparisons6 <- list(c("Severe", "Critical"))
  pb1<-ggboxplot(bar_tmp,
                 x="sam",
                 y="Expression",
                 color="sam",
                 fill=NULL,
                 add = "jitter",
                 bxp.errorbar.width = 0.6,
                 width = 0.4,
                 size=0.01,
                 font.label = list(size=30), 
                 palette = col)+theme(panel.background =element_blank())
  pb1<-pb1+theme(axis.line=element_line(colour="black"))+theme(axis.title.x = element_blank())
  pb1<-pb1+theme(axis.title.y = element_blank())+theme(axis.text.x = element_text(size = 15,angle = 45,vjust = 1,hjust = 1))
  pb1<-pb1+theme(axis.text.y = element_text(size = 15))+ggtitle(gene[i])+theme(plot.title = element_text(hjust = 0.5,size=15,face="bold"))
  pb1<-pb1+theme(legend.position = "NA")#
  pb1<-pb1+stat_compare_means(method="t.test",hide.ns = F,
                              comparisons =c(my_comparisons1,my_comparisons2,my_comparisons3,my_comparisons4,my_comparisons5,my_comparisons6),
                              label="p.signif")
  plist2[[i]]<-pb1 
}

plot_grid(plist2[[1]],plist2[[2]],plist2[[3]],
                plist2[[4]],plist2[[5]],plist2[[6]],
                plist2[[7]],plist2[[8]],plist2[[9]],
                plist2[[10]],plist2[[11]],plist2[[12]],ncol=4)#ncol=4表示图片排为几列

图片.png