参考CSDN博主「TS的美梦」的“复现《NC》图表（二）：R语言一键画表达量箱线图并添加显著性”（原文链接：https://blog.csdn.net/qq_42090739/article/details/121911002）利用自己数据进行了尝试。

#加载需要的R包： 

library(RColorBrewer)

library(ggpubr)

library(ggplot2)

library(cowplot)

#加载数据并进行处理：

func<-read.csv("function-FN.csv", header=T, row.names=1)

#选择几个基因做数据

gene<-c("aerobic_ammonia_oxidation", "aerobic_nitrite_oxidation", "nitrification", "chloroplasts", "manganese_oxidation", "predatory_or_exoparasitic")

gene <- as.vector(gene)

#数据标准化

func <- log2(func*100+1)

#提取需要作图得基因表达信息

func_plot <- func[,gene]

#加载分组信息

info<-read.csv("treatments.csv", header=T)

func_plot <-func_plot[info$Samples,]

func_plot$Samples=info$Treatments

func_plot$Samples <- factor(func_plot$Samples,levels=c("CK","F","N","FN"))

#设置分组颜色

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

#循环绘制每个变量图

plist2<-list()

for (i in 1:length(gene)){

  bar_tmp<-func_plot[,c(gene[i],"Samples")]

  colnames(bar_tmp)<-c("gene","Samples")

  my_comparisons1 <- list(c("CK", "F"))

  my_comparisons2 <- list(c("CK", "N"))

  my_comparisons3 <- list(c("CK", "FN"))

  my_comparisons4 <- list(c("F", "FN"))

  my_comparisons5 <- list(c("N", "FN"))

  my_comparisons6 <- list(c("F", "N"))

  pb1<-ggboxplot(bar_tmp,

                 x="Samples",

                 y="gene",

                 color="Samples",

                 fill=NULL,

                 add = "jitter",

                 bxp.errorbar.width = 1,

                 width = 0.8,

                 size=0.3,

                 font.label = list(size=20),

                 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

}

#分列排布

pall<-plot_grid(plist2[[1]],plist2[[2]],plist2[[3]],plist2[[4]],plist2[[5]],plist2[[6]],ncol=3)

#图片保存

ggsave(pall,filename = "FN.jpg",width = 12,height = 9)

#结果如下图所示