R|可视化|boxplot+beeswarm

实际科研中，往往需要联合箱式图（boxplot）和其他类型的图形样式，如蜂蜜图（beeswarm）进行数据展示，下面就联合boxplot+beeswarm来探索下。

方法一：

基础绘图函数boxplot，联合beeswarm::beeswarm绘制。

rm(list = ls())
library(limma)
library(tidyverse)
gene="ZEB1-AS1"

rt <- data.table::fread("uniq.symbol.txt",data.table = F) %>% 
  column_to_rownames("ID")

# FPKM to TPM
fpkm2tpm <- function(fpkm){
  exp(log(fpkm)-log(sum(fpkm))+log(1e6))
}
rt <- apply(rt, 2, fpkm2tpm)
rt1 <- log2(rt+1)
Type=c(rep("Normal",72),rep("Tumor",539))
single <- cbind(ID=colnames(rt1),expression=round(rt1[gene,],3),Type=Type)
single <- as.data.frame(single)
single$expression <- as.numeric(as.vector(single$expression))
# 开始画图
yMin=0                      #纵轴最小值
yMax= 5                    #纵轴最大值
ySeg=yMax*0.94
labels=c("Normal (n=72)","Tumor (n=539)")
wilcoxTest <- wilcox.test(expression~Type,data = single)
wilcoxP <- wilcoxTest$p.value
pvalue <- signif(wilcoxP,4)
pval=0
if(pvalue<0.001){
  pval=signif(pvalue,4)
  pval=format(pval,scientific = TRUE)
}else{
  pval=round(pvalue,3)
}

library(beeswarm)
par(mar = c(4,7,3,3))
boxplot(expression ~ Type, data = single,names=labels,
        xlab = NA,
        ylab = "ZEB1-AS1 expression log2(TPM+1)",
        cex.main=1.5,cex.lab=1.3,cex.axis=1.2,ylim=c(yMin,yMax),outline=FALSE)
beeswarm(expression ~ Type, data = single, col = c("blue","red"),lwd=0.2,
         pch = 16, add = TRUE, corral="wrap")
segments(1,ySeg, 2,ySeg);segments(1,ySeg, 1,ySeg*0.96);segments(2,ySeg, 2,ySeg*0.96)
text(1.5,ySeg*1.05,labels=paste("p=",pval,sep=""),cex=1.2)

boxplot_beeswarm