R语言之可视化-火山图

火山图可以方便直观地展示两个样本间基因差异表达的分布情况。通常横坐标用log2（fold change）表示，差异越大的基因分布在两端，纵坐标用-log10（pvalue）表示，T检验显著性P值的负对数。通常差异倍数越大的基因T检验越显著，所以往往关注左上角和右上角的值。我们根据计算结果在图上按照FDR和我们自定义的logFC值来将这部分显著变化的基因用不同颜色标示出来以区分，这类图像往往呈现类似火山爆发的样子，于是就被叫做“火山图”（volcano plot）了。

library(ggplot2)
diff <- read.csv("DEG.Out.csv",header = T)

logFC <-diff$logFC
adj <- diff$FDR

data <- data.frame(logFC=logFC,padj=padj)
data$sig[(data$padj > 0.05|data$padj=="NA")|(data$logFC < 0.5)& data$logFC > -0.5] <- "no"
data$sig[data$padj <= 0.05 & data$logFC >= 0.5] <- "up"
data$sig[data$padj <= 0.05 & data$logFC <= -0.5] <- "down"

# 选最大值作为xlim的上下边界
x_lim <- max(logFC,-logFC)
# 绘制火山图
library(ggplot2)
library(RColorBrewer)
pdf(file = "miRNA_volcano.pdf",width=8,height=8)
theme_set(theme_bw())
p <- ggplot(data,aes(logFC,-1*log10(padj),
                   color = sig))+geom_point()+
   xlim(-5,5) +  labs(x="log2(FoldChange)",y="-log10(FDR)")
p <- p + scale_color_manual(values =c("#0072B5","grey","#BC3C28"))+
  geom_hline(yintercept=-log10(0.05),linetype=4)+
  geom_vline(xintercept=c(-0.5,0.5),linetype=4)
p <- p +theme(panel.grid =element_blank())+
    theme(axis.line = element_line(size=0))+ylim(0,15)
p <- p  +guides(colour = FALSE)
p <- p +theme(axis.text=element_text(size=20),axis.title=element_text(size=20))
p
dev.off()
print(p)

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参考：
https://www.jianshu.com/p/efb41e5f0ee2