【R>>volcan】任意genelist，标注到火山图

刷微信公众号时，翻到《火山图|给你geneList, 帮我标注到火山图上》的推文，刚好最近在做火山图，下面就来一起学习。如有疑问请翻阅原文，在最下面参考链接。

核心点：将不需要标注的用NA表示，left_join的妙用。

普通版火山图

rm(list = ls())
library(ggrepel) #避免标签重复
library(ggsci)
load("DEseq2_DEG.Rdata")
rt <- DEG
rt$change <- as.factor(ifelse(rt$padj<0.01 & abs(rt$log2FoldChange)>1,
                              ifelse(rt$log2FoldChange>1,"UP","DOWN"),"STABLE"))

rt$sign <- ifelse(rt$padj < 0.001 & abs(rt$log2FoldChange)>2.5,rownames(rt),NA)
head(rt)

ggplot(data = rt, 
       aes(x = log2FoldChange, 
           y = -log10(padj))) +
  geom_point(alpha=1, size=3, 
             aes(color=change)) +
  ylab("-log10(FDR)")+
  xlab("log2(FoldChange)")+
  scale_color_manual(values=c("#0073C2CC", "#868686CC","#CD534CCC"))+
  geom_vline(xintercept=c(-1,1),lty=4,col="black",lwd=0.8) +
  geom_hline(yintercept = -log10(0.05),lty=4,col="black",lwd=0.8)+
  theme_light()+
  theme(legend.position="none")

加上label

rm(list = ls())
library(ggrepel) #避免标签重复
library(ggsci)
load("DEseq2_DEG.Rdata")
rt <- DEG
rt$change <- as.factor(ifelse(rt$padj<0.01 & abs(rt$log2FoldChange)>1,
                              ifelse(rt$log2FoldChange>1,"UP","DOWN"),"STABLE"))

rt$sign <- ifelse(rt$padj < 0.001 & abs(rt$log2FoldChange)>2.5,rownames(rt),NA)
head(rt)

ggplot(data = rt, 
       aes(x = log2FoldChange, 
           y = -log10(padj))) +
  geom_point(alpha=1, size=3, 
             aes(color=change)) +
  ylab("-log10(FDR)")+
  xlab("log2(FoldChange)")+
  scale_color_manual(values=c("#0073C2CC", "#868686CC","#CD534CCC"))+
  geom_vline(xintercept=c(-1,1),lty=4,col="black",lwd=0.8) +
  geom_hline(yintercept = -log10(0.05),lty=4,col="black",lwd=0.8)+
  theme_light()+
  theme(legend.position="none")

指定genelist

genelist <- data.frame(id=c("MKI67","PCNA","BCL2","GPX4","TFRC"),genelist=c("MKI67","PCNA","BCL2","GPX4","TFRC"))
rt1 <- rt %>% 
  rownames_to_column("id") %>% 
  left_join(genelist,by="id")

ggplot(data = rt1, 
       aes(x = log2FoldChange, 
           y = -log10(padj))) +
  geom_point(alpha=1, size=3, 
             aes(color=change)) +
  ylab("-log10(FDR)")+
  xlab("log2(FoldChange)")+
  scale_color_lancet(alpha = 0.8)+
  geom_vline(xintercept=c(-1,1),lty=4,col="black",lwd=0.8) +
  geom_hline(yintercept = -log10(0.05),lty=4,col="black",lwd=0.8)+
  theme_light()+
  theme(legend.position="none")+
  geom_label_repel(aes(label=genelist),
                   fontface="bold",
                   color="grey50",
                   box.padding = unit(0.35,"lines"),
                   point.padding = unit(0.5,"lines"),
                   segment.colour = "grey50",
                   size=3)

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参考链接：
火山图|给你geneList，帮我标到火山图上