下图是一篇文献中添加了基因标签的渐变色火山图，今天教大家如何使用R语言绘制一张类似的火山图。来自文章：Cell Rep. 2024;43(3):113784.
1.安装R包
local({r <- getOption("repos")r["CRAN"] <- "http://mirrors.tuna.tsinghua.edu.cn/CRAN/"options(repos=r)})package_list <- c("ggplot2","ggrepel","dplyr","devtools")for(p in package_list){if(!suppressWarnings(suppressMessages(require(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)))){install.packages(p, warn.conflicts = FALSE)suppressWarnings(suppressMessages(library(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)))}}
2.设置FC和FDR的阈值线
fc_cutoff <- 2fdr_cutoff <- 0.01
3.读入数据
setwd("/share/work")data<-read.table("Volcano.txt", header=TRUE,sep = "\t")
数据格式如下（表头不要改）：
ID FDR log2FC signTrans_newGene_1010 0.1719571 -0.327617885 NATrans_newGene_1013 9.65812E-10 -0.905601526 NATrans_newGene_1014 0.268121627 0.212668419 NATrans_newGene_1026 0.361458835 -0.371175921 NATrans_newGene_1027 0.514220593 -0.189095293 NATrans_newGene_1055 0.400366453 0.287239534 NATrans_newGene_1069 0.038485409 0.667683474 NATrans_newGene_1071 0.65302006 0.180040874 NATrans_newGene_1084 5.27862E-05 1.314071476 NA
第一列：基因ID；第二列：FDR值；第三列：log2FC值；第四列：要显示的基因名称，不显示的都用NA。
4.添加上下调信息列-regulated
data$regulated <- case_when(data$log2FC > log2(fc_cutoff) & data$FDR < fdr_cutoff ~ "up",data$log2FC < -log2(fc_cutoff) & data$FDR < fdr_cutoff ~ "down",abs(data$log2FC) <= log2(fc_cutoff) ~ "normal",data$FDR >= fdr_cutoff ~ "normal")head(data)
添加上下调信息后的数据：
#转换为因子data$regulated <- factor(data$regulated,levels = c("up","down","normal"),ordered = T)
5.ggplot2绘图
mycolor1 <- c("#008EBE","#FF890E")top.mar=0.2right.mar=0.2bottom.mar=0.2left.mar=0.2p <-ggplot(data=data,aes(log2FC,-log10(FDR),color=-log10(FDR))) +geom_point(size=2,alpha=0.9)+scale_colour_gradient2(low = mycolor1[1],mid = mycolor1[2],high = mycolor1[2],midpoint = 50, #midpoint = 75 指定颜色渐变的中点，这意味着在数值为75时颜色会是mid指定的颜色guide = "none") +geom_point(data = subset(data, !is.na(sign)),aes(x = log2FC, y = -log10(FDR)),shape = 1, size = 2, stroke = 1.2, color = "black") + # 描边的点geom_label_repel(aes(label=sign), fontface="bold",color="grey50", box.padding=unit(0.35, "lines"),point.padding=unit(0.5, "lines"), segment.colour = "grey50")+geom_hline(yintercept = c(-log10(fdr_cutoff)),linewidth = 0.5,color = "orange",lty = "dashed")+theme_classic()+theme(text=element_text(family = "sans",colour ="gray30",size = 10),axis.line = element_line(linewidth = 0.6,colour = "gray30"),axis.ticks = element_line(linewidth = 0.6,colour = "gray30"),axis.ticks.length = unit(1.5,units = "mm"),plot.margin=unit(x=c(top.mar,right.mar,bottom.mar,left.mar),units="inches"))p
结果如下图所示：
