ggplot2绘制火山图

今天通过ggplot2来绘制火山图，并且添加基因标签，代码如下：

1. 下载所需要的R包

install.packages(“ggplot2”)

install.packages(“tidyverse”)

install.packages(“ggrepel”)

install.packages(“cowplot”)

2. 导入需要的R包

library（ggplot2）

library(tidyverse)

library(ggrepel)

library(cowplot)

3. 示例数据

4.代码展示

#读取数据

df <- read.csv("easy_input_limma.csv", header = T)

#判断基因上调还是下调

df$group<-case_when(df$log2FC< -1 & df$PValue <0.05 ~"Down",

                    df$log2FC > 1 & df$PValue <0.05 ~"Up",

                    df$PValue >= 0.05 ~"no_signf",

                    abs(df$log2FC)<= 1 ~"no_signf")

#确定上下调基因因子顺序

df$group<-factor(df$group,levels=c("Up","Down","no_signf"))

#画基因标签的候选基因筛选

df1<-filter(df,log2FC>9)

#ggplot2开始绘图

ggplot(data=df,aes(x=log2FC,y=-log10(PValue)))+

geom_point(aes(color=group),

           size=4)+

#画水平线

geom_hline(yintercept = -log10(0.05),

           linetype="dashed",

           color="grey30")+

#画垂直线

geom_vline(xintercept = c(-1,1),

           linetype="dashed",

           color="grey30")+

#添加基因标签

geom_text_repel(data=df1,

                aes(x= log2FC,y= -log10(PValue),label= gene_id))+

scale_color_manual(values = c("#FF9999","#99CC00","grey80"))+

theme_half_open()