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今天通過ggplot2來繪制火山圖，并且添加基因標(biāo)簽，代碼如下：

1.?下載所需要的R包

install.packages(“ggplot2”)

install.packages(“tidyverse”)

install.packages(“ggrepel”)

install.packages(“cowplot”)

2.?導(dǎo)入需要的R包

library（ggplot2）

library(tidyverse)

library(ggrepel)

library(cowplot)

3.?示例數(shù)據(jù)

4.代碼展示

#讀取數(shù)據(jù)

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

#判斷基因上調(diào)還是下調(diào)

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")

#確定上下調(diào)基因因子順序

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

#畫基因標(biāo)簽的候選基因篩選

df1<-filter(df,log2FC>9)

#ggplot2開始繪圖

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

geom_point(aes(color=group),

???????????size=4)+

#畫水平線

geom_hline(yintercept = -log10(0.05),

???????????linetype="dashed",

???????????color="grey30")+

#畫垂直線

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

???????????linetype="dashed",

???????????color="grey30")+

#添加基因標(biāo)簽

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()

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