ggplot2 绘制火山图

使用 ggplot包 绘制火山图，需要一个dataframe并包含如下信息：

1. log2FoldChange：绘制x轴
2. pvalue或padj：绘制y轴
3. Change：元素为up、down或none，用于散点上色

library("ggplot2")

一、添加"Change"列

View(result)

 

log2FC阈值：0.5；padj阈值：0.05

thres_log2FC=0.5
thres_p=0.05

result[which(result$log2FoldChange >= thres_log2FC & result$padj < thres_p),'Change'] <- 'up'
result[which(result$log2FoldChange <= -thres_log2FC & result$padj < thres_p),'Change'] <- 'down'
result[which(abs(result$log2FoldChange) <= thres_log2FC | result$padj >= thres_p),'Change'] <- 'none'

 View(result)

write.csv(result,file = "gleason high vs low_result.csv",quote = FALSE) 

二、ggplot2作图

p <- ggplot(data = result, aes(x = log2FoldChange, y = -log10(padj), color = Change)) +
  geom_point(size = 1) +  #绘制散点图
  scale_color_manual(values = c('red', 'gray', 'green'), limits = c('up', 'none', 'down')) +  #自定义点的颜色
  labs(x = 'log2 Fold Change', y = '-log10 adjust p-value', title = 'gleason high vs low', color = '') +  #坐标轴标题
  theme(plot.title = element_text(hjust = 0.5, size = 14), panel.grid = element_blank(), #背景色、网格线、图例等主题修改
        panel.background = element_rect(color = 'black', fill = 'transparent'), 
        legend.key = element_rect(fill = 'transparent')) +
  geom_vline(xintercept = c(-thres_log2FC, thres_log2FC), lty = 3, color = 'black') +  #添加阈值线
  geom_hline(yintercept = -log10(thres_p), lty = 3, color = 'black') 
  #+ xlim(-5, 5) + ylim(0, 15)  #定义刻度边界

p