火山图

作者

[编辑] 郑虎;

[审核] .

注记

Hiplot 网站

本页面为 Hiplot Volcano 插件的源码版本教程，您也可以使用 Hiplot 网站实现无代码绘图，更多信息请查看以下链接:

https://hiplot.cn/basic/volcano?lang=zh_cn

火山图是一种直观展示两个样本间基因差异表达的分布图。

环境配置

  • 系统: Cross-platform (Linux/MacOS/Windows)

  • 编程语言: R

  • 依赖包: ggpubr

# 安装包
if (!requireNamespace("ggpubr", quietly = TRUE)) {
  install.packages("ggpubr")
}

# 加载包
library(ggpubr)

数据准备

载入数据为基因名称及其对应的 logFC 和 p.value。

# 加载数据
data <- read.delim("files/Hiplot/183-volcano-data.txt", header = T)

# 整理数据格式
## 对差异p(adj.P.Val一列)进行log10转换
data[, "logP"] <- -log10(as.numeric(data[, "P.Value"]))
data[, "logFC"] <- as.numeric(data[, "logFC"])
## 新加一列Group
data[, "Group"] <- "not-significant"
## Up and down
data$Group[which((data[, "P.Value"] < 0.05) & (data$logFC >= 2))] <- "Up-regulated"
data$Group[which((data[, "P.Value"] < 0.05) & (data$logFC <= 2 * -1))] <- "Down-regulated"
## 新加一列Label
data[["Label"]] <- ""
## 对差异表达基因的p值进行从小到大排序
data <- data[order(data[, "P.Value"]), ]
## 高表达的基因中，选择adj.P.Val最小的10个
up_genes <- head(data[, "Symbol"][which(data$Group == "Up-regulated")], 10)
down_genes <- head(data[, "Symbol"][which(data$Group == "Down-regulated")], 10)
not_sig_genes <- NA
## 将up_genes和down_genes合并，并加入到Label中
deg_top_genes <- c(as.character(up_genes), as.character(not_sig_genes),
as.character(down_genes))
deg_top_genes <- deg_top_genes[!is.na(deg_top_genes)]
data$Label[match(deg_top_genes, data[, "Symbol"])] <- deg_top_genes

# 查看数据
head(data)
    Symbol     logFC  P.Value     logP           Group    Label
1      LTB  2.580831 1.17e-14 13.93181    Up-regulated      LTB
2    CDCA5 -2.326302 2.46e-13 12.60906  Down-regulated    CDCA5
3 C10orf54  3.307901 3.53e-13 12.45223    Up-regulated C10orf54
4    CAPN7  2.514235 1.04e-12 11.98297    Up-regulated    CAPN7
5     OIP5 -2.166620 1.43e-12 11.84466  Down-regulated     OIP5
7     PKIG -1.560504 1.58e-12 11.80134 not-significant

可视化

# 火山图
options(ggrepel.max.overlaps = 100)
p <- ggscatter(data, x = "logFC", y = "logP", color = "Group", 
               palette = c("#2f5688", "#BBBBBB", "#CC0000"), size = 1, 
               alpha = 0.5, font.label = 8, repel = TRUE, label=data$Label,
               xlab = "log2(Fold Change)", ylab = "-log10(P Value)",
               show.legend.text = FALSE) +
  ggtitle("Volcano Plot") +
  geom_hline(yintercept = -log(0.05, 10), linetype = "dashed") +
  geom_vline(xintercept = c(2, -2), linetype = "dashed") +
  theme_bw() +
  theme(text = element_text(family = "Arial"),
        plot.title = element_text(size = 12,hjust = 0.5),
        axis.title = element_text(size = 12),
        axis.text = element_text(size = 10),
        axis.text.x = element_text(angle = 0, hjust = 0.5,vjust = 1),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10))

p
图 1: 火山图

横轴用 log2（fold change）表示，差异越大的基因分布在图片两端。纵坐标用 -log10（p.value）表示，取值为 T 检验显著性 P 值的负对数。蓝色的点代表下调的基因，红色的点代表上调的基因，灰色的点代表差异不显著的基因。