GO气泡图

作者

[编辑] 郑虎;

[审核] .

修改于

2026-01-27

注记

Hiplot 网站

本页面为 Hiplot GOBubble Plot 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/gobubble?lang=zh_cn

GO气泡图用于显示按z-score或adjusted p-value的负相对序列的Z-score彩色气泡图。

环境配置

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

  • 编程语言: R

  • 依赖包: data.table; jsonlite; GOplot; ggplotify

# 安装包
if (!requireNamespace("data.table", quietly = TRUE)) {
  install.packages("data.table")
}
if (!requireNamespace("jsonlite", quietly = TRUE)) {
  install.packages("jsonlite")
}
if (!requireNamespace("GOplot", quietly = TRUE)) {
  install.packages("GOplot")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# 加载包
library(data.table)
library(jsonlite)
library(GOplot)
library(ggplotify)
sessioninfo::session_info("attached")
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.2 (2025-10-31)
 os       Ubuntu 24.04.3 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       UTC
 date     2026-01-27
 pandoc   3.1.3 @ /usr/bin/ (via rmarkdown)
 quarto   1.8.27 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 data.table   * 1.18.0  2025-12-24 [1] RSPM
 ggdendro     * 0.2.0   2024-02-23 [1] RSPM
 ggplot2      * 4.0.1   2025-11-14 [1] RSPM
 ggplotify    * 0.1.3   2025-09-20 [1] RSPM
 GOplot       * 1.0.2   2016-03-30 [1] RSPM
 gridExtra    * 2.3     2017-09-09 [1] RSPM
 jsonlite     * 2.0.0   2025-03-27 [1] RSPM
 RColorBrewer * 1.1-3   2022-04-03 [1] RSPM

 [1] /home/runner/work/_temp/Library
 [2] /opt/R/4.5.2/lib/R/site-library
 [3] /opt/R/4.5.2/lib/R/library
 * ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

数据准备

加载的数据是具有七个列的GO富集的结果：category, GO id, GO term, gene count, gene name, logFC, adjust pvalue and zscore。

# 加载数据
data <- data.table::fread(jsonlite::read_json("https://hiplot.cn/ui/basic/gobubble/data.json")$exampleData$textarea[[1]])
data <- as.data.frame(data)

# 整理数据格式
colnames(data) <- c("category","ID","term","count","genes","logFC","adj_pval","zscore")
data <- data[data$category %in% c("BP","CC","MF"),]
data <- data[!is.na(data$adj_pval),]
data$adj_pval <- as.numeric(data$adj_pval)
data$zscore <- as.numeric(data$zscore)

# 查看数据
head(data)
  category         ID              term count  genes      logFC adj_pval
1       BP GO:0007507 heart development    54   DLC1 -0.9707875 2.17e-06
2       BP GO:0007507 heart development    54   NRP2 -1.5153173 2.17e-06
3       BP GO:0007507 heart development    54   NRP1 -1.1412315 2.17e-06
4       BP GO:0007507 heart development    54   EDN1  1.3813006 2.17e-06
5       BP GO:0007507 heart development    54 PDLIM3 -0.8876939 2.17e-06
6       BP GO:0007507 heart development    54   GJA1 -0.8179480 2.17e-06
      zscore
1 -0.8164966
2 -0.8164966
3 -0.8164966
4 -0.8164966
5 -0.8164966
6 -0.8164966

可视化

# GO气泡图
p <- function () {
  GOBubble(data, display = "single", title = "GO Enrichment Bubbleplot",
           colour = c("#FC8D59","#FFFFBF","#99D594"),
           labels = 0,  ID = T, table.legend = T, table.col = T, bg.col = F) + 
  theme(plot.title = element_text(hjust = 0.5))
}
p <- as.ggplot(p)

p
图 1: GO气泡图

如示例图所示，图的x轴表示z-score。y轴上显示了 adjusted p-value 的负对数（对应于该 term 的重要性）。绘制圆圈的面积与分配给该 term 的基因数量成正比。每个圆都根据其类别进行着色，并用 ID 或 term 名称标记。