矩阵气泡图

作者

[编辑] 郑虎;

[审核] .

修改于

2026-01-17

注记

Hiplot 网站

本页面为 Hiplot Matrix Bubble 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/matrix-bubble?lang=zh_cn

彩色矩阵气泡用于可视化不同细胞（列）中多个基因（行）的表达矩阵数据。

环境配置

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

  • 编程语言: R

  • 依赖包: data.table; jsonlite; ggalluvial; ggplot2

# 安装包
if (!requireNamespace("data.table", quietly = TRUE)) {
  install.packages("data.table")
}
if (!requireNamespace("jsonlite", quietly = TRUE)) {
  install.packages("jsonlite")
}
if (!requireNamespace("ggalluvial", quietly = TRUE)) {
  install.packages("ggalluvial")
}
if (!requireNamespace("ggplot2", quietly = TRUE)) {
  install.packages("ggplot2")
}

# 加载包
library(data.table)
library(jsonlite)
library(ggalluvial)
library(ggplot2)
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     2026-01-18
 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
 ggalluvial * 0.12.5  2023-02-22 [1] RSPM
 ggplot2    * 4.0.1   2025-11-14 [1] RSPM
 jsonlite   * 2.0.0   2025-03-27 [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

数据结构：

  • <1st-col>: (String) 单元格样本名称作为 X 轴
  • <2nd-col>: (String) 基因名作为Y轴
  • <3rd-col>: (Numeric) 基因表达
  • <4rd-col>: (Numeric) 组
# 加载数据
data <- data.table::fread(jsonlite::read_json("https://hiplot.cn/ui/basic/matrix-bubble/data.json")$exampleData$textarea[[1]])
data <- as.data.frame(data)

# 整理数据格式
data[, 1] <- factor(data[, 1], levels = unique(data[, 1]))
data[, 2] <- factor(data[, 2], levels = unique(data[, 2]))

# 查看数据
head(data)
      x     y value  group
1 cell1 gene1     1 groupC
2 cell1 gene2     5 groupC
3 cell1 gene3    10 groupC
4 cell1 gene4    15 groupC
5 cell1 gene5    20 groupC
6 cell1 gene6    25 groupC

可视化

# 矩阵气泡图
p <- ggplot(data = data, aes(x = x, y = y, size = value, color = y)) +
  geom_point(alpha = 1) +
  labs(title = "Matrix Bubble") +
  guides(color = FALSE) +
  theme(panel.background = element_blank(),
        panel.grid.major = element_line(colour = "gray"),
        strip.background = element_blank(),
        panel.border = element_rect(colour = "black", fill = NA),
        panel.spacing = unit(0, "lines"),
        plot.title = element_text(size = 12, hjust = 0.5),
        text = element_text(family = "Arial"),
        legend.title = element_text(size = 10),
        axis.text.x = element_text(angle=0, hjust=0.5, vjust=1)) +
  facet_grid(~group, scales = 'fixed', margins = F) +
  scale_color_manual(values = c(
    "#3B4992FF","#EE0000FF","#008B45FF","#631879FF","#008280FF","#BB0021FF",
    "#5F559BFF","#A20056FF","#808180FF","#1B1919FF"))

p
图 1: 矩阵气泡图