弦图

作者

[编辑] 郑虎;

[审核] .

修改于

2026-01-27

注记

Hiplot 网站

本页面为 Hiplot Chord 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/chord?lang=zh_cn

复杂的数据关系交互作用以和弦图的形式表现出来。

环境配置

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

  • 编程语言: R

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

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

# 加载包
library(data.table)
library(jsonlite)
library(circlize)
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     2026-01-28
 pandoc   3.1.3 @ /usr/bin/ (via rmarkdown)
 quarto   1.8.27 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package    * version date (UTC) lib source
 circlize   * 0.4.17  2025-12-08 [1] RSPM
 data.table * 1.18.0  2025-12-24 [1] RSPM
 ggplotify  * 0.1.3   2025-09-20 [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

基因与通路或基因本体相互作用的数据框架或矩阵。

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

# 整理数据格式
row.names(data) <- data[, 1]
data <- data[, -1]
data <- as.matrix(data)

# 查看数据
head(data)
   E1 E2 E3 E4 E5
S1  4 16 12 18 11
S2  7 11  2 15 10
S3  9  2 17 16 11
S4 14  9 12  3 17
S5  1  1  7  1 12
S6 10 18  9 13  9

可视化

# 弦图
Palette <- c("#E64B35FF","#4DBBD5FF","#00A087FF","#3C5488FF","#F39B7FFF",
             "#8491B4FF","#91D1C2FF","#DC0000FF","#7E6148FF","#B09C85FF")
grid.col <- c(Palette, Palette, Palette[1:5])
p <- as.ggplot(function() {
  chordDiagram(
    data, grid.col = grid.col, grid.border = NULL, transparency = 0.5,
    row.col = NULL, column.col = NULL,  order = NULL,
    directional = 0, # 1, -1, 0, 2
    direction.type = "diffHeight", # diffHeight and arrows
    diffHeight = convert_height(2, "mm"), reduce = 1e-5, xmax = NULL, 
    self.link = 2, symmetric = FALSE, keep.diagonal = FALSE, 
    preAllocateTracks = NULL,
    annotationTrack = c("name", "grid", "axis"),
    annotationTrackHeight = convert_height(c(3, 3), "mm"),
    link.border = NA, link.lwd = par("lwd"), link.lty = par("lty"), 
    link.sort = FALSE, link.decreasing = TRUE, link.largest.ontop = FALSE,
    link.visible = T, link.rank = NULL, link.overlap = FALSE,
    scale = F, group = NULL, big.gap = 10, small.gap = 1
    )
  })

p
图 1: 弦图