MA 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 EnhancedMA 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/pseudo-enhanced-ma?lang=zh_cn

差异表达基因可视化。

环境配置

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

  • 编程语言: R

  • 依赖包: data.table; jsonlite; EnhancedVolcano

# 安装包
if (!requireNamespace("data.table", quietly = TRUE)) {
  install.packages("data.table")
}
if (!requireNamespace("jsonlite", quietly = TRUE)) {
  install.packages("jsonlite")
}
if (!requireNamespace("EnhancedVolcano", quietly = TRUE)) {
  remotes::install_github('kevinblighe/EnhancedVolcano')
}

# 加载包
library(data.table)
library(jsonlite)
library(EnhancedVolcano)
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
 data.table      * 1.18.0  2025-12-24 [1] RSPM
 EnhancedVolcano * 1.29.1  2025-12-03 [1] Github (kevinblighe/EnhancedVolcano@b1f351b)
 ggplot2         * 4.0.1   2025-11-14 [1] RSPM
 ggrepel         * 0.9.6   2024-09-07 [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

# 加载数据
data <- data.table::fread(jsonlite::read_json("https://hiplot.cn/ui/basic/pseudo-enhanced-ma/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$baseMeanNew <- 1 / (10^log(data$baseMean + 1))

# 查看数据
head(data)
              baseMean log2FoldChange      lfcSE       stat       pvalue
COL6A3    8.494143e+04    -0.34453583 0.07607842 -4.5305972 5.881720e-06
ZNF157    2.456747e+00    -0.42976616 0.33693867 -1.2957785 1.950518e-01
RPL23P11  0.000000e+00             NA         NA         NA           NA
SCARNA10  4.406548e-01    -0.05657159 0.15265730 -0.2329492 8.158009e-01
RNU6-857P 0.000000e+00             NA         NA         NA           NA
TOPORS    5.331777e+02     0.10709656 0.12572643  0.8549637 3.925712e-01
                  padj  baseMeanNew
COL6A3    6.207728e-05 4.469624e-12
ZNF157              NA 5.750056e-02
RPL23P11            NA 1.000000e+00
SCARNA10            NA 4.314220e-01
RNU6-857P           NA 1.000000e+00
TOPORS    6.148749e-01 5.239278e-07

可视化

# MA 图
p <- EnhancedVolcano(
  data, lab = rownames(data), title = "MA plot", subtitle = "EnhancedMA",
  x = 'log2FoldChange', y = 'baseMeanNew', xlab = bquote(~Log[2]~ 'fold change'),
  ylab = bquote(~Log[e]~ 'base mean + 1'), ylim = c(0,12),
  pCutoff = as.numeric(1e-05), FCcutoff = 1, pointSize = 3.5,
  labSize = 4, boxedLabels = T, colAlpha = 1,
  legendLabels = c('NS', expression(Log[2]~FC),
                   'Mean expression', 
                   expression(Mean-expression~and~log[2]~FC)),
  legendPosition = "bottom", legendLabSize = 16, legendIconSize = 4.0,
  encircleCol = 'black', encircleSize = 2.5, encircleFill = 'pink',
  encircleAlpha = 1/2) + 
  coord_flip() +
  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.title = element_text(size = 10),
        legend.text = element_text(size = 10))

p
图 1: MA 图