如何按组堆叠箱线图：同组并列、不同组上下排列

问题背景 #

现有一个包含12列的data.frame，按列名分为3组：

• 前4列：Gene_1组（列名以Gene_1开头）
• 第5-8列：Gene_2组（列名以Gene_2开头）
• 第9-12列：Gene_3组（列名以Gene_3开头）

所有列均为连续数值型数据，需求是：

• 同组内的4个箱线图并列展示
• 不同组的箱线图上下堆叠成3行

之前尝试的ggplot2代码导致所有箱线图并列显示，X轴混乱，需要修正实现方式。

数据示例（子集） #

df <- structure(list(Gene_1_TL1= c(0.382992297410965, 0.460950464010239, 
0.447804838418961, 0.447804838418961, 0.460950464010239, 0.447804838418961, 
0.369836807250977, 0.447804838418961, 0.369836807250977, 0.447804838418961
), Gene_1_TL2= c(0.460011065006256, 0.52004611492157, 0.253930300474167, 
0.222006008028984, 0.302200853824615, 0.485153168439865, 0.20485857129097, 
0.350892871618271, 0.331338971853256, 0.295754462480545), Gene_1_TL3= c(0.277256995439529, 
0.425392180681229, 0.182383552193642, 0.253527283668518, 0.329186052083969, 
0.305586904287338, 0.188975885510445, 0.238625407218933, 0.497761845588684, 
0.342641144990921), Gene_1_TL4= c(0.565486133098602, 
0.564990341663361, 0.164183273911476, 0.15946152806282, 0.234778091311455, 
0.396436214447021, 0.172556579113007, 0.257463246583939, 0.43759897351265, 
0.200696632266045), Gene_2_TL1= c(0.0779446139931679, 0.274154871702194, 
0.0718425810337067, 0.0718425810337067, 0.274154871702194, 0.0718425810337067, 
0.160841777920723, 0.0718425810337067, 0.160841777920723, 0.0718425810337067
), Gene_2_TL2= c(0.0662130266427994, 0.258626192808151, 0.0601647943258286, 
0.060332003980875, 0.141631454229355, 0.113691322505474, 0.0786028951406479, 
0.0668068528175354, 0.171470999717712, 0.0754544585943222), Gene_2_TL3= c(0.144175127148628, 
0.145591989159584, 0.0984272509813309, 0.0906868129968643, 0.28544145822525, 
0.138114541769028, 0.091837003827095, 0.0904595032334328, 0.211963757872581, 
0.163982316851616), Gene_2_TL4= c(0.118267595767975, 
0.199180424213409, 0.0867970511317253, 0.0653180256485939, 0.203389659523964, 
0.149213299155235, 0.126333728432655, 0.0975232273340225, 0.256154090166092, 
0.146669581532478), Gene_3_TL1= c(0.287342727184296, 0.417357206344604, 
0.255898356437683, 0.255898356437683, 0.417357206344604, 0.255898356437683, 
0.471998482942581, 0.255898356437683, 0.471998482942581, 0.255898356437683
), Gene_3_TL2= c(0.299634903669357, 0.418549239635468, 0.424916654825211, 
0.432371437549591, 0.584436595439911, 0.296403467655182, 0.563782930374146, 
0.3688924908638, 0.578023612499237, 0.278784334659576), Gene_3_TL3= c(0.314525783061981, 
0.343217849731445, 0.315391361713409, 0.353350460529327, 0.562197327613831, 
0.292534917593002, 0.616392850875854, 0.284660279750824, 0.532478809356689, 
0.341239869594574), Gene_3_TL4= c(0.216887220740318, 
0.283130913972855, 0.248720198869705, 0.421182304620743, 0.564142644405365, 
0.204288363456726, 0.778401911258698, 0.272624760866165, 0.511143803596497, 
0.186424404382706)), row.names = c("04d83340b8bd", "122T", "1c2a5ac94492", 
"1d209304d988", "212T", "24ab7fecc92e", "356T", "379fe8924c51", 
"39T", "3ec4d3fc8bd1"), class = "data.frame")

错误代码分析 #

之前的代码存在两个关键问题：

1. facet_grid(. ~ gsub("\\d", "", variable)) 使用列方向分面，导致所有组的箱线图横向并列，不符合上下堆叠的需求
2. gsub("\\d", "", variable) 的正则表达式错误，会把Gene_1变成Gene_，无法正确区分Gene_1/Gene_2/Gene_3三组

正确实现代码 #

library(reshape2)
library(ggplot2)

# 1. 融化数据
df_melted <- melt(df)

# 2. 拆分列名，生成基因组和TL编号两个变量
df_melted$gene_group <- gsub("_TL\\d+", "", df_melted$variable)
df_melted$tl <- gsub("Gene_\\d+_", "", df_melted$variable)

# 3. 绘制分组箱线图
boxplot <- ggplot(df_melted, aes(x = tl, y = value)) +
  geom_boxplot(fill = "#619CFF") +
  # 按gene_group分行，上下堆叠
  facet_grid(gene_group ~ ., scales = "free_y") +
  labs(x = "TL编号", y = "数值") +
  theme_bw() +
  theme(
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.border = element_blank(),
    axis.line = element_line(colour = "black"),
    strip.text.y = element_text(size = 12, face = "bold")
  )

print(boxplot)

代码说明 #

• 拆分列名：通过正则表达式分别提取gene_group（Gene_1/Gene_2/Gene_3）和tl（TL1/TL2/TL3/TL4），让ggplot能明确区分分组和同组内的类别
• 分面设置：使用facet_grid(gene_group ~ .)实现行方向分面，不同基因组的箱线图上下堆叠；scales = "free_y"允许每行的Y轴刻度独立，适配不同组的数据范围
• 样式调整：添加了填充色、坐标轴标签和分面标题样式，提升图表可读性

内容的提问来源于stack exchange，提问作者Programming Noob