如何在同一张多箱线图中为各标记的不同地点添加统计显著性标记？

要实现每种标记（category）内部不同地点（place）的显著性比较，且不跨标记比较，可以借助ggsignif包的geom_signif函数，它能针对分组变量单独设置组内比较，同时通过位置对齐匹配箱线图的排列。

修改后的完整代码 #

library(ggplot2)
library(dplyr)
library(tidyr)
library(ggpubr)
library(ggsignif)  # 新增包，用于分组添加显著性标记

data <- data.frame(
  fat = rep(c("Lake A", "Lake B", "Lake C"), each = 50),
  zon = c(rnorm(50, mean = 5, sd = 1), rnorm(50, mean = 5.5, sd = 1), rnorm(50, mean = 4.5, sd = 1)),
  cal = c(rnorm(50, mean = 6, sd = 1.5), rnorm(50, mean = 6.5, sd = 1.5), rnorm(50, mean = 5.5, sd = 1.5)),
  si = c(rnorm(50, mean = 7, sd = 1), rnorm(50, mean = 7.5, sd = 1), rnorm(50, mean = 6.5, sd = 1)), 
  other1 = rnorm(150),other2 = rnorm(150))

data_selected <- data %>% select(place = fat, zon, cal, si)
data_long <- pivot_longer(data_selected, cols = c("zon", "cal", "si"), names_to = "category", values_to = "value")

ggplot(data_long, aes(x = place, y = value, fill = category)) +
  geom_boxplot(position = position_dodge(width = 0.8)) +  # 指定箱线图间距，用于后续对齐
  labs(title = NULL,
       x = "Location",
       y = "Marker level (Log-values)",
       fill = "Marker") +
  theme_bw() +
  theme(legend.position = "top") +
  # 添加分组显著性标记
  geom_signif(
    aes(group = category),  # 指定按标记分组，仅在组内比较地点
    comparisons = list(c("Lake A", "Lake B"), c("Lake A", "Lake C"), c("Lake B", "Lake C")),  # 组内两两比较组合
    test = "t.test",  # 沿用原代码的检验方法
    map_signif_level = TRUE,  # 显示显著性符号（*、**等）而非原始p值
    size = 1,  # 显著性横线的粗细
    textsize = 5,  # 符号大小
    position = position_dodge(width = 0.8)  # 和箱线图间距对齐，确保标记对应正确分组
  )

关键说明 #

• position_dodge(width = 0.8)：保证箱线图和显著性标记的位置完全对齐，避免标记错位。
• aes(group = category)：限制显著性比较仅在同一个标记组内进行，不会跨标记绘制对比线条。
• comparisons参数：定义每个标记组内需要比较的地点组合，这里包含了三个地点的所有两两对比。

内容的提问来源于stack exchange，提问作者mschmidt