序

本文记录了：
小提琴图+箱形图的绘制，箱形图放置小提琴图内部，并进行显著性差异检验。

成图如下所示：

加载所需要的包

library(ggplot2)
library(ggpubr)
library(ggsci)
library(ggsignif)

查看示例数据

str(iris)
'data.frame':   150 obs. of  5 variables:
 $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
 $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
 $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
 $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
 $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

table(iris$Species)
    setosa versicolor  virginica 
        50         50         50 

成图

ggplot(iris, aes(x = Species, y = Sepal.Length, fill = Species)) +
  geom_violin(trim = FALSE, alpha = 0.5) +
  geom_boxplot(
    width = 0.1, # 箱子宽度，使其能缩进在小提琴里
    fill = "white",
    outlier.shape = 0 # 将离群点画为一个小方块，要隐藏则设置为NA
  ) +
  # 添加误差线
  stat_boxplot(
    geom = "errorbar",
    position = position_dodge(width = 0.1),
    width = 0.1
  ) +
  # 添加散点
  geom_jitter(
    width = 0.2, alpha = 0.3
  )+
  # ggpubr
  theme_pubr() + # 主题先设置，不然会覆盖后续的微调。
  labs(
    title = "Violin Plot with Boxplot",
    subtitle = "Fisher's Iris Data",
    x = "Species",
    y = "Sepal Length",
    caption = "Statistics: Pairwise Wilcoxon rank sum test; *** p < 0.001"
  ) +
  theme(                     
    axis.text.x = element_text(angle = 45, hjust = 1),
    legend.title = element_blank()
  )+
  # ggsci
  scale_fill_manual(
    values = ggsci::pal_aaas()(3)
  ) +
  # ggsignif
  geom_signif(
    test = "wilcox.test", # default.
    comparisons = list(
      c("setosa", "versicolor"), # 设置谁与谁比较
      c("setosa", "virginica"),
      c("versicolor", "virginica")
      ),
    step_increase = 0.1, # 当有多个对比线时，每根线向上错开 10%，防止重叠
    map_signif_level = FALSE # 设置为F(default)，表示直接显示具体的 P 值数值，而不是星号（***）
  )