How to add p-values to a grouped ggplot in R

Question

fish_ID	颜色	安装	时间
1	蓝色	inst_0	136
1	绿色	inst_0	40
1	红色	inst_0	111
1	黄色	inst_0	20
1	蓝色	inst_3	112
1	绿色	inst_3	13
1	红色	inst_3	15
1	黄色	inst_3	90
2	蓝色	inst_0	110
2	绿色	inst_0	80
2	红色	inst_0	11
2	黄色	inst_0	34
2	蓝色	inst_3	19
2	绿色	inst_3	130
2	红色	inst_3	15
2	黄色	inst_3	88

我这里以一部分数据为例。我有很多这样的鱼 ID 号。我想做一个配对 t 检验，比较每个颜色集在 inst_0 和 inst_3 之间花费的平均时间。我能够用这段代码很好地比较它们：

library(ggplot2)
library(ggprism)

ggplot(mydata , aes(x = factor(inst), y = time, fill = color)) +
 geom_boxplot(position = position_dodge(width = 0.75)) +
 scale_fill_manual(values = c("blue" = "blue", "green" = "green", "red" = "red", "yellow" = 
 "yellow")) +
 theme_prism()

我还想从图中的配对 t 检验结果中添加 p 值，但我不确定如何对每个颜色集应用成对比较（例如 inst_0 和 inst_3 之间的蓝色比较）。我会很感激你的建议。谢谢！

Answer 1

请注意，您可以在使用

rstatix

后对齐 p 值的位置。

df <- data.frame(
  stringsAsFactors = FALSE,
           fish_ID = c(1L,1L,1L,1L,1L,1L,1L,1L,
                       2L,2L,2L,2L,2L,2L,2L,2L),
             Color = c("blue","green","red",
                       "yellow","blue","green","red","yellow","blue","green",
                       "red","yellow","blue","green","red","yellow"),
              inst = c("inst_0","inst_0","inst_0",
                       "inst_0","inst_3","inst_3","inst_3","inst_3","inst_0",
                       "inst_0","inst_0","inst_0","inst_3","inst_3",
                       "inst_3","inst_3"),
              time = c(136L,40L,111L,20L,112L,13L,
                       15L,90L,110L,80L,11L,34L,19L,130L,15L,88L)
)

library(rstatix)
library(ggplot2)
library(ggprism)

df_p_val <- df |> 
  group_by(Color) |>  
  t_test(time ~ inst) |>  
  add_xy_position()

# align positions of p-values
df_p_val <- df_p_val |> 
  mutate(group1 = c(0.7,0.9, 1.1, 1.3),
         group2 = c(1.7, 1.9, 2.1,2.3))

colors <- unique(df$Color) # to manually select fill, color scales
ggplot(df, aes(x=factor(inst), y=time)) + 
  geom_boxplot(aes(fill=Color)) +
  theme_prism() +
  add_pvalue(df_p_val, fontface="bold", 
             colour = "Color", 
             show.legend=F) +
  scale_fill_manual(values =colors) +
  scale_color_manual(values=colors)

^{创建于 2023-05-05 与 reprex v2.0.2}