Add "p = " in front of geom_boxplot p-value in ggplot2-CodePudding

P-values can be added to ggplot2 figures using the function ggpubr::stat_compare_mean(). However I cannot get the text "p = " to show up in front of the p-values. There are examples of how to add "p = " in front of p-values on the help page for the function but they do not seem to work.

Example

library(ggplot2)
library(ggpubr)
library(dplyr)

data("Cars93")

# List of the comparisons I would like to make for which p-values will be derived

my_comparisons <- list(c("Front", "Rear"),
                       c("Front", "4WD"),
                       c("Rear", "4WD"))

# creates the figure with p-value but no label indicating the values are p-values

Cars93 %>%
  mutate(DriveTrain = factor(DriveTrain, levels = c("Front","Rear","4WD"))) %>%
  ggplot(aes(x = DriveTrain, y = Price))  
  stat_compare_means(paired = F,
                     comparisons = my_comparisons)  
  geom_boxplot(outlier.colour="white", outlier.fill = "white", outlier.shape = 1, outlier.size = 0)  
  geom_jitter(shape=1, position=position_jitter(0.2), color = "black", fill = "white", size = 2)  
  theme_bw()  
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())

following the example at the bottom of the ?stat_compare_means page suggests using aes(label = paste0("p = ", ..p.format..) which does not work.

?stat_compare_means

Cars93 %>%
  mutate(DriveTrain = factor(DriveTrain, levels = c("Front","Rear","4WD"))) %>%
  ggplot(aes(x = DriveTrain, y = Price))  
  stat_compare_means(paired = F,
                     comparisons = my_comparisons,
                     aes(label = paste0("p = ", ..p.format..)))  
  geom_boxplot(outlier.colour="white", outlier.fill = "white", outlier.shape = 1, outlier.size = 0)  
  geom_jitter(shape=1, position=position_jitter(0.2), color = "black", fill = "white", size = 2)  
  theme_bw()  
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())

If you look at the label argument on the ?stat_compare_means help page it says the allowed values include "p.signif" or "p.format" which made me think ..p.format.. was deprecated, so I tried adding in "p.format" which also did not work.

Cars93 %>%
  mutate(DriveTrain = factor(DriveTrain, levels = c("Front","Rear","4WD"))) %>%
  ggplot(aes(x = DriveTrain, y = Price))  
  stat_compare_means(paired = F,
                     comparisons = my_comparisons,
                     aes(label = paste0("p = ", "p.format")))  
  geom_boxplot(outlier.colour="white", outlier.fill = "white", outlier.shape = 1, outlier.size = 0)  
  geom_jitter(shape=1, position=position_jitter(0.2), color = "black", fill = "white", size = 2)  
  theme_bw()  
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())

In the end I would like the p-values to be preceded by p = such that the labels would say p = 0.00031, p = 0.059, and p = 0.027.

CodePudding user response：

When you use a list of comparisons, stat_compare_means defaults to using geom_signif from the ggsignif package, essentially acting as a glorified wrapper function. In so doing, you lose some of the formatting flexibility. Better in this case to use geom_signif directly:

library(ggsignif)

Cars93 %>%
  mutate(DriveTrain = factor(DriveTrain, levels = c("Front","Rear","4WD"))) %>%
  ggplot(aes(x = DriveTrain, y = Price))  
  geom_signif(y_position = c(55, 60, 65),
              comparisons = my_comparisons,
              map_signif_level = function(x) paste("p =", scales::pvalue(x)))  
  geom_boxplot(outlier.colour="white", outlier.fill = "white", 
               outlier.shape = 1, outlier.size = 0)  
  geom_jitter(shape=1, position=position_jitter(0.2), 
              color = "black", fill = "white", size = 2)  
  theme_bw()  
  theme(axis.text.x = element_text(size = 16, color = "black"),
        axis.text.y = element_text(size = 16, color = "black"),
        axis.title = element_text(size = 16, color = "black"),
        axis.title.x = element_text(vjust = -0.5),
        panel.grid = element_blank(),
        panel.background = element_blank())