在geom_boxplot p-值前面添加ggplot2中的"p =“

Question

P-值可以使用函数ggplot2添加到ggpubr::stat_compare_mean()图中。但是，我不能让文本"p =“出现在p-值前面。在函数的帮助页面中，如何在p-值前面添加"p =“的例子有一些，但是它们似乎不起作用。

示例

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())

遵循?stat_compare_means页面底部的示例，建议使用不起作用的aes(label = paste0("p = ", ..p.format..)。

?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())

如果您查看label帮助页面上的?stat_compare_means参数，它说允许的值包括"p.signif"或"p.format"，这使我认为..p.format..是不推荐的，所以我尝试在"p.format"中添加也不起作用的值。

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())

最后，我希望在p-值之前加上p =，这样标签就可以说p= 0.00031，p= 0.059，p= 0.027。

Answer 1

当您使用比较列表时，stat_compare_means默认使用来自ggsignif包的geom_signif，实质上是一个美化的包装函数。这样做，您就失去了一些格式化灵活性。在这种情况下，最好直接使用geom_signif：

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())

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