r - 将自定义注释添加到 p 值标签到 ggpubr stat_compare_means()

Question

我尝试制作显示 p 值的箱线图

my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len")+ 
  stat_compare_means(comparisons = my_comparisons, method = "wilcox.test")

结果是

但是如何向计算的 p 值添加额外的文本？我想添加 "p = " 如下所示

我怎样才能做到？

upd. 下面的变体不起作用

my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )

ggboxplot(ToothGrowth, x = "dose", y = "len")+ 
  stat_compare_means(comparisons = my_comparisons, method = "wilcox.test", aes(label=paste("p=",scientific(as.numeric(..p.format..)))))

ggboxplot(ToothGrowth, x = "dose", y = "len")+ 
  stat_compare_means(comparisons = my_comparisons, method = "wilcox.test", aes(label = paste("p =", ..p.format..)))

ggboxplot(ToothGrowth, x = "dose", y = "len")+ 
  stat_compare_means(comparisons = my_comparisons, method = "wilcox.test", aes(label = paste0("p =", ..p.format..)))

Answer 1

我相信这可能是 ggpubr 中的潜在错误。该文档提供了一个示例，说明如何将自定义文本添加到您的 p 值。当将多个比较传递给标记函数时，这开始失败。我认为该错误可能是 ggplot 不知道将哪个表达式解析为标签(请参阅下面的 r-lang 警告)。还有一些关于可能相关的 p 值计算的警告。

也就是说，我觉得大多数关于 ggpubr 的问题都与具有多个 p 值的注释有关，我确实觉得您可能需要重新考虑 (a) 您的统计数据和 (b) 您的可视化。

library(ggpubr)
#> Loading required package: ggplot2
library(tidyverse)

## This works as expected. Only one test
ggboxplot(ToothGrowth, x = "supp", y = "len") + 
  stat_compare_means(aes(label = paste0("p = ", ..p.format..)))

看到大量警告 - 开始失败。

my_comparisons <- list( c("0.5", "1"), c("1", "2"), c("0.5", "2") )
ggboxplot(ToothGrowth, x = "dose", y = "len") +
  stat_compare_means(comparisons = my_comparisons, 
                     aes(label = paste0("p = ", ..p.format..)))
#> Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
#> Please use `as_label()` or `as_name()` instead.
#> This warning is displayed once per session.
#> Warning in wilcox.test.default(c(4.2, 11.5, 7.3, 5.8, 6.4, 10, 11.2, 11.2, :
#> cannot compute exact p-value with ties
#> Warning in wilcox.test.default(c(4.2, 11.5, 7.3, 5.8, 6.4, 10, 11.2, 11.2, :
#> cannot compute exact p-value with ties
#> Warning in wilcox.test.default(c(16.5, 16.5, 15.2, 17.3, 22.5, 17.3, 13.6, :
#> cannot compute exact p-value with ties

通过分别为每个比较组创建一个图，这又开始起作用了。

ls_tg <- ToothGrowth %>%
  split(., .$dose)

lapply(my_comparisons, function(x) bind_rows(ls_tg[x])) %>%
  map(~ggboxplot(., x = "dose", y = "len") + 
        stat_compare_means(aes(label = paste0("p = ", ..p.format..)))) %>%
  patchwork::wrap_plots()

^{由 reprex package 创建于 2021-12-07 (v2.0.1)}