删除平均值低于指定值的组的 p 值

Question

我想知道是否有一种方法可以指定在 R 中的 ggpubr 包中的 ggboxplot 上显示哪些 p 值，但我一直没有成功尝试这样做。

我发现的唯一选择是预先过滤数据，但我不想在制作图表时排除这些组。即，我只想显示平均值 > 我的参考组的组的 p 值，但我仍然想查看所有数据。

在我的示例中，我希望“lo”组隐藏其显着性水平，同时仍保留在图表上，因为其平均值低于参考组

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

Plant<-c("ref","ref","ref","ref","ref","ref","ref","ref","ref",
         "hi","hi","hi","hi","hi","hi","hi","hi","hi",
         "lo","lo","lo","lo","lo","lo","lo","lo","lo")
Delta.CCI<-c(11.05,11.45,9.65,10.65,10.15,8.95,8.95,12.45,8.95,
             20.56,20.66,19.76,20.36,20.26,20.06,19.16,19.16,19.06,
             2.18,1.58,2.98,1.11,1.91,0.21,1.68,2.11,0.51)
df<-data.frame(Plant,Delta.CCI)

#generate a list of comparisons for the data frame
cdf<-compare_means(Delta.CCI ~ Plant, 
                   data = df, 
                   ref.group = "ref")
#make a new list
my_list <- vector()
#for every other comparison put a 1 in the list
#this is so I can stagger the p-values later since there are so many in my actual data set
for(i in 1:nrow(cdf)+1){
  if(i %% 2 == 0){
    my_list[i] <- 1
  } else {
    my_list[i] <- 0
  }
}

#Make the box plot
p<-ggboxplot(df,
             title = "A",
             x="Plant",
             y="Delta.CCI")+
  #rotate the text so it is legible
  rotate_x_text(angle = 90)+
  #make a line showing where the mean of the LBA/GFP group is
  geom_hline(yintercept = mean(df$Delta.CCI[df$Plant=="ref"]), linetype = 2)+
  #add out p-values to the plot as significance labels
  stat_compare_means(label="p.signif",label.y=my_list+28,ref.group="ref")
p

Answer 1

一种选择是使用

stat_pvalue_manual

。为此，我使用

rstatix

包中的较低级别函数来创建测试统计数据的 data.frame。您可以轻松地向此 df 添加 y 位置，而无需创建单独的向量。此外，通过参数

detailed=TRUE

wilcox_test

允许添加对均值差异的估计，以有条件地用空字符串替换不需要的标签：

library(ggplot2)
library(ggpubr)
library(dplyr, warn=FALSE)
library(rstatix)

cdf <- df |>
  wilcox_test(Delta.CCI ~ Plant, ref.group = "ref",
              detailed = TRUE) |>
  add_significance("p") |>
  mutate(
    y.position = 28 + (row_number() %% 2 == 0),
    p.signif = if_else(estimate < 0, p.signif, "")
  )

p <- ggboxplot(df,
  title = "A",
  x = "Plant",
  y = "Delta.CCI"
) +
  rotate_x_text(angle = 90) +
  geom_hline(yintercept = mean(df$Delta.CCI[df$Plant == "ref"]), linetype = 2) +
  stat_pvalue_manual(
    cdf,
    label = "p.signif",
    x = "group2"
  )
p