R-使用'stat_compare_means'在ggplot中重新格式化P值

2024-05-17 • 问答

我想在多面ggplot中将p值绘制到每个面板。如果p值大于0.05，我想按原样显示p值。如果p值小于0.05，我想以科学计数法显示该值（即0.0032-> 3.20e-3； 0.0000425-> 4.25e-5）。

我为此编写的代码是：

   p1 <- ggplot(data = CD3,aes(location,value,color = factor(location),fill = factor(location))) + 
  theme_bw(base_rect_size = 1) +
  geom_boxplot(alpha = 0.3,size = 1.5,show.legend = FALSE) +
  geom_jitter(width = 0.2,size = 2,show.legend = FALSE) +
  scale_color_manual(values=c("#4cdee6","#e47267","#13ec87")) +
  scale_fill_manual(values=c("#4cdee6","#13ec87")) +
  ylab(expression(paste("Density of clusters,",mm^{-2}))) +
  xlab(NULL) +
  stat_compare_means(comparisons = list(c("CT",'N'),c("IF","N")),aes(label = ifelse(..p.format.. < 0.05,formatC(..p.format..,format = "e",digits = 2),..p.format..)),method = 'wilcox.test',show.legend = FALSE,size = 10) +
  #ylab(expression(paste('Density,/',mm^2,)))+
  theme(axis.text = element_text(size = 10),axis.title = element_text(size = 20),legend.text = element_text(size = 38),legend.title = element_text(size = 40),strip.background = element_rect(colour="black",fill="white",size = 2),strip.text = element_text(margin = margin(10,10,10),size = 40),panel.grid = element_line(size = 1.5))
plot(p1)

此代码运行无错误，但是数字的格式未更改。我究竟做错了什么？

我附加了数据以重现该图：donwload data here

编辑

structure(list(value = c(0.931966449207829,3.24210526315789,3.88811650210901,0.626860993574675,4.62085308056872,0.477508650519031,0.111900110501359,3.2495164410058,4.06626506024096,0.21684918139434,1.10365086026018,4.66666666666667,0.174109967855698,0.597625869832174,2.3758865248227,0.360751947840548,1.00441501103753,3.65168539325843
),Criteria = structure(c(2L,2L,2L),.Label = c("Density","Density of cluster","nodular count","Elongated count"),class = "factor"),Case = structure(c(1L,1L,3L,4L,5L,6L,6L),.Label = c("Case 1A","Case 1B","Case 2","Case 3","Case 4","Case 5"),Mark = structure(c(1L,1L),.Label = c("CD3","CD4","CD8","CD20","FoxP3"),location = structure(c(3L,.Label = c("CT","IF","N"),class = "factor")),row.names = c(91L,92L,93L,106L,107L,108L,121L,122L,123L,136L,137L,138L,151L,152L,153L,166L,167L,168L),class = "data.frame")

我认为您的问题来自stat_compare_means和comparisons的使用。我不太确定，但是我会猜测stat_compare_means的p值的输出与compare_means不同，因此，您不能将其用于{{ 1}}。

让我用您的示例解释一下，您可以像这样修改p.value的显示：

aes

您可以正确显示p.value，但丢失了柱线。因此，如果使用label参数，则会得到：

library(ggplot2)
library(ggpubr)
ggplot(df,aes(x = location,y = value,color = location))+
  geom_boxplot()+
  stat_compare_means(ref.group = "N",aes(label = ifelse(p < 0.05,sprintf("p = %2.1e",as.numeric(..p.format..)),..p.format..)))

因此，现在您得到的是条形，但显示不正确。

要解决此问题，您可以使用comparisons函数在ggplot2之外执行统计，并使用软件包library(ggplot2) library(ggpubr) ggplot(df,color = location))+ geom_boxplot()+ stat_compare_means(comparisons = list(c("CT","N"),c("IF","N")),..p.format..)))来显示正确的显示。

在这里，我正在使用compare_means和函数ggsignif创建新列，但是您可以在dplyr R中轻松地做到这一点。

mutate

然后，您可以绘制它：

base

它看起来像您要绘制的内容吗？

R-使用'stat_compare_means'在ggplot中重新格式化P值

linda881633 回答：R-使用'stat_compare_means'在ggplot中重新格式化P值

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