Tukey 在 ggplot 箱线图上的 post-hoc

Question

好的，所以我认为我已经很接近这个了，但是当我最后尝试构建箱形图时出现错误。我的目标是在每个箱线图上方放置表示时间点之间统计关系的字母。我在这个网站上看到了两个对此的讨论，并且可以从他们的代码中重现结果，但不能将其应用于我的数据集。

套餐

library(ggplot2)
library(multcompView)
library(plyr)

这是我的数据：

dput(WaterConDryMass)
structure(list(ChillTime = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 
2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L), .Label = c("Pre_chill", 
"6", "13", "24", "Post_chill"), class = "factor"), dmass = c(0.22, 
0.19, 0.34, 0.12, 0.23, 0.33, 0.38, 0.15, 0.31, 0.34, 0.45, 0.48, 
0.59, 0.54, 0.73, 0.69, 0.53, 0.57, 0.39, 0.8)), .Names = c("ChillTime", 
"dmass"), row.names = c(NA, -20L), class = "data.frame")

ANOVA 和 Tukey Post-hoc

Model4 <- aov(dmass~ChillTime, data=WaterConDryMass)
tHSD <- TukeyHSD(Model4, ordered = FALSE, conf.level = 0.95)
plot(tHSD , las=1 , col="brown" )

函数：

generate_label_df <- function(TUKEY, flev){

  # Extract labels and factor levels from Tukey post-hoc 
  Tukey.levels <- TUKEY[[flev]][,4]
  Tukey.labels <- multcompLetters(Tukey.levels)['Letters']
  plot.labels <- names(Tukey.labels[['Letters']])

  boxplot.df <- ddply(WaterConDryMass, flev, function (x) max(fivenum(x$y)) + 0.2)

  # Create a data frame out of the factor levels and Tukey's homogenous group letters
  plot.levels <- data.frame(plot.labels, labels = Tukey.labels[['Letters']],
                            stringsAsFactors = FALSE) 

  # Merge it with the labels
  labels.df <- merge(plot.levels, boxplot.df, by.x = 'plot.labels', by.y = flev, sort = FALSE)
  return(labels.df)
}

箱线图：

ggplot(WaterConDryMass, aes(x = ChillTime, y = dmass)) +
  geom_blank() +
  theme_bw() +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
  labs(x = 'Time (weeks)', y = 'Water Content (DM %)') +
  ggtitle(expression(atop(bold("Water Content"), atop(italic("(Dry Mass)"), "")))) +
  theme(plot.title = element_text(hjust = 0.5, face='bold')) +
  annotate(geom = "rect", xmin = 1.5, xmax = 4.5, ymin = -Inf, ymax = Inf, alpha = 0.6, fill = "grey90") +
  geom_boxplot(fill = 'green2', stat = "boxplot") +
  geom_text(data = generate_label_df(tHSD), aes(x = plot.labels, y = V1, label = labels)) +
  geom_vline(aes(xintercept=4.5), linetype="dashed") +
  theme(plot.title = element_text(vjust=-0.6))

错误：

Error in HSD[[flev]] : invalid subscript type 'symbol'

Answer 1

我想我找到了您正在学习的教程，或者非常相似的内容。您可能最好将整个内容复制并粘贴到您的工作 space、函数和所有内容中，以避免遗漏一些小差异。

基本上我完全按照教程 (http://www.r-graph-gallery.com/84-tukey-test/) 进行了操作，并在最后添加了一些必要的调整。它添加了几行额外的代码，但它有效。

generate_label_df <- function(TUKEY, variable){

  # Extract labels and factor levels from Tukey post-hoc 
  Tukey.levels <- TUKEY[[variable]][,4]
  Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])

  #I need to put the labels in the same order as in the boxplot :
  Tukey.labels$treatment=rownames(Tukey.labels)
  Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
  return(Tukey.labels)
}

model=lm(WaterConDryMass$dmass~WaterConDryMass$ChillTime )
ANOVA=aov(model)

# Tukey test to study each pair of treatment :
TUKEY <- TukeyHSD(x=ANOVA, 'WaterConDryMass$ChillTime', conf.level=0.95)

labels<-generate_label_df(TUKEY , "WaterConDryMass$ChillTime")#generate labels using function

names(labels)<-c('Letters','ChillTime')#rename columns for merging

yvalue<-aggregate(.~ChillTime, data=WaterConDryMass, mean)# obtain letter position for y axis using means

final<-merge(labels,yvalue) #merge dataframes

ggplot(WaterConDryMass, aes(x = ChillTime, y = dmass)) +
  geom_blank() +
  theme_bw() +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
  labs(x = 'Time (weeks)', y = 'Water Content (DM %)') +
  ggtitle(expression(atop(bold("Water Content"), atop(italic("(Dry Mass)"), "")))) +
  theme(plot.title = element_text(hjust = 0.5, face='bold')) +
  annotate(geom = "rect", xmin = 1.5, xmax = 4.5, ymin = -Inf, ymax = Inf, alpha = 0.6, fill = "grey90") +
  geom_boxplot(fill = 'green2', stat = "boxplot") +
  geom_text(data = final, aes(x = ChillTime, y = dmass, label = Letters),vjust=-3.5,hjust=-.5) +
  geom_vline(aes(xintercept=4.5), linetype="dashed") +
  theme(plot.title = element_text(vjust=-0.6))

Tukey 在 ggplot 箱线图上的 post-hoc

Tukeys post-hoc on ggplot boxplot

r

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boxplot