title: Tukeys post-hoc on ggplot boxplot
body: <p>Ok, so I think I'm pretty close with this, but I'm getting an error when I try to construct my box plot at the end. My goal is to place letters denoting statistical relationships among the time points above each boxplot. I've seen two discussion of this on this site, and can reproduce the results from their code, but can't apply it to my dataset.</p>
  
  <p>Packages</p>
  
  <pre><code>library(ggplot2)
  library(multcompView)
  library(plyr)
  </code></pre>
  
  <p>Here is my data:</p>
  
  <pre><code>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")
  </code></pre>
  
  <p>ANOVA and Tukey Post-hoc</p>
  
  <pre><code>Model4 &lt;- aov(dmass~ChillTime, data=WaterConDryMass)
  tHSD &lt;- TukeyHSD(Model4, ordered = FALSE, conf.level = 0.95)
  plot(tHSD , las=1 , col="brown" )
  </code></pre>
  
  <p>Function:</p>
  
  <pre><code>generate_label_df &lt;- function(TUKEY, flev){
  
    # Extract labels and factor levels from Tukey post-hoc 
    Tukey.levels &lt;- TUKEY[[flev]][,4]
    Tukey.labels &lt;- multcompLetters(Tukey.levels)['Letters']
    plot.labels &lt;- names(Tukey.labels[['Letters']])
  
    boxplot.df &lt;- 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 &lt;- data.frame(plot.labels, labels = Tukey.labels[['Letters']],
                              stringsAsFactors = FALSE) 
  
    # Merge it with the labels
    labels.df &lt;- merge(plot.levels, boxplot.df, by.x = 'plot.labels', by.y = flev, sort = FALSE)
    return(labels.df)
  }  
  </code></pre>
  
  <p>Boxplot:</p>
  
  <pre><code>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))
  </code></pre>
  
  <p>Error:</p>
  
  <pre><code>Error in HSD[[flev]] : invalid subscript type 'symbol'
  </code></pre>