title: ggplot2 grouped boxplot doesn't separate groups for different timepoints
body: <p>I have a simple data set with two groups and a value for each group at 4 different time points. I want to display this data set as grouped boxplots over time but ggplot2 doesn't separate the time points. </p>
  
  <p>This is my data:</p>
  
  <pre><code> matrix
      Replicate Line Day Treatment  X A WT     Marker Proportion
              1    C  10       low NA      HuCHuD_Pos       8.62
              2    C  10       low NA      HuCHuD_Pos         NA
              1    C  18       low NA      HuCHuD_Pos      30.50                                                    
              3    C  18       low NA      HuCHuD_Pos         NA
              2    C  18       low NA      HuCHuD_Pos         NA
              1    C  50       low NA      HuCHuD_Pos      26.10
              2    C  50       low NA      HuCHuD_Pos      31.90
              1    C  80       low NA      HuCHuD_Pos      12.70
              2    C  80       low NA      HuCHuD_Pos      26.20
              1    C  10    normal NA      HuCHuD_Pos         NA
              2    C  10    normal NA      HuCHuD_Pos      17.20
              1    C  18    normal NA      HuCHuD_Pos       3.96
              2    C  18    normal NA      HuCHuD_Pos         NA
              1    C  50    normal NA      HuCHuD_Pos      25.60
              2    C  50    normal NA      HuCHuD_Pos      17.50
              1    C  80    normal NA      HuCHuD_Pos      19.00
             NA    C  80    normal NA      HuCHuD_Pos         NA
  </code></pre>
  
  <p>And this is my code:</p>
  
  <pre><code>matrix = as.data.frame(subset(data.long, Line == line_single &amp; Marker == marker_single &amp; Day != "30"))
  
  pdf(paste(line_name_single, marker_name_single, ".pdf"), width=10, height=10)
  plot &lt;- 
  ggplot(data=matrix,aes(x=Day, y=Proportion, group=Treatment, fill=Treatment)) +
  geom_boxplot(position=position_dodge(1))   
  print(plot)
  dev.off()
  </code></pre>
  
  <p>What do I do wrong?</p>
  
  <p>What I want</p>
  
  <p><img src="https://i.stack.imgur.com/jcf4q.png" alt=""></p>
  
  <p>What I get</p>
  
  <p><img src="https://i.stack.imgur.com/glG1c.png" alt=""></p>
  
  <p>Thanks very much for your help!</p>
  
  <p>Cheers, 
  Paula </p>