title: ggplot2 & stat_ellipse: Draw ellipses around multiple groups of points
body: <p>This might be a simple one, but I'm trying to draw ellipses around my treatments on my PCoA plot.</p>
  
  <p>My data frame (sc) is:</p>
  
  <pre><code>             MDS1        MDS2 Treatment
  X1xF1 -0.19736183 -0.24299825   1xFlood
  X1xF2 -0.17409568 -0.29727596   1xFlood
  X1xF3 -0.15272444 -0.28553837   1xFlood
  S1    -0.06643271  0.47049959     Start
  S2    -0.15143350  0.31152966     Start
  S3    -0.26156297  0.12296849     Start
  X3xF1  0.29840827  0.04581617  3xFloods
  X3xF2  0.50503749 -0.07011503  3xFloods
  X3xF3  0.20016537 -0.05488630  3xFloods
  </code></pre>
  
  <p>and my code is:</p>
  
  <pre><code>ggplot(data=sc,(aes(x=MDS1,y=MDS2,colour = Treatment)))+geom_point(size=3)+
    ggtitle("PCoA of samples at 'class' level(method='Bray')\n",sep=''))+
    theme_bw()+guides(colour = guide_legend(override.aes = list(size=3)))+
    stat_ellipse()
  </code></pre>
  
  <p>It plots the PCoA okay up until stat_ellipse(). I've tried it with various parameters and at best I can get one ellipse for the whole plot (although I can't seem to reproduce that now).</p>
  
  <p>What I'm after is three CI ellipses for the three treatments, coloured the same as the treatments. Any help would be very appreciated!</p>
  
  <p>Thanks.</p>