title: plotting variables of procrustes analysis in r?
body: <p>I have performed non-metric multidimensional scaling (NMDS) on two data frames, each containing different variables but for the same sites. I am using the vegan package:</p>
  
  <pre><code>&gt; head (ResponsesS3)
     R1_S3 R10_S3 R11_S3 R12_S3 R2_S3 R3_S3 R4_S3 R6_S3 R7_S3 R8_S3 R9_S3
  4      0      0      0      0     0     1     0     0     0     0     0
  5      0      0      0      0     0     1     0     0     0     0     0
  7      1      0      0      1     0     0     0     0     0     0     0
  12     0      0      0      0     0     1     0     0     0     0     0
  14     2      2      0      0     0     0     2     0     0     0     0
  16     0      0      1      0     0     0     0     0     0     1     0
  
  
  &gt; head (EnvtS3)
       Dep_Mark  Dep_Work   Dep_Ext   Use_For Use_Fish    Use_Ag Div_Prod
  4  0.06222836 1.0852315 0.8367309 1.1415929 1.644670 0.1006964 0.566474
  5  0.25946808 1.3342266 0.0000000 1.7123894 0.822335 0.0000000 0.283237
  7  2.20668862 0.0000000 0.8769881 0.4280973 0.822335 0.5244603 0.849711
  12 2.26323697 0.0000000 0.8090991 1.1415929 0.000000 1.4957609 1.416185
  14 1.65107675 0.5195901 0.2921132 0.5707965 0.822335 1.7873609 0.849711
  16 1.82230225 0.4760163 0.1915366 2.2831858 0.000000 1.6614904 0.849711
  
  
  &gt; ResponsesS3.mds = metaMDS (ResponsesS3, k =2, trymax = 100)
  
  &gt; EnvtS3.mds = metaMDS (EnvtS3, k =2, trymax = 100)
  </code></pre>
  
  <p>I fit the results using a procrustean superimposition</p>
  
  <pre><code>&gt; pro.ResponsesS3.EnvtS3.mds &lt;- procrustes(ResponsesS3.mds,EnvtS3.mds)
  </code></pre>
  
  <p>I am most interested in understanding how the variables from each dataset fit together. I would like to use the plot() function to return a graph of the variables from ResponsesS3 and from EnvtS3, rather than the sites (which is what the plot function returns by default). </p>
  
  <p>Is this possible?</p>