title: Problems with output plot of PCA+environmental factors (with envfit) with vegan
body: <p>I have a dataset from 6 samples with lots of species (12k) and some environmental factors (7 factors). I am trying to do a PCA ordination of the species and then add the environmental factors to the analysis and to the plot using <code>vegan</code> package. What I do is the following:</p>
  
  <pre><code>&gt;pca.spec &lt;- rda(spec) 
  &gt;groups &lt;- factor(rownames(spec)) 
  &gt;plot(pca.spec) 
  &gt;text(pca.spec, labels=groups)
  </code></pre>
  
  <p>And then</p>
  
  <pre><code>&gt; env_fact &lt;- read.csv("env_fact.csv") 
  &gt; ef &lt;- envfit(pca.spec, env_fact, permu=999)
  &gt; plot(ef) 
  </code></pre>
  
  <p>The output is the following:</p>
  
  <pre><code>***VECTORS
  
                         PC1      PC2     r2 Pr(&gt;r)
  pH                -0.55984 -0.82860 0.1914 0.7556
  NH4                0.00204  1.00000 0.3108 0.5319
  NO2               -0.51192  0.85904 0.5042 0.3000
  NO3               -0.86533  0.50121 0.0857 0.9361
  Total.inorganic.N -0.18298  0.98312 0.2164 0.6500
  X..N.total        -0.49702  0.86774 0.2600 0.4806
  X..C.total        -0.47205  0.88157 0.2618 0.4931
  Permutation: free
  Number of permutations: 720
  
  ***FACTORS:
  
  Centroids:
             PC1     PC2
  SSPIA0 -2.0704  3.2416
  SSPIA1 -1.8165 -4.1363
  SSPIA2 -1.0806 -7.0426
  SSPIA3  9.2544  0.7544
  SSPIA4 -2.1292  3.6535
  SSPIA5 -2.1578  3.5293
  
  Goodness of fit:
     r2 Pr(&gt;r)
  SS  1      1
  Permutation: free
  Number of permutations: 720
  </code></pre>
  
  <p>And a plot with the 'Centroids' represented in the same position as the samples itself (duplicated information) and the arrows without the name of the factor they represent in a position that allows to identify them (they seems to appear too far from the end of the arrow). </p>
  
  <p><img src="https://i.stack.imgur.com/8OAzF.jpg" alt="enter image description here"></p>
  
  <p>How can I move the names closer to their corresponding arrows? How can I remove 'centroids' ('factors') from the plot?</p>
  
  <p>I'm also not sure whether I carried out the analysis correctly.</p>
  
  <p>Thanks a lot.</p>