[R-sig-eco] biplot with most important species

2016-10-12 Thread Bjorn
Hi all, there might be a simple solution to do this, but I don't seem to manage to find it. I have done a PCA using vegan. I now want to create a biplot with only those species that explain a certain (cumulative) amount of the variation along the first 2 PC axes (in order to keep things

Re: [R-sig-eco] biplot with most important species

2016-10-12 Thread stephen sefick
Hi Bjorn, I have done this in the past using ggplot2. I think that I plotted everything, but only labeled those that were above some threshold. In other words, I changed the label in the input data to "". I think that is how I solved this problem. HTH, Stephen On Wed, Oct 12, 2016 at 5:44 AM,

Re: [R-sig-eco] biplot with most important species

2016-10-12 Thread syrovat
Hi Bjorn, A common practice in simplifying ordinatin plots is to keep species that show the best fit into the ordination space. The position of such species in the ordination diagram really (may) tell something. In linear methods like PCA a linear fit is suitable. This can be computed using