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I've completed PCA analysis, in R with VEGAN package, of some ecological data on tree health. There are 80 trees total (so, 80 'sites') divided into four treatment categories. I've got the data plotted with color coded points--colors according to the treatment groups. Rather than plotting individual sites/trees on PCA biplot, I'd like to make something like a box-and-whisker plot that has four 'crosses' that show the centroid for each group and the SE in both PCA dimensions. I've seen figures like this in papers, but I can't seem to find an R script for plotting this way. Any suggestions?

I guess an alternative would be to just take the site scores and manually find the means and SE's and create my own plot, but I'd rather find a script for it, if possible.

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  • $\begingroup$ if this doesn't get answered here, you could flag it and ask for it to be moved to stackoverflow. $\endgroup$ – TooTone Mar 20 '14 at 18:16
  • $\begingroup$ Thanks, I'm new here and I appreciate the suggestion. I was under the impression that stackoverflow was more for just programming questions--which I guess this sort of is, but I assumed a practical stats audience would be better. Also, I don't speak code very well, so I get a little overwhelmed there. But thanks again for the suggestion. $\endgroup$ – Jas Max Mar 20 '14 at 18:27
  • $\begingroup$ Well it could go either way. I suggest you add the visualization tag to your post as well. You might get more interest if you add pictures to your post, both the ones you have already and (if you can) examples of what you'd like. (If you put this on SO you'd want to have some code in your post.) $\endgroup$ – TooTone Mar 20 '14 at 18:31
  • $\begingroup$ here's an example of a stackoverflow question with a great answer v similar to yours. Whether or not it stays here I hope you can see it's a good idea to get illustrative images in your question. $\endgroup$ – TooTone Mar 21 '14 at 3:06
  • $\begingroup$ Thanks for the suggestion, I appreciate your time. I'll go ahead and try it over there. $\endgroup$ – Jas Max Mar 21 '14 at 16:25

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