Hi Listers,
I am trying to reflect a PCA biplot in the x-axis (i.e. PC1) but am not
having much success. In theory I believe all I need to do is multiply the
site and species scores for the PC1 by -1, which would effectively flip the
biplot.
I am creating a blank plot using the plot command and accessing the results
from a call to rda. I then use the calls to scores to obtain separate site
and species coordinates and I have worked out how to multiply the
appropriate PC1 scores by -1 to create the site and species scores I want.
However I am not sure how to change the call to plot which accesses the
results of the call to rda to draw the blank plot. The coordinates it is
accessing are for the unreflected ordination and this does not match the new
site and species scores that I have.
> fish.pca <- rda(fish.hel)
> fish.site <- scores(fish.pca,display="sites",scaling=3)
> fish.spp <- scores(fish.pca,display="species",scaling=3)
> fish.site[,"PC1"] <- -1*(fish.site[,"PC1"])
> fish.spp[,"PC1"] <- -1*(fish.spp[,"PC1"])
> graph <- plot(fish.pca,display=c("sites","species"),type="n",scaling=3) #
how do I get the plot to draw up the blank display based on the reversed
site and species scores?
Any help appreciated.
cheers
Andy
--
Andrew Halford Ph.D
Associate Research Scientist
Marine Laboratory
University of Guam
Ph: +1 671 734 2948
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