reflecting a PCA biplot
Something like opar<- par(mfcol = c(1, 2)) z<- prcomp(USArrests, scale = TRUE) biplot(z, cex = 0.5) z$x[,1]<- -z$x[,1] z$rotation[,1]<- -z$rotation[,1] biplot(z, cex = 0.5, xlab = "-PC1") par(opar) perhaps? Allan
On 09/08/11 13:57, Andrew Halford wrote:
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