Biplot, depending on what parameters you give it, scales the data in a certain way.
See http://stat.ethz.ch/R-manual/R-patched/library/stats/html/biplot.princomp.html scale The variables are scaled by lambda ^ scale and the observations are scaled by lambda ^ (1-scale) where lambda are the singular values as computed by princomp. Normally 0 <= scale <= 1, and a warning will be issued if the specified scale is outside this range. Am 07.05.2012 um 16:01 schrieb Christian Cole: > Hi Jessica, > > Yes, that does help. It confirms my digging around in the prcomp object. > > I was plotting $x, but wasn't sure whether this was appropriate. Mainly > because the data ranges are different in $x than when plotted by biplot() > - as I mentioned my reply to Bryan. Do you know if this difference is data > range matters? > Many thanks, > > Chris > > > > On 07/05/2012 14:24, "Jessica Streicher" <j.streic...@micromata.de> wrote: > >> That depends on what you want to plot there. Basically, you could just >> use plot() with pcaResult$x. You might need to define which PCs you want >> to plot there though. >> >> pcaResult<-prcomp(iris[,1:4]) >> plot(pcaResult$x) # gives the first 2 PCs >> plot(pcaResult$x[,2:3]) #gives the second vs the 3rd PC >> >> or if you want to see more you can use pairs() >> >> pairs(pcaResult$x) >> >> if you want things colored, theres the col parameter that works for both >> functions: >> >> pairs(pcaResult$x,col=iris[,5]) >> >> Does this help? >> >> Am 07.05.2012 um 12:22 schrieb Christian Cole: >> >>> I have a decent sized matrix (36 x 11,000) that I have preformed a PCA >>> on >>> with prcomp(), but due to the large number of variables I can't plot the >>> result with biplot(). How else can I plot the PCA output? >>> >>> I tried posting this before, but got no responses so I'm trying again. >>> Surely this is a common problem, but I can't find a solution with >>> google? >>> >>> >>> The University of Dundee is a registered Scottish Charity, No: SC015096 >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
