How to plot PCA output?
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 $x than when plotted by biplot() - as I mentioned my reply to Bryan. Do you know if this difference is data range matters? Many thanks, Chris
On 07/05/2012 14:24, "Jessica Streicher" <j.streicher at micromata.de> wrote:
That depends on what you want to plot there. Basically, you could just use plot() with pcaResult$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 at 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 at 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