I suggest that you re-post your question, but this time make it easy for
readers to help you by providing a simple reproducible example of your
problem. Provide some fake data, or a small subset of your data using,
for example, the function dput(). Trim the fat from your code. Get rid
of any arguments or functions that are not necessary to demonstrate your
problem. Include in your code the function library() or require() to load
any needed packages. If you make it so that a reader can simply copy and
paste your code into R, you will get more help.
Jean
Barbara Doll <bd...@ncsu.edu> wrote on 08/15/2012 01:29:09 PM:
>
> I'm using R for PCA and? factor analysis. I want to create biplots of
> varimax rotated factors that color-code points by their classification.
> My research is on streams that are urban and rural. So, I want to color
> code them by this classification. If you just do a biplot from prcomp or
> princomp, you cannot add this color. So, I have used some code developed
> by a graduate student in our statistics department here at NC State
> University. However, when you compare the two biplots, the observed
> points are not in the same location. The variable vectors match up, but
> not the points. I'm not sure why. The code is below. Please help.
>
>
> label=data[,"Urban.Rural"]
> indexU<-which(label=="U")
> indexR<-which(label=="R")
>
> collab<-rep(0,length(data[,1]))
> collab[indexU]<-"Blue"
> collab[indexR]<-"Green"
>
> library(psych)
>
> fit <- principal(mydata, nfactors = num.fac, rotate="varimax", scores =
> TRUE)
>
> z1 <- sum(fit2$loadings[,1]^2) ### need to scale scores and loadings by
> these factors
> z2 <- sum(fit2$loadings[,2]^2)
>
> biplot(fit$scores[,c(1,2)]/c(z1, z2), loadings(fit)[,c(1,2)]*c(z1, z2),
> xlabs=rep("", length(collab)), col = c("black", "orange"))
> legend(x="bottomright", legend=c("Urban","Rural"),
> text.col=c("Blue","Green"), bg="Grey90")
>
> ### scale the plot parameters
> rrr<-apply(fit$scores[,1:2],2, range)
> (abs(rrr)+.1)*sign(rrr)
> par(usr=as.vector(rrr))
>
> ### now include the colored points
> points(fit$scores[,c(1,2)], col=collab, pch=20)
[[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.
