R help - Sep 2012 - PCA legend outside of PCA plot

Hi All,

I have been trying to get to plot my PCA legend outside of the PCA plot,
but success still alludes me.

Can you guys please advise how I can achieve this. I used locater() to
obtain coordinates for below the Comp.1 axis. Using these coordinates the
legend disappears.

Below is the code for the PCA and legend.

Thanks in advance for the help.

Regards
Tinus


r.cols <- rainbow(length(unique(SEData$Seamount)))
pca1 <- princomp(SEData3, scores=TRUE, cor=TRUE)
biplot(pca1, var.axes= TRUE,
xlabs=rep("",nrow(SEData3)),main="Seamounts
PCA")
rrr <- apply(pca1$scores[,1:2],2, range)
par(usr=as.vector(rrr))
points(pca1$scores[,1:2], col=r.cols , pch=20)
legend(-8, 2.95, sm, col = r.cols, text.col = "black", lty = NULL,
pch = 20,horiz = F,)


-- 
M.J. Sonnekus
PhD Candidate (The Phytoplankton of the southern Agulhas Current Large
Marine Ecosystem (ACLME))
Department of Botany
South Campus
Nelson Mandela Metropolitan University
PO Box 77000
Port Elizabeth
South Africa
6031

Cell: 082 080 9638
E-mail: tsonnekus@gmail.com

	[[alternative HTML version deleted]]

Try adding the parameter xpd=TRUE to your legend() statement. Without
reproducible code it is pretty hard to be sure what the problem is.

----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Tinus Sonnekus
> Sent: Sunday, September 09, 2012 1:37 PM
> To: r-help at r-project.org
> Subject: [R] PCA legend outside of PCA plot
> 
> Hi All,
> 
> I have been trying to get to plot my PCA legend outside of the PCA
> plot,
> but success still alludes me.
> 
> Can you guys please advise how I can achieve this. I used locater() to
> obtain coordinates for below the Comp.1 axis. Using these coordinates
> the
> legend disappears.
> 
> Below is the code for the PCA and legend.
> 
> Thanks in advance for the help.
> 
> Regards
> Tinus
> 
> 
> r.cols <- rainbow(length(unique(SEData$Seamount)))
> pca1 <- princomp(SEData3, scores=TRUE, cor=TRUE)
> biplot(pca1, var.axes= TRUE,
> xlabs=rep("",nrow(SEData3)),main="Seamounts
> PCA")
> rrr <- apply(pca1$scores[,1:2],2, range)
> par(usr=as.vector(rrr))
> points(pca1$scores[,1:2], col=r.cols , pch=20)
> legend(-8, 2.95, sm, col = r.cols, text.col = "black", lty =
NULL,
> pch = 20,horiz = F,)
> 
> 
> --
> M.J. Sonnekus
> PhD Candidate (The Phytoplankton of the southern Agulhas Current Large
> Marine Ecosystem (ACLME))
> Department of Botany
> South Campus
> Nelson Mandela Metropolitan University
> PO Box 77000
> Port Elizabeth
> South Africa
> 6031
> 
> Cell: 082 080 9638
> E-mail: tsonnekus at gmail.com
> 
> 	[[alternative HTML version deleted]]
> 
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