On 10/28/2009 11:21 AM, trz wrote:
Hi There,
I'm attempting to plot 10 values on a three-dimensional PCA with text labels
next to each point. While i have no trouble doing this on 2D plots using the
'text' or 'textxy' function, I cannot find a function to do this on a 3D
plot.
I am using princomp for my PCA:
PCA<-princomp(eucdata, cor=TRUE)
PCA$scores [,1:3] # the three principal components i want to plot
Then i am using 'scatterplot3d' to plot my first 3 principal components:
scatterplot3d(PCA$scores [,1:3],xlab="Component 1 (26.9%)",main="My 3D
PCA",ylab="Component 2
+ (17.9%)", zlab="Component 3
(12.4%)",type="h",box=FALSE,pch=21,bg=color)
And i get this:
http://www.nabble.com/file/p26096592/myPCA.jpeg
'text' and 'textxy' only accept 2D coordinates so they do not label my
points in a way that makes sense.
I'm open to other 3D plotting functions in R, i just think this one is easy
to visually understand. In addition, If there is any way to move the grid up
to z=0 please let me know. To be clear i am trying to make my PCA look more
like this one i found in a journal article (Trejaut et al., 2005):
http://www.nabble.com/file/p26096592/journal.pbio.0030247.g003.png
scatterplot3d will return a function that can transform 3D coordinates
to 2D so you can plot labels in the right place; see its man page.
Alternatively, you could use the rgl package. Using the
example(princomp) results, the call is similar to what you had, with
some extra work for embellishment:
plot3d(pc.cr$scores [,1:3],xlab="Component 1",main="My 3D
PCA",ylab="Component 2", zlab="Component 3", type="h", box=F, axes=F)
spheres3d(pc.cr$scores[,1:3], radius=0.1, col="pink")
grid3d(side="z", at=list(z=0))
text3d(pc.cr$scores[,1:3], text=rownames(pc.cr$scores), adj=1.3)
This looks too crowded, but maybe you have fewer points to plot.
Duncan Murdoch
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