Thank you Duncan! That is very helpful, after posting this i did figure out how to convert the 2d coordinates into 3d. I was initially hesitant about using rgl because i thought it looked messy. With the modifications you suggested for the plot, it actually looks very clear now in rgl! And it rotates :-D
Thanks again! Tom Rzeszutek MSc. Candidate McMaster University Duncan Murdoch-2 wrote: > > 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 > > ______________________________________________ > [email protected] 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. > > -- View this message in context: http://www.nabble.com/Labelling-individual-points-on-3D-PCA-scatterplot-tp26096592p26101737.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ [email protected] 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.
