[BioC] RE: PCA plots

[Jeff Sorenson]

For a simple 3-D scatter plot, I've settled on a perl script that converts
any three principle components (calculated by R) into a 3-D VRML scatterplot
(.wrl) file that can viewed with most web browsers.  The script is adapted
from an online tutorial
http://staff.washington.edu/larryg/Classes/Rvrml/zz-hand.html.  This suits
my needs nicely, since our lab uses a web interface to most of our data.
I'm interested in how people are using ggobi for microarray work.

Jeff Sorenson


>
> Message: 1
> Date: Tue, 28 Jan 2003 07:30:57 -0500
> From: Robert Gentleman <rgentlem@jimmy.harvard.edu>
> To: Laurent Gautier <laurent@cbs.dtu.dk>
> Cc: Michael Benjamin <msb1129@bellsouth.net>,
> bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] PCA plots
>
>
>  I think that we are likely to leave that to ggobi -- they have done a
> lot of stuff and the interface to R is pretty reasonable these days.
>
> On Tue, Jan 28, 2003 at 05:55:31AM +0100, Laurent Gautier wrote:
> > On Mon, Jan 27, 2003 at 11:29:39PM -0500, Michael Benjamin wrote:
> > > Hi, all.
> > >
> > > Are there any plans to spice up the principal components
> analysis tools
> > > in R?  Many commercial packages offer interactive manipulation of 3D
> > > biplots.  We are almost there already, with a fast (if homely-looking)
> > > biplot in "princomp."  Any takers?
> >
> > AFAIK, R can interface with ggobi. By linking selections of individuals
> > in different planes of projection, you should be able to achieve it
> > (and go beyond "only" 3 dimensions, if I understood what you meant
> > by "interactive manipulation").
> > Check the screenshots at www.ggobi.org to get an idea.
> >
> >
> > Hopin' it helps,
> >
> >
> > L.
> >
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>
> --
> +-----------------------------------------------------------------
> ----------+
> | Robert Gentleman                 phone : (617) 632-5250
>           |
> | Associate Professor              fax:   (617)  632-2444
>           |
> | Department of Biostatistics      office: M1B20
> | Harvard School of Public Health  email:
> rgentlem@jimmy.dfci.harvard.edu   |
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