In R, to get and use a package (i.e. ade4), then find out about a function,
try this:

> install.packages('ade4')
# ...time passes...
> library(ade4)
> ?dudi.coa

You might want to read the following paper, too:

Use and misuse of correspondence analysis in codon usage
studies<http://nar.oxfordjournals.org/content/30/20/4548.full>

Hope this helps... the 'made4' package would seem to be useful (it was
created for similar purposes) but Aedin Culhane, one of the authors,
suggested *not* using it recently, and I assume that she knows a great deal
more about the situation than I do, so if you do use it, perhaps you might
contact her.


On Thu, Mar 8, 2012 at 9:20 AM, aoife doherty <aoife.m.doherty@gmail.com>wrote:

> Many thanks. I tried this:
>
> table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11,
>    8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1",
>    "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2",
>    "codon3")))
>
> library(ca)
>
> plot(ca(table,suprow=c(4,5)))
>
> This will give me a ca plot, where the nodes of interest 4,5 are open
> circles.
>
> However i have two questions.
>
> 1. Is it possible instead of manually typing in 4 and 5 to somehow get R to
> read in a list of nodes of interest. Basically is it possible to change:
>
> c(4,5) to c(all the nodes that are in a file)
>
> and
>
> 2. Is it possible instead of the individual nodes of interest being open
> circles, if the area encompassing all the nodes of interest could be shaded
> differently/highlighted.
> i THINK this is where your suggestion of:
>
> Your best bet is to use the package ade4
> using res=dudi.coa(data)
> then
> s.class(res$li,group)
> where group is your grouping variable you want to highlight.
>
> comes in, but i am completely new at R, i have genuinely tried to
> understand the packages from the manual, I am confused however.
>
> Aoife
>
>
>
>
>
> On Wed, Mar 7, 2012 at 12:45 PM, Susan Holmes <susan@stat.stanford.edu
> >wrote:
>
> >
> > Your best bet is to use the package ade4
> > using res=dudi.coa(data)
> > then
> > s.class(res$li,group)
> > where group is your grouping variable you want to highlight.
> > Best
> > Susan Holmes
> > Statistics
> > Stanford
> >
> >
> > On Wed, 7 Mar 2012, aoife [guest] wrote:
> >
> >
> >> Hey guys, Can anyone help?
> >>
> >> I did a correspondance analysis and made a plot.
> >>
> >> I also have a specific list of nodes that i want to find in my plot and
> >> want to either color the nodes that appear in my list differently, or
> put
> >> some kind of border around that group of nodes...
> >>
> >> Would anyone know how to do this?
> >>
> >>
> >>
> >>
> >> -- output of sessionInfo():
> >>
> >> n/a
> >>
> >> --
> >> Sent via the guest posting facility at bioconductor.org.
> >>
> >> ______________________________**_________________
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> >> Bioconductor@r-project.org
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> http://news.gmane.org/gmane.science.biology.informatics.conductor>
> >>
> >>
>
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>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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