Hi Martin,

thanks a lot for the help, I really appreciate it!

When I used the code below that you suggested it worked fine for creating
pdf files with just one plot, but it wouldn't create a pdf file with more
figures.

> options(device="pdf")
> consensus(<your args here>)
> dev.off()

What I did was to reproduce the plot.consensus.kmean function but without
the 'get(getOption("device"))()' term. This makes the plotting in R less
practical (because one image overwrites the other) but works great for
creating pdf files.

Once again thank you for your help and sorry for capitalizing the name of
the package!

All the best,

Artur


On Jan 22, 2008 3:32 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Artur
>
> It looks like 'consensus' uses (in plot.consensus.kmeans) the command
>
> get(getOption("device"))()
>
> at the start of it's plotting routine. So try
>
> > options(device="pdf")
> > consensus(<your args here>)
> > dev.off()
>
> once you've navigated R's concept of its working directory (using
> setwd) to point to where you'd like the pdf to be saved. It will
> create a file Rplots.pdf. (you could get fancier here, writing your
> own function as a kind of pseudo-device to forward the right arguments
> to pdf, mypdf=function() pdf("testfile.pdf") and set
> options(device="mypdf")). Not sure why maanova does things this way,
> or whether this will work for all plots.
>
> Also it's the 'maanova' package.
>
> Hope that helps
>
> Martin
>
>
> "Artur Veloso" <abveloso@gmail.com> writes:
>
> > Dear all,
> >
> > I am using the MAANOVA package to create k-means clusters and wanted to
> save
> > the graphs produced by the function "consensus" in a PDF file. I don't
> get
> > any error messages when I write my code, but when I try to open the file
> I
> > get a message that it can't be opened because there are no pages in the
> > document. Am I doing something wrong? Does anyone know of a way to go
> around
> > this?
> >
> > Thanks a lot!
> >
> > Artur Veloso
> > Masters in Marine Biology Candidate
> > College of Charleston, South Carolina
> >
> > # this works fine, so I don't think the problem is creating the pdf file
> > pdf("test_file.pdf")
> > plot(1:10,1:10)
> > dev.off()
> >
> > # this also works, but the pdf file does not get the consensus plot
> > library(maanova)
> > dolphin.maanova <- read.madata
> >
> ("maanova_males_data.txt","maanova_males_design.txt",arrayType="oneColor",
> >                    probeid=1,intensity=2)
> > dolphin.maanova.fit <- fitmaanova(madata=dolphin.maanova
> ,formula=~+Sample)
> > genes <- read.csv("bioc.males.numbers.csv",header=T)
> > genes.cluster <- macluster(dolphin.maanova.fit,term="Sample" ,
> > idx.gene=genes[,2],what="gene",method="kmean",kmean.ngroup=8)
> > pdf("teste.pdf")
> > bioc.males.consensus <- consensus(bioc.males.cluster,0.5)
> > dev.off()
> >
> >
> >> sessionInfo()
> > R version 2.6.1 (2007-11-26)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] maanova_1.8.0
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.6.1
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>

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