This should work...

# save defaults for resetting
def.par <- par(no.readonly = TRUE)
# Set the layout
par(mfrow=c(2,3))
# Set the size of the outer margin
par(oma=c(0,0,2,0))
# Add a title to the top of the outer margin, using a bolf-face font
# Margin text is by default set to the side 3, which is the top, 1 = bottom,
2 = left, 4 = right
mtext("A nice title", outer = TRUE, font=2)
# do all the plotting
#
# reset to default par
par(def.par)

On 7/5/06, J.delasHeras@ed.ac.uk <J.delasHeras@ed.ac.uk> wrote:
>
>
> Hi Ulrik,
>
> thanks for your reply.
>
> I haven't managed to make it work the way you describe, unfortunately.
> It seems to affect only the last plot, not the whole figure... I guess
> I need to investigate this further. If you can send me the example that
> worked for you I'd appreciate that, as it may help me find out why it
> doesn't work for me.
> The link about Rgraphics is quite good, thanks for that!
>
> Just for teh record, this is one example of the plots I would like to
> add text to:
>
> par(mfrow=c(2,3))
> for (i in 1:3) {
> plot(log2(RG$Rb[,i]),log2(RG$R[,i]),pch=".")
> abline(0,1,col="blue")}
> for (i in 1:3) {
> plot(log2(RG$Gb[,i]),log2(RG$G[,i]),pch=".")
> abline(0,1,col="blue")}
>
> so that gives me 6 plots in the same figure. I want to be able to add a
> title to the whole figure... or maybe add other text here and there...
> using the whole figure, not the individual plots.
>
> Thanks for your help!
>
> Jose
>
>
>
> Quoting Ulrik Stervbo <ulriks@ruc.dk>:
>
> > I can't remember syntax exactly, but using the omi argument to par to
> > set the top outer margin and then mtext, to set some margin text,
> > works very well
> >
> > something like
> > par(omi=c(0,0,0.1,0)) # omi is for inches, oma (usage oma=c(0,0,3,0))
> > is for lines
> > mtext(label="Something")
> >
> > Maybe this link will help you:
> > http://www.stat.auckland.ac.nz/~paul/Talks/Rgraphics.pdf
> >
> > I have a working solution on my home computer I can share if needed
> >
> > Ulrik
> >
> > On 7/4/06, James W. MacDonald <jmacdon@med.umich.edu> wrote:
> >> You might also consider using the 'xpd' argument to par().
> >>
> >>  > par(xpd = NA)
> >>  > plot(1:10)
> >>  > plot(1:10)
> >>  > plot(1:10)
> >>  > plot(1:10)
> >>  > plot(1:10)
> >>  > plot(1:10)
> >>  > text(-12,28,"A header string")
> >>
> >> The only problem with this solution is finding where to put things. An
> >> alternative is to use
> >>
> >>  > text(locator(1), "A header string") and then place it where you
> want.
> >>
> >> HTH,
> >>
> >> Jim
> >>
> >>
> >> Ana Conesa wrote:
> >> > Hi Jose,
> >> >
> >> > I came across this same problem some time ago and I figured out a
> quite
> >> > rudimentary solution, I guess. Probably there are more elgant ones
> >> (I would
> >> > love to know them!!!)
> >> > Basically what I do is:
> >> > - Split my device up into one more row, very narrow, at the upper
> part, to
> >> > host the general title, and then set my first figure to spand across
> this
> >> > first row.
> >> > - Then plot a "ghost" plot in which I have made everything not
> visible but
> >> > the Title. Normally you have to adjust the margins for this first
> >> "plot" in
> >> > advance.
> >> > - Resest the margins
> >> > - Plot the other plots
> >> >
> >> > For example, for a title, plus 4 figures you could use:
> >> >
> >> >>layout(matrix(c(1,1,2,3,4,5),3,2, byrow=T),heights=c(1,6,6))
> >> >>par(mar=c(0.1,0.1,2,0.1))
> >> >>plot(0, main="Your Title", xaxt="n", yaxt="n", xlab="",
> >> >
> >> > ylab="",bty="n",col="white")
> >> >
> >> >>par(mar=c(c(4, 4, 4, 2)))
> >> >>plot...what ever...
> >> >
> >> >
> >> > You have to play a bit with the heights parameter of layout to get
> the
> >> > division you are happy with (the function layout.show() shows you the
> >> > position of each plot in your screen). And play also with the
> >> margins, maybe.
> >> >
> >> > Hope this is of some use to you...
> >> >
> >> > Ana
> >> >
> >> >
> >> > On Tue, 04 Jul 2006 18:12:56 +0100, J.delasHeras wrote
> >> >
> >> >>This is a bit off-topic, as it's purely R, I suppose...
> >> >>
> >> >>I am making figures containing 6 plots (MA plots, in this case),
> using:
> >> >>
> >> >>par(mfrow=c(2,3))
> >> >>
> >> >>now, I would like to add a title, for instance, to the whole figure,
> >> >>not to the individual plots... how does one do that? I can only seem
> >> >>to add text, title etc to each plot...
> >> >>
> >> >>thanks for any pointers!
> >> >>
> >> >>Jose
> >> >>
> >> >>--
> >> >>Dr. Jose I. de las Heras                      Email:
> J.delasHeras@ed.ac.uk
> >> >>The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131
> 6513374
> >> >>Institute for Cell & Molecular Biology        Fax:   +44 (0)131
> 6507360
> >> >>Swann Building, Mayfield Road
> >> >>University of Edinburgh
> >> >>Edinburgh EH9 3JR
> >> >>UK
> >> >>
> >> >>_______________________________________________
> >> >>Bioconductor mailing list
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> >> >>https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >>Search the archives:
> >> >
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >> >
> >> > --
> >> > IVIA (http://www.ivia.es)
> >> > Open WebMail Project (http://openwebmail.org)
> >> > Debian Project (http://www.debian.org)
> >> >
> >> > _______________________________________________
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> >>
> >>
> >> --
> >> James W. MacDonald
> >> University of Michigan
> >> Affymetrix and cDNA Microarray Core
> >> 1500 E Medical Center Drive
> >> Ann Arbor MI 48109
> >> 734-647-5623
> >>
> >>
> >>
> >> **********************************************************
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> >> not be used for urgent or sensitive issues.
> >>
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> >>
> >
> >
> > --
> > Blog: http://ulrikstervbo.blogspot.com
> > Mailing-list: http://www.coollist.com/group.cgi?l=ulrik_i_berlin
> >
> > _______________________________________________
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> >
>
>
>
> --
> Dr. Jose I. de las Heras                      Email: J.delasHeras@ed.ac.uk
> The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
> Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
>
>


-- 
Blog: http://ulrikstervbo.blogspot.com
Mailing-list: http://www.coollist.com/group.cgi?l=ulrik_i_berlin

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