[BioC] OT: question about plots, general R, really...

[Ulrik Stervbo]

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 at 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 at 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
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> >>UK
> >>
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> --
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
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