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

Wed Jul 5 14:39:21 CEST 2006

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 at 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 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
>> >>Swann Building, Mayfield Road
>> >>University of Edinburgh
>> >>Edinburgh EH9 3JR
>> >>UK
>> >>
>> >>_______________________________________________
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>> >
>> > --
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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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>
>
> --
> Blog: http://ulrikstervbo.blogspot.com
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>
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-- 
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
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK