Hi Steve,
I don't know if there is a function that makes a figure like that, but
with
a little bit of work you should be able to plot a figure extremely
similar
to the one you showed. I couldn't see what your example looked like
because
you didn't define the object scores, but I created a little example
that
looks a little bit like what you want it to look like.
I hope this helps.
Cheers,
Artur Veloso
Master's Candidate
College of Charleston
Charleston, SC
cp <- colorRampPalette(c('darkblue', 'darkred'))(30)
layout(matrix(c(1,2,3,4,4,0),ncol=2),widths=c(0.8,0.2))
par(mar=c(5, 6, 4, 2) + 0.1)
#creates the top image
image(x=seq(0,1,0.1),z=matrix(rnorm(10)),xaxt="n",yaxt="n",bty="n",xla
b="",col=cp)
axis(side=3,at=seq(0,0.9,0.1)+.05,labels=paste("gene",1:10),las=2,tick
="F")
axis(side=2,at=0,labels="Condition 1",las=2,tick=F)
#creates the middle image
image(x=seq(0,1,0.1),z=matrix(rnorm(10)),xaxt="n",yaxt="n",bty="n",xla
b="",col=cp)
axis(side=3,at=seq(0,0.9,0.1)+.05,labels=paste("gene",1:10),las=2,tick
="F")
axis(side=2,at=0,labels="Condition 2",las=2,tick=F)
#creates the bottom image
image(x=seq(0,1,0.1),z=matrix(rnorm(10)),xaxt="n",yaxt="n",bty="n",xla
b="",col=cp)
axis(side=3,at=seq(0,0.9,0.1)+.05,labels=paste("gene",1:10),las=2,tick
="F")
axis(side=2,at=0,labels="Condition 3",las=2,tick=F)
#creates the side bar
par(mar=c(5, 2, 4, 3) + 0.1)
image(y=1:10,z=matrix(1:10,ncol=10),xaxt="n",yaxt="n",bty="n",ylab="",
col=cp)
axis(side=4,at=1:10,labels=1:10,las=2,tick=F)
On Tue, Jun 17, 2008 at 3:09 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:
> Hi,
>
> I'm trying to recreate a figure from a publication[1] that looks
like this:
>
http://cbio.mskcc.org/~lianos/images/barfig.png<http: cbio.mskcc.or="" g="" %7elianos="" images="" barfig.png="">
>
> I have some vectors with "scores" (that you see is plotted
horizontally
> there) that I'd just like to turn into some colored
representation/heatmap
> like that. I'd also like to then display the legend of the heatmap
on the
> right there. It would be great if we can add the labels too, but if
it's
> overkill to do, then I'll deal without them.
>
> I have code that is my crude attempt at plotting on of those bars,
but I
> think I'm going about it the wrong way. I'm also at a loss at
finding the
> magic incantation is to get the colorbar up on the side (the
equivalent to
> MATLAB's `colorbar` call[2], I guess).
>
> nboxes <-length(scores)
> cp <- colorRampPalette(c('darkblue', 'darkred'))(30)
> plot(1, 1, xlim=c(0, 50), ylim=c(-1,1), type="n", axes=FALSE,
bty="n",
> xlab=names(scores), ylab="")
> rect(xlef=0:nboxes, ybottom=1, xright=(0:nboxes)+1, ytop=1.8,
> col=cp[1:nboxes], border='light grey')
>
> I looked trough the R graphics gallery[3] to see if I could find
something
> similar, but I'm not finding anything that's helping ...
>
> Some code examples would be great, but some general pointers to
places I
> should be looking into would also be a big help.
>
> Thanks,
> -steve
>
> [1] Bild et al. Oncogenic pathway signatures in human cancers as a
guide to
> targeted, Nature 2006.
> [2]
>
http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/ac
cess/helpdesk/help/techdoc/ref/colorbar.html
> [3]
http://addictedtor.free.fr/graphiques/
>
> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics, and Systems Biology
> Weill Medical College, Cornell University
>
>
http://cbio.mskcc.org/~lianos <http: cbio.mskcc.org="" %7elianos="">
>
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