[R] heatmap help
Paul Lepp
pwlepp at pmgm2.stanford.edu
Wed Sep 8 20:06:33 CEST 2004
Thanks Marta (and Andy). Between the two of you I think I got the result I
was looking for. I ended up doing the following:
heatmap(x, distfun=function(x) as.dist(x))
Thanks again.
> -----Original Message-----
> From: Marta Rufino [mailto:mrufino at ipimar.ualg.pt]
> Sent: Wednesday, September 08, 2004 2:22 AM
> To: pwlepp at pmgm2.Stanford.EDU
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] heatmap help
>
>
> Hello,
>
>
> I was just doing heatmaps myself ;-) and I had the same problem.
> It would be
> nice to have such an example in the help file because it is not
> clear (thank
> you).
> you use (for example... this is my case, which I am doing the distance
> matrix using vegdist function with Bray curtis similarity):
>
> heatmap(matrix, scale="none", distfun=function(m) vegdist(m,
> method="bray"),
> hclustfun=function(m) hclust(m, method="average"), col=
> grey(seq(0.8,0,l=5)))
>
> or you can put directly the distance matrix that you may want, but I found
> it worst. To have the right labels on I found that the best way
> would be to
> have them in the matrix directely, because if we put it after it does not
> work well...
>
> I have been having difficulties in producing the scale that I
> want and doing
> the correct legend...
> I found an email with a function (image.scale()), but it does not work
> entirely well.
> How can I define the values I want in the scale, for example, use
> red for 1
> g, blue for 2 g, etc...
> Is there a simpler way of doing the legend?
>
> thank you very much,
> Marta
>
>
> > Dear R wizards,
> > Hopeful someone can help me with what I believe is a pretty simple task.
> I
> > pretty new to R so some (much) of the obvious escapes me. How do I get a
> > distance matrix into heatmap? What do I tell distfun if what I'm trying
> to
> > map is already an ordered distance matrix? I tried >heatmap(x,
> > distfun=as.dist(x)) where x is the distance matrix but R gave
> me an error.
> > Thanks in advance for any help.
> >
> > Paul Lepp
> >
> > `-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-.
> > `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`
> > >==/ >==/ >==/ >==/ >==/
> > ,=,-<=`. ,=,-<=`. ,=,-<=`. ,=,-<=`. ,=,-<=`. ,=,
> > ,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-'
> > Paul Lepp, Ph.D. Stanford School of Medicine
> >
> > VAPAHCS, 154T Dept. of Microbiology & Immunology
> > 3801 Miranda Ave Stanford University
> > Palo Alto, CA 94304 Stanford, CA
> > (650) 493-5000 x66762 fax: (650) 852-3291
> > http://cmgm.stanford.edu/~pwlepp pwlepp at cmgm.stanford.edu
> >
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