[BioC] Heatmap

[Laurent Gautier]

You may want to tell us what are 'gclus' and 'sclus'... the problem
might be there...
(Note that 'Matrix[,]' can be replaced elegantly by 'Matrix'.)

Otherwise apparently it works (R-1.8.1):
m <- matrix(rnorm(100), 20, 5)
heatmap(m, Rowv=as.dendrogram(hclust(dist(m))), Colv=as.dendrogram(hclust(dist(t(m)))))


Regards,


L.


-- 
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent


On Fri, Jan 02, 2004 at 10:04:14AM +0100, Johan Lindberg wrote:
> I am trying to plot a matrix of m-values in a heatmap with "average 
> linkage". The rows are M-values of genes and the columns are my slides.
> I do the following and get the following error message:
> 
> > heatmap(Matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus), 
> col=rbg)
> Error in match.fun(FUN) : evaluation is nested too deeply: infinite 
> recursion?
> Error: evaluation is nested too deeply: infinite recursion?
> #But this is not the case since I can plot the rows (genes) if I plot them 
> without my columns (slides).
> plot(sclus, main = paste("Dendrogram: Coph = " , round(coph1columns, 2)))
> #This works, why?????????? Strange????
> And even more strange, it works if I choose another distance method like 
> "single" or "complete" linkage.
> 
> I would really appreciate som help :)
> 
> / Johan
> 
> 
> *******************************************************************************************
> Johan Lindberg
> Royal Institute of Technology
> AlbaNova University Center
> Stockholm Center for Physics, Astronomy and Biotechnology
> Department of Molecular Biotechnology
> 106 91 Stockholm, Sweden
> 
> Phone (office): +46 8 553 783 45
> Fax: + 46 8 553 784 81
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