[BioC] Heatmap

[Johan Lindberg]

Ok, sorry, I guess I have to take it from the beginning :)
I have a matrix of M-values that I want to visualize with the heatmap function.
Since I get the best cophenetic correlation between my slides (my columns 
in the matrix) with euclidean distance and average linkage I want to use 
that in my plot.

#########This works:
#The distance between the columns.
sampdist <- dist(t(matrix[,]), method="euclidean")
sclus <- hclust(sampdist, method="complete")
#The distance between the rows.
genedist <- dist(Matrix[,], method="euclidean")
gclus <- hclust(genedist, method="complete")
heatmap(MatrixwithoutentirerowofNA[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus))

#########But this does not work???
sampdist <- dist(t(matrix[,]), method="euclidean")
sclus <- hclust(sampdist, method="average")
#The distance between the rows.
genedist <- dist(Matrix[,], method="euclidean")
gclus <- hclust(genedist, method="average")
heatmap(MatrixwithoutentirerowofNA[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus))
Error in match.fun(FUN) : evaluation is nested too deeply: infinite recursion?
Error: evaluation is nested too deeply: infinite recursion?

#But this works??
plot(glus) #from gclus <- hclust(genedist, method="average")
plot(sclus) #from sclus <- hclust(sampdist, method="average")
#Obviously I can plot the dendograms seperately but not together in a Heatmap.

What am I doing wrong? Once again, I really appreciate any help I can get.

/ Johan


1CC2:30 2004-01-02 +0100, you wrote:
>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
> > Visiting adress: Roslagstullsbacken 21, Floor 3
> > Delivery adress: Roslagsvägen 30B
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

*******************************************************************************************
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
Visiting adress: Roslagstullsbacken 21, Floor 3
Delivery adress: Roslagsvägen 30B