Sorry, I noticed that I had the wrong name on the matrix :( Here comes the correct version. 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(Matrix[,],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(Matrix[,],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 At 14:29 2004-01-02 +0100, you wrote: >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: Roslagsv?gen 30B >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@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: Roslagsv?gen 30B > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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: Roslagsv?gen 30B