Hi all, I have got a 8000*200 gene expression matrix. I am clustering rows and columns with hclust. I want to plot something like generated by 'heatmap' which means an heatmap with corresponding array and gene trees. So, the fact is that the gene tree should be horizontal. With 'plot' function applied to an hclust object, the dendrogram is always vertical. But plotting the tree is really fast. To plot the gene tree horizontal, I saw that coercing the hclust object with as.dendrogram allows one to use the option horiz=TRUE in 'plot'. That's pretty true but plotting the dendrogram for 8000 genes requires then an infinity of time. I see each branch of the tree be slowly drawn one by one. Why this difference in calculation time ? And is there a way to plot a horizontal tree as quick as 'plot(hclust_object,...)' does ? best regards, tony [[alternative HTML version deleted]]

Hi Anthony just out of interest, what graphics device are you using to view the heatmap with 8000 rows and the tree with 8000 branches? I wonder because if you will spend 1 mm per row, 8000 rows are 8 metres [that's 4 centiinch and 26.2 feet in the US]. Best wishes Wolfgang Anthony Ferrari ha scritto: > Hi all, > > I have got a 8000*200 gene expression matrix. I am clustering rows and > columns with hclust. > > I want to plot something like generated by 'heatmap' which means an heatmap > with corresponding array and gene trees. So, the fact is that the gene tree > should be horizontal. > > With 'plot' function applied to an hclust object, the dendrogram is always > vertical. But plotting the tree is really fast. > > To plot the gene tree horizontal, I saw that coercing the hclust object with > as.dendrogram allows one to use the option horiz=TRUE in 'plot'. That's > pretty true but plotting the dendrogram for 8000 genes requires then an > infinity of time. I see each branch of the tree be slowly drawn one by one. > > Why this difference in calculation time ? > And is there a way to plot a horizontal tree as quick as > 'plot(hclust_object,...)' does ? > > > best regards, > > tony > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber