[BioC] Plotting trees - hclust object vs dendrogram

[Wolfgang Huber]

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]]
> 
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber