[BioC] Outputting dendrogram with large numbers of genes without losing resolution

[Marie Chehani Alles]

Dear Listserv,

I’m attempting to do heatmaps on large lists of genes (often well over 500 genes in each list) using heatmap.2(). Does anyone know how to output a large heatmap without losing resolution in the dendrogram? When a large list of genes is clustered (with genes on the horizontal axis), the horizontal dendrogram is often squashed so that the lines become indistinct, even when the plot area is set to its maximum. 

I am wondering if there is some way of setting up the R graphics so that I can assign a fixed width to each arm of the dendrogram... say a height of x pixels per gene? Or does anyone know of any other work-arounds for this issue? This must be a common problem so maybe I'm googling the wrong words!

Please let me know if this is an issue for the R-listserv rather than Bioconductor.

Thanks,
Che

Marie Alles
Cancer Research Program
Garvan Institute of Medical Research
384 Victoria Street, Darlinghust, Sydney, NSW 2010, AUSTRALIA