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

[Sean Davis]

Marie Chehani Alles wrote:
> 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.

Unfortunately, screen size is limited.  If you really must use R for
this task, then try making a large pdf or png of the same plot (say 35
inches high by 10 inches wide).  Then, you can use an external program
to view the resulting file.

The better alternative is to use a program such as TreeView (and,
potentially its close relative "cluster") to interact with such large
heatmaps.  It is available for free and is a java program, so it works
on many platforms.

Sean