[BioC] Problems with heatmap on genes...

jeffrey rasmussen rasmuss at u.washington.edu
Tue Nov 9 18:14:23 CET 2004

Hi Giulio,

If you have access to Adobe Illustrator, you could write your heatmap to a 
postscript file using postscript() and then open and edit the file in 
Illustrator. I've found that in many cases this is much easier than 
wrangling with the plotting parameters in R, in particular when it comes 
to fonts. Otherwise, trying to display > 50 genes on a heatmap becomes 
prohibitively difficult.


On Tue, 9 Nov 2004, Giulio Di Giovanni wrote:

> Hi,
> I'm trying to have a clear figure of gene clusters using heatmaps, but with 
> more than 100-200 genes it's not possible to do it, with default options (and 
> I would like to do that with 1500 genes or so...). Gene names (and branchs 
> too) collapse together...
> I tried, setting new device dimensions (jpeg() or png() height and width), 
> and modifying par() options (fin, etc..), to have long cluster figures (to be 
> clear, dChip style). Well, it works for others high-level graphical 
> functions, but it doesn't work for heatmaps().  I always obtain big figures, 
> but with exactely the same squared heatmap inside.
> I spent long time on the documentation and searching the web, and when I 
> found something, it was always some heatmaps for 50-100 genes at max
> I trust that someone working on gene clustering is confidential on this,
> and I will appreciate a lot any suggestion... I almost became crazy on that 
> !!!
> Thanks in advance,
> Giulio
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