[BioC] GAGE heatmap pdf question...

Luo Weijun luo_weijun at yahoo.com
Wed Mar 21 03:09:37 CET 2012

Hi Alan,
The sample names (columns) and KEGG pathway names (rows) are actually not clipped, except that they extend beyond the visible area. You may open your PDF file in Adobe Illustrator, and you can see and edit the heatmaps for better effects. 
The relevant function called here is gs.heatmap, which further calls heatmap2. Both of these functions are internal functions, and have been optimized for the common cases and are not intended to be changed. If you have really long sample names, you may try to make them shorter. If you really want to adjust the margins through these functions, you need to change the values of argument "margins" where heatmap2 is called within gs.heatmap. For details, type in gage:::gs.heatmap . I would suggest to make copies of these functions first then you make these changes on your own copies.
Weijun Luo

> (Sorry if this is a duplicate message. It looks like the original send
> of this message didn't go through. Anyway....)
> Is there a way to adjust the borders of the heatmap output by the
> sigGeneSet function in the gage package? When I run my data (3 treated
> samples against 3 controls) using kegg.gs, I get very few significant
> hits, so when the heatmap file is generated, most of both the sample
> names (along the bottom) and the KEGG pathway names (along the right
> side) are clipped off... Is there some way to effectively "zoom out"
> so that more of the annotations are visible?
> Thanks,
> Alan

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