Entering edit mode
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.
HTH.
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