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Old 03-23-2014, 02:15 PM   #55
bigmw
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Location: US

Join Date: Aug 2013
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Forgot that sigGeneSet function has been updated to give users more control on the margin and font size. sigGeneSet calls a internal function heatmap2 to generate the heatmaps. So check the argument for this function
args(gage:::heatmap2)
The argument two relevant arguments here are margins and cexRow, which control the margins for column/row names and row name font size, you may do something like:
kegg.sig<-sigGeneSet(cnts.kegg.p,outname="~/RNAseq/13_Acute-Changes/14_GAGE_native_A1A2/A1A2All/A1A2All.kegg",pdf.size = c(7,12), margins = c(5,10))


Quote:
Originally Posted by sindrle View Post
Another question... How to alter the heatmaps text-part size (KEGG pathway names)?
The names are all capped, its unreadable.. The "pdf.size" - option only regualtes the graphic part.

###################################################
### significant.genesets
###################################################
kegg.sig<-sigGeneSet(cnts.kegg.p, outname="~/RNAseq/13_Acute-Changes/14_GAGE_native_A1A2/A1A2All/A1A2All.kegg",pdf.size = c(7,12))
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