[BioC] Visualise KEGG pathway and highlight genes

Marc Carlson mcarlson at fhcrc.org
Thu Apr 16 18:32:36 CEST 2009

Daniel Brewer wrote:
> Hello,
> >From a couple of interesting gene lists I have found KEGG pathways which
> contain genes from both lists.  Does anyone know how to visualise this?
>  I was thinking something along the lines of the KEGG pathway being
> plotted and the genes from the two lists highlighted in different colours.
> I can cope with this not being done in bioconductor but would prefer it
> if the final image was exported as PDF.  I have searched around without
> much luck ... it seems possible that KEGGgraph maybe able to do it but
> it is not clear from vignette.
> Dan
Hi Daniel,

>From your post it is a little bit unclear to me exactly what you want to
happen.  KEGGgraph (which you mentioned), has a few vignettes that might
help you.  One of them is actually about plotting KEGG pathways. You can
find those here:


It also seems that you may have some plot that you want to push into PDF
format and are unsure how you might do that.  Is that right?  If so,
then you should only need to do something like this:

##turn on the pdf device to start output flowing to "myfile.pdf"

##then call plot() with the appropriate arguments.
plot(Appropriate arguments here)

##then turn off that pdf device (now that you have captured the output).

I hope this helps,


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