[BioC] Visualise KEGG pathway and highlight genes

[Georg Otto]

Hi Daniel,

Daniel Brewer <daniel.brewer at icr.ac.uk>
writes:

>
>>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. 

if a non-bioconductor solution is ok for you, you should have a look at
pathvisio or genmapp. These programs are able to visualize expression
data in a pathway context. Some pathways KEGG pathways can directly be
used from wikipathways, others you have to convert yourself.

http://www.pathvisio.org/Main_Page

http://www.genmapp.org/


Hope that helps,

Georg