[BioC] Visualise KEGG pathway and highlight genes

Saroj K Mohapatra smohapat at vbi.vt.edu
Thu Apr 16 17:13:08 CEST 2009


Hi Daniel:

This is also something in which I am interested, but have not found an easy way yet. 

If KEGG allows the network images to be downloaded in SVG format (currently I found only GIF), then I think there is a way of manually modifying the color of the nodes.

Within the KEGGSOAP package, there is a function called "mark.pathway.by.objects" 

Client-side interface to obtain an url for a KEGG pathway diagram with a given set of genes marked
Description
    Given a KEGG pathway id and a set of KEGG gene ids, the functions return the URL of a KEGG
    pathway diagram with the elements corresponding to the genes marked by red or specified color

I used the example code given there in:
---------------------------------------------------
url <- mark.pathway.by.objects("path:eco00260",
                c("eco:b0002", "eco:c00263"))
if(interactive()){
     browseURL(url)
}
url <- color.pathway.by.objects("path:eco00260",
                c("eco:b0002", "eco:c00263"),
                c("#ff0000", "#00ff00"), c("#ffff00"
---------------------------------------------------
And it creates an image at http://soap.genome.jp/tmp/mark_pathway_www2_api14063/eco00260.gif with the nodes marked.

Best wishes,

Saroj

----- Original Message -----
From: "Daniel Brewer" <daniel.brewer at icr.ac.uk>
To: "Bioconductor mailing list" <bioconductor at stat.math.ethz.ch>
Sent: Thursday, April 16, 2009 6:50:44 AM GMT -05:00 US/Canada Eastern
Subject: [BioC] Visualise KEGG pathway and highlight genes

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

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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