[BioC] plotting multiple genes on a genome

Jarek Bryk bryk at evolbio.mpg.de
Wed Oct 21 13:32:26 CEST 2009


I would like to plot a list of interesting genes (located on different 
chromosomes) on a genome. I extracted their genomic coordinates with 
biomaRt (see table below) and now I am looking for a way to send them 
all to some plotting function.

So I have a matrix like this:

                  chromosome_name start_position end_position strand band
gene1               1      295038550    295099001     1   H6
gene2               2      8660648    8693244     -1 E3.1
gene3               X       880698     929632     -1   A3
gene4               4       84109214     84109545      1 C1.1
gene5               4       35964995     35982539     -1 C1.2

and now I want to plot all these genes on a genome to have a visual 
representation of their position.

I've tried to do this with GenomeGraph, but it seems to allow only for 
extraction of all genes/transcripts etc. from a given region of a single 
chromosome, and not just from a user-supplied gene list.

Could anyone please suggest a package/way to do this?


   Jarek Bryk
   Max Planck Institute for Evolutionary Biology
   August Thienemann Str. 2 | 24306 Plön, Germany
   tel. +49 4522 763 287 | bryk at evolbio.mpg.de

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