[BioC] plotting multiple genes on a genome
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?
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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