[Bioperl-l] Using Bioperl Graphics to create a heat map of sequence hits

[Scott Cain]

Hi,

You should be able to do that with wiggle_density and wiggle_xyplot  
glyphs.  See

   http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks

for instructions on constructing wiggle plots.  After you have a  
wiggle plot, you'll need the wiggle2gff3.pl script (which is part of  
GBrowse, but it will should run fine on its own), which you can get  
from GMOD's cvs:

   http://gmod.cvs.sourceforge.net/viewvc/*checkout*/gmod/Generic-Genome-Browser/bin/wiggle2gff3.pl

which will convert the wig file to a binary file.  Then you can create  
Bio::SeqFeatureI objects that will work with Bio::Graphics to draw the  
density or xyplot.  Note as well that Bio::Graphics is no longer part  
of the main BioPerl distribution, so you'll need to get the most  
recent version from CPAN.

Also, fair warning: I've never actually done this; I've only used  
wiggle plots in the context of GBrowse, but it should work pretty much  
as described.

Scott

On Aug 10, 2009, at 2:54 PM, OjoLoco wrote:

>
> Hello all,
>   I have found matching sequences between two genomes and I would  
> now like
> to create a graphic that contains a heat map-like track that will  
> show areas
> of the genome that were found more often than others.  For every nt  
> I have
> the number of times it was found, so if it was found very often it  
> would be
> a darker color than say a nt that wasn't found at all.  Is there any  
> way to
> achieve this using built in BioPerl graphics? Thank you for your time.
> -- 
> View this message in context: http://www.nabble.com/Using-Bioperl-Graphics-to-create-a-heat-map-of-sequence-hits-tp24905417p24905417.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research