Bioperl newbie - Bio::Graphics::Glyph::xyplot

daverave has asked for the wisdom of the Perl Monks concerning the following question:

Hello dear monks,

I am new to bioperl and seek your assistance, as I have spent the lat hour reading heavy documentatiion and could not find examples that will help me start off.

I wish to create a plot where the X axis will be some genome (I will give Genbank file, I want genes to be displayed below the X axis), and the Y axis will represent some score. I have generated files containing for evey position in the genbank a numeric score, and I want to plot these data.

from what I can tell, this sounds like a work for Bio::Graphics::Glyph::xyplot, but I could not find a descent start point, for example how to get from a Genbank file + a file containing a numeric value fo each nucleotide in the genbank to a plot.

There are so many structures and sub-structures I could not find my hands... So, how do I get started? I guess it should not be so complicated.

Thank you !

Comment on Bioperl newbie - Bio::Graphics::Glyph::xyplot

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Re: Bioperl newbie - Bio::Graphics::Glyph::xyplot by Khen1950fx (Canon) on Jun 28, 2010 at 01:01 UTC
A good place to start would be GBrowse. You could use the glyph options to get a better idea of what's going on. For questions, just refer to the GMOD wiki. Read through the info there, play with it, then try Bio::Graphics::Glyph::xyplot. There's also the documentation on doc.bioperl.org.	[reply]
Re^2: Bioperl newbie - Bio::Graphics::Glyph::xyplot by daverave (Scribe) on Jun 28, 2010 at 05:56 UTC
Thanks, I've done some reading on GBrowse. Doesn't it require runing an apache server etc.? I just want it for local use.	[reply]
Re^3: Bioperl newbie - Bio::Graphics::Glyph::xyplot by Khen1950fx (Canon) on Jun 28, 2010 at 08:31 UTC
Yes. It requires an Apache server. If you can't use Apache, then use this to get going. I pulled it from the docs. #!/usr/bin/perl use strict; use warnings; use Bio::DB::GFF; use Bio::Graphics::Panel; use Bio::DB::GFF::Aggregator; use Bio::Graphics::Glyph::xyplot; my $agg = Bio::DB::GFF::Aggregator->new(-method => 'repeat_density', - +sub_parts => 'density:repeat'); my $db = Bio::DB::GFF->new(-dsn => 'mydatabase', -aggregators => $agg); my $segment = $db->segment('Chr1'); my $features = $segment->features('repeat_density'); my $panel = Bio::Graphics::Panel::->new(-pad_left=>40,-pad_right=>40); $panel->add_track($features, -glyph => 'xyplot', -graph_type => 'points', -point_symbol => 'disc', -point_radius => 4, -scale => 'both', -height => 200, ); [download]	[reply] [d/l]