in reply to Bioperl newbie - Bio::Graphics::Glyph::xyplot

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.
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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]
      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,
);

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