[Bioperl-l] using graphics xyplot
Shawn Hoon
shawnh at stanford.edu
Mon Dec 15 22:35:00 EST 2003
hi,
I'm trying to use the SVG/PNG component for drawing xyplots along a
segment. Its not clear to me how to do it
without going through a Bio::DB::GFF::Aggregator. If I just have a
bunch of scores (i.e. features) that I want plot along a segment of
dna.
Something like this doesn't seem to be possible since there is a call
to $feat->parts in xyplot.pm :
my $panel = Bio::Graphics::Panel->new(-length => 1000,
-key_style => 'between',
-width => 800,
-pad_left => 10,
-pad_right => 10,
-image_class=>'GD::SVG'
);
$panel->add_track(arrow =>
Bio::SeqFeature::Generic->new(-start=>1,-end=>1000),
my $feat = Bio::SeqFeature::Generic->new();
while($i < 1000){
my $f= Bio::SeqFeature::Generic->new(-start=>$i,
-end=>$i+50,
-strand=>1,
-score=>int(rand(100)));
$feat->add_sub_SeqFeature($f,'EXPAND');
$i+=50;
}
$panel->add_track($feat,
-graph_type=>'line',
-bump=>0,
-glyph =>'xyplot');
my $gd = $panel->gd;
print $gd->svg;
am I trying to use it wrongly?
thanks,
shawn
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