[Bioperl-l] Please help with Bio::Graphics
Lucas Quincy Ton
lton at nd.edu
Mon Feb 3 17:53:38 EST 2003
Dear all,
I have recently started using the Bio::Graphics module to render a png
picture from an embl-formatted file. Everything so far looks fine but when I
coded the 'dna' glyph to render GC-content plot, I get the plot but with just
a straight line in the middle (50%) from lelf to right. Would someone please
gear me to the right direction? My code is as follow:
#I create a SeqFeature::Generic object
my $gcfeature = Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length,);
#here I attach the whole DNA sequence referenced by $seq to the feature
#I do this because I read perldoc on dna.pm which specified that "the feature
#must return a DNA sequence string in response to the dna() method -- so I
made
#my best guess as to its meaning
$gcfeature->attach_seq($seq);
#now I create a track for GC content
$panel->add_track($gcfeature,
-glyph => 'dna',
-fgcolor => 'black',
-height => 100,
-bgcolor => 'red',
-do_gc => 'true',
-gc_bins => 10,
-axis_color=> 'blue',
-strand => 'forward',);
Any response will be greatly appreciated.
Lucas Ton.
More information about the Bioperl-l
mailing list