[Bioperl-l] background layer is not supported in Bioperl 1.6 for Bio::Graphics::Glyph
Xianjun Dong
Xianjun.Dong at bccs.uib.no
Fri Jun 12 20:38:50 UTC 2009
HI,
I am not sure this is the right place I can get help.
I've suffered by a problem for several days: I want to highlight parts
of regions in my track, using a different background color. To do that,
I defined a glyph named "background", based on the
'Bio::Graphics::Glyph::generic' module. I override the draw_component()
method, by adding code like below:
$gd->filledRectangle($left,0,$right,$gd->height,
$self->factory->translate_color($color));
# the script is pasted at the end
This will draw a rectangle with top=0, bottom=$gd->height. I made the
highlight regions into a list of features, and add_track with
-glyph=>'background'. (see the following script, test.pl) This really
works as I expect, which will add a colored block at background of all
tracks in a panel (including the ruler arrow). You can see the output
image in attached file "test.bioperl1.2.3.png"
Now, the problem comes: when I switch to Bioperl 1.5 (or 1.6), it does
not work. Well, it works, but the highlight part only shrink to a low
height, instead of covering all tracks in the panel. I also attached the
output here, see the file "test.bioperl1.6.png".
I tried to think about the reason, the 'background' module is based on
the generic module. What can cause the difference? Is it because
$gd->height is different, or the tracks followed with 'background' track
can not draw from the first position?
Well. I can stick to use Bioperl 1.2.3 to avoid the problem. ("Smart
person solve problem, wise person avoid problem"...) But another problem
is coming: Bio::Graphics in Bioperl 1.2.3 does not support
$panel->create_web_map() function, which means I have to use some higher
version if I want to create web map for my graphics, but then I have to
give up using highlight background.
OK. It's long enough for my first-time submission here. Hope someone can
throw me some clue.
Thanks ahead!!
Xianjun
==================== test.pl =======================
#!/usr/bin/perl
use strict;
use lib "$ENV{HOME}/lib";
use Bio::Graphics;
use Bio::Graphics::Feature;
my $ftr= 'Bio::Graphics::Feature';
# processed_transcript
my $trans1 =
$ftr->new(-start=>50,-end=>10,-name=>'ZK154.1',-type=>"3'-UTR");
my $trans2 = $ftr->new(-start=>100,-end=>50,-name=>'ZK154.2',-type=>'CDS');
my $trans3 =
$ftr->new(-start=>350,-end=>225,-name=>'ZK154.3',-type=>'CDS',
-source=>'a');
my $trans4 =
$ftr->new(-start=>650,-end=>500,-name=>'ZK154.3',-type=>'CDS',
-source=>'a');
my $trans5 =
$ftr->new(-start=>700,-end=>650,-name=>'ZK154.3',-type=>"5'-UTR");
my $trans =
$ftr->new(-segments=>[$trans1,$trans2,$trans3,$trans4,$trans5]);
# hightlight
my $trans31 =
$ftr->new(-start=>240,-end=>450,-name=>'hightlight1',-type=>'background',
-source=>'a');
my $trans41 =
$ftr->new(-start=>650,-end=>600,-name=>'hightlight2',-type=>'multihourglass',
-source=>'b');
my $panel= Bio::Graphics::Panel->new(-width=>1200,
-length=>1050,
-start =>0,
-pad_left=>12,
-pad_right=>12);
# the following track works as I expected in bioperl 1.2.3, but not in
1.5 and 1.6
$panel->add_track([$trans41,$trans31],
-glyph => 'background',
-block_bgcolor => sub{return (shift->source eq
'a')?'#cccccc':'#fffc22'},
);
$panel->add_track($ftr->new(-start=>100,-end=>1000),
-glyph=>'arrow',
-double=>1,
-tick=>2);
$panel->add_track($trans,
-glyph => 'transcript2', # 'transcript2', #process_5utr',
-fgcolor => 'darkred',
-bgcolor => 'darkred',
-title => '$source',
-link =>
'http://www.ensembl.org/Homo_sapiens/transview?transcript=$name', #EnsEMBL
);
print $panel->png;
# the following part works in bioperl 1.5 and 1.6, but not work in
Bioperl 1.2.3
my $map = $panel->create_web_map("image");
$panel->finished();
1;
==================== background.pm =======================
package Bio::Graphics::Glyph::background;
use strict;
use base 'Bio::Graphics::Glyph::generic';
sub pad_top{
return 0;
}
sub draw_component {
my $self = shift;
#$self->SUPER::draw_component(@_);
my ($gd,$dx,$dy) = @_;
my ($left,$top,$right,$bottom) = $self->bounds($dx,$dy);
# draw an arrow to indicate the direction of transcript
my $color = $self->option('block_bgcolor') || '#cccccc';
$gd->filledRectangle($left,0,$right,$gd->height,
$self->factory->translate_color($color));
}
1;
--
==========================================
Xianjun Dong
PhD student, Lenhard group
Computational Biology Unit
Bergen Center for Computational Science
University of Bergen
Hoyteknologisenteret, Thormohlensgate 55
N-5008 Bergen, Norway
E-mail: xianjun.dong at bccs.uib.no
Tel.: +47 555 84022
Fax : +47 555 84295
==========================================
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