[Bioperl-l] background layer is not supported in Bioperl 1.6 for Bio::Graphics::Glyph
Xianjun Dong
Xianjun.Dong at bccs.uib.no
Sat Jun 13 08:05:53 EDT 2009
Hi, Scott
Thanks for your reply first.
I still have question: I dig out the code from GBrowse (which I paste
below). Method make_postgrid_callback gets all highlight region and then
use hilite_regions_closure function to draw them out, using the
following GD function:
$gd->filledRectangle($left+$start,0,$left+$end,$bottom,
$panel->translate_color($h_color));
where the $bottom=$panel->bottom. This is the only difference from my
code, where I use $gd->height. I guess they are almost same (except the
pad_bottom), we can see this in the code of
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html#CODE22
OK. Anyway, I change to use $panel->bottom, instead of $gd->height, for
my highlight regions. The output is same, when using the library of
Bioperl 1.6 (or 1.5). You can see the attached image ("test.bioperl1.6.png")
OK. I might have not explained my question explicitly. My question is:
if using bioperl 1.2.3 (actually the Bio::Graphics in bioperl 1.2.3), I
can get the right image I want (see the attached file
"test.bioperl1.2.3.png"), where the highlight range will go from the
roof to the floor. While in bioperl 1.5 (or 1.6), I only can see the
highlight region in its own track, not the whole panel. OK, did I
explain clearly now? you can see the difference of the two images.
[I am not sure the mailist allow to attach image, otherwise, I put them
in the following links:
test.bioperl1.6.png: http://translog.genereg.net/test.bioperl1.6.png
test.bioperl1.2.3.png:
http://translog.genereg.net/test.bioperl1.2.3.png ]
You can test it and see the difference if you have both 1.2.3 and 1.6 on
your computer?
Really want to know how this works in bioperl 1.2.3 (Even though this
might be a bug at that version, or whatever)
Thanks
Xianjun
=============================================
# this generates the callback for highlighting a region
sub make_postgrid_callback {
my $settings = shift;
return unless ref $settings->{h_region};
my @h_regions = map {
my ($h_ref,$h_start,$h_end,$h_color) =
/^(.+):(\d+)\.\.(\d+)(?:@(\S+))?/;
defined($h_ref) && $h_ref eq $settings->{ref}
? [$h_start,$h_end,$h_color||'lightgrey']
: ()
}
@{$settings->{h_region}};
return unless @h_regions;
return hilite_regions_closure(@h_regions);
}
# this subroutine generates a Bio::Graphics::Panel callback closure
# suitable for hilighting a region of a panel.
# The args are a list of [start,end,color]
sub hilite_regions_closure {
my @h_regions = @_;
return sub {
my $gd = shift;
my $panel = shift;
my $left = $panel->pad_left;
my $top = $panel->top;
my $bottom = $panel->bottom;
for my $r (@h_regions) {
my ($h_start,$h_end,$h_color) = @$r;
my ($start,$end) = $panel->location2pixel($h_start,$h_end);
if ($end-$start <= 1) { $end++; $start-- } # so that we always see
something
# assuming top is 0 so as to ignore top padding
$gd->filledRectangle($left+$start,0,$left+$end,$bottom,
$panel->translate_color($h_color));
}
};
}
Scott Cain wrote:
> Hello Xianjun,
>
> I don't think that approach will work. What you almost certainly need
> to do is a postgrid callback that does the drawing of the highlighted
> region. For example code of how to do this, take a look at the
> make_postgrid_callback subroutine in GBrowse 1.69. The option
> -postgrid is a method of Bio::Graphics::Panel.
>
> Scott
>
>
>
>
> On Fri, Jun 12, 2009 at 4:38 PM, Xianjun Dong<Xianjun.Dong at bccs.uib.no> wrote:
>
>> 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
>> ==========================================
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
>
>
>
--
==========================================
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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