[Bioperl-l] background layer is not supported in Bioperl 1.6 for Bio::Graphics::Glyph
Xianjun Dong
Xianjun.Dong at bccs.uib.no
Thu Jun 18 06:15:47 EDT 2009
Hi, Scott,
Do you mind to have a look of the code (below my signature) if I use the
-postgrid callback correctly?
I still cannnot get the background for the whole panel.
Thanks
Xianjun
Xianjun Dong wrote:
> Hi, Scott
>
> Before I gave up my own whole solution to use GBrowse, I still want to
> bother you once:
>
> As you suggested, I put -postgrid option when the panel, which will
> call a function to draw the background. The code below is almost
> copied from the online POD of Bio::Graphics::Panel (see
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html
> )
>
> But it still does not work. Could you help to have a look? I paste it
> below. (BTW, the above page of POD, the -postgrid=>\&draw_gap, while
> the gap drawing function is gap_it, not draw_gap. I guess it's a typo.
> or not?)
>
> THanks
>
> Xianjun
>
> ----------------------------------------------- mytestcode.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
> -postgrid=>\&gap_it);
>
> sub gap_it {
> my $gd = shift;
> my $panel = shift;
> my ($gap_start,$gap_end) = $panel->location2pixel(500,600);
> my $top = $panel->top;
> my $bottom = $gd->height, #panel->bottom;
> my $gray = $panel->translate_color('red');
> $gd->filledRectangle($gap_start,$top,$gap_end,$bottom,$gray);
> }
> # 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();
>
>
>
>
>
>
>
>
>
>
> Scott Cain wrote:
>> Hi Xianjun,
>>
>> I understand what you want to do, as the current version of gbrowse
>> does this, which uses bioperl 1.6. Without digging through the code,
>> I can't tell you exactly how this works and you didn't send your code
>> that uses this callback, so I can't try it either.
>>
>> One thing that is different between your code and gbrowse is that each
>> of the tracks is actually a seperate panel (to allow track dragging),
>> so it possible that this sort of callback doesn't work for
>> Bio::Graphics any more.
>>
>> Scott
>>
>> On Saturday, June 13, 2009, Xianjun Dong <Xianjun.Dong at bccs.uib.no>
>> wrote:
>>
>>> 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
>>> ==========================================
>>>
>>>
>>>
>>
>>
>
--
==========================================
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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