[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 10:15:47 UTC 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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