[Bioperl-l] Bio::Graphics - Howto Show Negative Start-End and Enable Connector

[Siddhartha Basu]

Hi,

Wijaya Edward wrote:
> Dear expert,
> 
> My figure here: http://defiant.i2r.a-star.edu.sg/~ewijaya/misc/foo2.png <http://defiant.i2r.a-star.edu.sg/%7Eewijaya/misc/foo2.png> 
> is created with the script (down below).
> 
> How can I modify the script such that:
> 
> 1. The arrow track is represented in negative form.
>    I.e. instead of 1 to 300, we use -300 to 0.
> 
> I tried this, but won't do:
> 
> my $flen = Bio::SeqFeature::Generic->new(
>        -start => -300,
>        -end => 0, );

It works if you pass the 'SeqFeature' object to the '-segment' option of 
  "Bio::Graphics::Panel".

  my $panel = Bio::Graphics::Panel->new(
    -length    => 300,
   -width     => 500,
   -pad_left  => 70,
   -pad_right => 70,
    -key_style => 'left',
   -connector => 'solid',
      -segment => $flen,
);

For more, read one of the previous posting,
http://article.gmane.org/gmane.comp.lang.perl.bio.general/1721/match=negative+seqfeature

-siddhartha

> 
> And how can I make these number to appear
> for every gridpoints (not just two as I have now).
> 
> 
> 2. How can I enable the connector with grid just like
>   I had in the first panel? (as you can see, my script
>   has connector added, but still doesn't show).
> 
> All, in all, I am trying to mimic this figure:
> http://nar.oxfordjournals.org/content/vol31/issue13/images/large/gkg56702.jpeg <http://nar.oxfordjournals.org/content/vol31/issue13/images/large/gkg56702.jpeg> 
> 
> And here is my script:
> 
> __BEGIN__
> #!/usr/bin/perl -w
> use strict;
> use Data::Dumper;
> use Bio::Graphics;
> use Bio::SeqFeature::Generic;
> use List::Compare;
> use List::Util qw(max);
> 
> my %nofseq = ( 0 => 300, 1 => 300, 2 => 300, 3 => 300, 4 => 300, 5 => 300 );
> my @seqid = keys %nofseq;
> my @lenlist = values %nofseq;
> my $maxlen = max (@lenlist);
> #print Dumper \@seqid ;
> 
> my $panel = Bio::Graphics::Panel->new(
>    -length    => 300,
>    -width     => 500,
>    -pad_left  => 70,
>    -pad_right => 70,
>    -key_style => 'left',
>    -connector => 'solid',
> );
> 
> my $flen = Bio::SeqFeature::Generic->new(
>        -start => 1,   # tried -300
>        -end => 300, # and 0, but failed.
> );
> 
>    my $track1 = $panel->add_track(
>        $flen,
>        -glyph   => 'arrow',
>        -tick    => 2,
>        -fgcolor => 'black',
>        -double  => 1,
>    );
> 
> 
> 
> my %nlist;
> 
> while ( <DATA> ) {
>    chomp;
>    next if /^\#/;
>    my ($sqi,$pos,$str,$progname) = split /\,/;
>    my $start = $pos + $nofseq{$sqi};
>    my $end = $start + length($str) + 1;
>    push @{$nlist{$sqi}}, $start." ".$end." ".$progname;
> }
> 
> # Check which sequence has no motifs;
> my @bssi = keys %nlist;
> 
> my $lc = List::Compare->new(\@seqid, \@bssi);
> my @comp = $lc->get_unique;
> 
> 
> foreach my $comp ( @comp  ) {
>    push @{$nlist{$comp}}, '0'." ".'0'." "."NONE";
> 
> }
> 
> my %prog_color = ( "WEEDER" => 3000, "MEME" => 200, "NONE" => 0 );
> 
> foreach my $seqid ( sort keys %nlist ) {
> 
> 
>    my $track = $panel->add_track(
>        -glyph     => 'graded_segments',
>        -key       => "SEQ ". $seqid,
>        -connector => "dashed"
>        -label     => 1,
>        -bgcolor   => 'blue',
>                -bump      =>  +1,
>                -height    =>  8,
>        -min_score => 0,
>        -max_score => 5000
>    );
> 
> 
>    foreach my $range ( @{$nlist{$seqid}} ) {
> 
>        my ($st,$en,$progname) = split(" ", $range);
>        my $dname = " ";
>        if ( $st != 0 and $en !=0  ) {
>           $dname = "Seq ". $seqid;
>        }
> 
>        my $score;
>        if ( $progname eq "WEEDER" ) {
>            $score = $prog_color{$progname};
> 
>        }
>        elsif ($progname eq "MEME" ) {
>            $score = $prog_color{$progname};
>        }
> 
>        my $feature = Bio::SeqFeature::Generic->new(
>            -display_name => $dname,
>            -start        => $st,
>            -end          => $en,
>            -score        => $score
>        );
> 
>        $track->add_feature($feature);
> 
>    }
> 
> }
> 
> print $panel->png;
> 
> #The DATA is simply just list of string and its location in their
> respective sequence.
> # The figure is just the plot of it out.
> __DATA__
> # sequence number,pos,binding sites,program
> 4,-63,AGCTTTCTCT,MEME
> 0,-22,AACTTTGTAC,WEEDER
> 1,-13,AAGTTTCTCT,WEEDER
> 5,-228,ACCTTTGCCA,MEME
> 5,-121,AAGTTTGTCT,WEEDER
> 5,-88,AAGTTTTTCC,SPACE
> 3,-148,AACTTAGTCA,MEME
> 0,-184,AACTTTGTCT,MEME
> __END__
> 
> 
> Thanks and hope to hear from you again.
> 
> --
> Regards,
> 
> Edward WIJAYA
> 
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