Summary

Bio::Graphics::Glyph::redgreen_box - The "redgreen_box" glyph

Package variables

Inherit

Bio::Graphics::Glyph::generic

Synopsis

  See Bio::Graphics::Panel and Bio::Graphics::Glyph.

Description

This glyph is similar to the graded_segments glyph except that it
generates a green->red gradient suitable for use with microarray data.
A feature score of 0 is full green; a feature score of 1.0 is full
red; intermediate scores are shades of yellow. The following options are standard among all Glyphs. See
Bio::Graphics::Glyph for a full explanation.

  Option      Description                      Default
  ------      -----------                      -------

  -fgcolor      Foreground color	       black

  -outlinecolor	Synonym for -fgcolor

  -bgcolor      Background color               turquoise

  -fillcolor    Synonym for -bgcolor

  -linewidth    Line width                     1

  -height       Height of glyph		       10

  -font         Glyph font		       gdSmallFont

  -connector    Connector type                 0 (false)

  -connector_color
                Connector color                black

  -label        Whether to draw a label	       0 (false)

  -description  Whether to draw a description  0 (false)

  -hilite       Highlight color                undef (no color)

The following glyph-specific option is recognized:

  -border       Draw a fgcolor border around   0 (false)
                the box

  -color_subparts
               Give each subpart a separate    0 (false)
               color based on its score

If the -color_subparts option is true, then the glyph will
individually coloriz each of its subparts. In addition, internal
bumping of features will be turned off. This will produce an effect
similar to graded_segments.

Methods

Methods description

None available.

Methods code

sub bgcolor {

  my $self = shift;
  $self->{force_bgcolor};

}

sub fgcolor {

  my $self = shift;
  return $self->option('border') ? $self->SUPER::fgcolor : $self->{force_bgcolor};

}

sub color_subparts {

 shift->option('color_subparts')

}

sub bump {

  my $self = shift;
  return 0 if $self->color_subparts;
  return $self->SUPER::bump;

}

sub draw {

  my $self = shift;
  my $val  = $self->feature->score;

  # we're going to force all our parts to share the same colors
  # unless otherwise requested
  my @parts = $self->parts;
  @parts    = $self if !@parts && $self->level == 0;
  unless ($self->color_subparts) {
    my @rgb   = map {int($_)} HSVtoRGB(120*(1-$val),1,255);
    my $color =  $self->panel->translate_color(@rgb);
    $_->{force_bgcolor} = $color foreach @parts;
  } else {
    foreach (@parts) {
      my $val    = $_->feature->score;
      my @rgb    = map {int($_)} HSVtoRGB(120*(1-$val),1,255);
      my $color  =  $self->panel->translate_color(@rgb);
      $_->{force_bgcolor} = $color;
    }
  }

  $self->SUPER::draw(@_);

}

sub HSVtoRGB {

($$$) {  my ($h,$s,$v)=@_;
  my ($r,$g,$b,$i,$f,$p,$q,$t);

  if( $s == 0 ) {
    ## achromatic (grey)
    return ($v,$v,$v);
  }

  $h /= 60;                       ## sector 0 to 5
  $i = int($h);
  $f = $h - $i;                   ## factorial part of h
  $p = $v * ( 1 - $s );
  $q = $v * ( 1 - $s * $f );
  $t = $v * ( 1 - $s * ( 1 - $f ) );
  
  if($i<1) {
    $r = $v;
    $g = $t;
    $b = $p;
  } elsif($i<2){
    $r = $q;
    $g = $v;
    $b = $p;
  } elsif($i<3){
    $r = $p;
    $g = $v;
    $b = $t;
  } elsif($i<4){
    $r = $p;
    $g = $q;
    $b = $v;
  } elsif($i<5){
    $r = $t;
    $g = $p;
    $b = $v;
  } else {
    $r = $v;
    $g = $p;
    $b = $q;
  }
  return ($r,$g,$b);

}

sub mMin {

        my $n=10000000000000;
        map { $n=($n>$_) ? $_ : $n } @_;
        return($n);

}

sub mMax {

        my $n=0;
        map { $n=($n<$_) ? $_ : $n } @_;
        return($n);

}

General documentation

Please report them.

Bio::Graphics::Panel,
Bio::Graphics::Glyph,
Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::cds,
Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond,
Bio::Graphics::Glyph::dna,
Bio::Graphics::Glyph::dot,
Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow,
Bio::Graphics::Glyph::generic,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments,
Bio::Graphics::Glyph::line,
Bio::Graphics::Glyph::pinsertion,
Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect,
Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::ruler_arrow,
Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2,
Bio::Graphics::Glyph::translation,
Bio::Graphics::Glyph::triangle,
Bio::DB::GFF,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
GD

Lincoln Stein <lstein@cshl.org>
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.