merged_alignment documentation.

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

No package variables defined.

This glyph acts like graded_segments but the bgcolor of segments
(sub-feature) is controlled by binned scores. It also supports
semantic zooming to optimize glyph drawing for larger sequence
displays. 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)

In addition, the merged-alignment glyph recognizes the following
glyph-specific options:

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

  -max_score  Maximum value of the         Calculated
              feature's "score" attribute

  -min_score  Minimum value of the         Calculated
              feature's "score" attribute

  -bincolors  Colors assigned to bins      lightgrey powderblue cornflowerblue blue
              (in order)

  -bins       Bins to which scores are     Calculated
              assigned

  -merge_parts                             0 (false)
              Whether to simplify the 
              alignment at low magnification

  -max_gap    Do not merge across gaps     Calculated
              that exceed this threshold

If max_score and min_score are not specified, then the glyph will
calculate the local maximum and minimum scores at run time.
If the bins are not specified, they will be calculated
based on the number of colors assigned and the local
(or user-specified) minimum and maximum scores.
Calculated bins are equal in size.
User-specified bins are expressed as ranges,

  bins  = 0-50 50-70 70-90 90-100

where each range means greater than the lower number and
less than or equal to the higher number. The "merge_parts" option is used for semantic zooming.
Specifically, if features are small and dense, they
will not be displayed very well for large segments and the
color-coding will be lost. If merge-parts is set to a
true value, adjacent alignment parts will be merged until a gap
exceeding a calculated or user-specified value is encountered.
Unless specified, the maximum gap allowed for merging adjacent features is
calculated as (L/10000)*(L/500), where L = the length of the sequence
displayed in the browser. The exponentially increasing gap threshold
allows more aggressive merging of alignment features as the size of
the displayed sequence grows larger.
The score of the merged feature is calculated as a weighted average.
For example, consider two adjacent HSPs that are each 400 bp in
length and have scores of 60% and 70%. If the merge_parts option
is set to a true value, the two HSPs would be merged in the display to
a single 800 bp alignment block with an average score of 65%.
The merge_parts option is turned off by default. Sample gbrowse configuration stanzas for an alignment feature
using this glyph. The scores are assumed to be expressed
as percent identity (0-100).

 # base configuration
 [BLASTZ]
 feature      = blastz_alignment
 glyph        = merged_alignment
 bincolors    = #A0A0A0 powderblue cornflowerblue blue
 bins         = 60-70 70-80 80-90 90-100
 category     = Sequence Similarity Tracks
 height       = 6
 bump         = 1
 label        = 1
 fgcolor      = black
 key          = BLASTZ

Semantic zooming with defined maximum gap between
merged features for different zoom levels

 # if the displayed segment is >= 20000 in length,
 # use the merge_parts option to simplify the alignment
 # display
 [BLASTZ:20000]
 feature      = blastz_alignment
 merge_parts  = 1
 max_gap      = 50 # do not merge across gaps > 50 bp

 # if the displayed segment is >= 50000 in length
 [BLASTZ:50000]
 feature      = blastz_alignment
 merge_parts  = 1
 max_gap      = 500 # do not merge across gaps > 500 bp

--OR--
Semantic zooming with dynamically calculated maximum
gap

 # if the displayed segment is >= 20000 in length,
 [BLASTZ:20000]
 feature      = blastz_alignment
 merge_parts  = 1

sub draw {

  my $self = shift;

  # bail out if this isn't the right kind of feature
  # handle both das-style and Bio::SeqFeatureI style,
  # which use different names for subparts.
  my @parts = $self->parts;
  @parts    = $self if !@parts && $self->level == 0;
  return $self->SUPER::draw(@_) unless @parts;

  my $cols = $self->option('bincolors') || COLORS;
  my @cols = split /\s+/, $cols;
  my $bins = $self->option('bins');
  my @bins = $bins ? split /\s+/, $bins : $self->get_bins(\@parts, @cols);
  my %color;
  @color{@bins} = @cols;

  @parts = $self->merge_parts(@parts) if $self->option('merge_parts');

  # figure out the colors
  for my $part (@parts) {
      my ($bin) = grep { $part->in_range($_) } @bins;
    
      my $idx   = $bin ? $self->panel->translate_color($color{$bin}) 
	  : $self->panel->translate_color('white');
      $part->{partcolor} = $idx;
  }
  
  $self->{parts} =\@ parts;

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

}

sub in_range {

    my $self = shift;
    my $range = shift;
    my ($low,$high) = split '-', $range;
    my $s = $self->score || shift;
    return 1 if $s > $low && $s <= $high;
    return 0;

}

sub bgcolor {

    my $self = shift;
    return $self->{partcolor} || 'white';

}

sub get_bins {

    my $self  = shift;
    my $parts = shift;
    my $cols  = @_;
    my ($min,$max) = $self->minmax($parts);
    my $range = $max - $min;
    return ($max) if $range == 0;
    my $increment = $range/$cols;
    
    my ($score,@bins) = $min;
    until ($score >= $max) {
	my $range = "$score-";
	$score += $increment;
	$range .= $score;
	push @bins, $range;
    }
    
    return @bins;

}

sub keyglyph {

  my $self = shift;

  my $scale = 1/$self->scale;  # base pairs/pixel

  # two segments, at pixels 0->50, 60->80
  my $offset = $self->panel->offset;
  
  my $feature =
    Bio::Graphics::Feature->new(
				-segments=>[ [ 0*$scale +$offset,25*$scale+$offset],
					     [ 25*$scale +$offset,50*$scale+$offset],
					     [ 50*$scale+$offset, 75*$scale+$offset]
					   ],
				-name => $self->option('key'),
				-strand => '+1');

  my @scores = $self->example_scores;
  my @segments = $feature->segments;
  for ($feature->segments) {
      $_->score(shift @scores);
  }

  my $factory = $self->factory->clone;
  $factory->set_option(label => 1);
  $factory->set_option(bump  => 0);
  $factory->set_option(connector  => 'solid');
  my $glyph = $factory->make_glyph(0,$feature);

}

sub example_scores {

    my $self = shift;
    my $bins = $self->option('bins');

    if ($bins) {
	my @bins = split /\s+/, $bins;
	$bins[0] =~ s/(\S+)\-\S+/$1/;
	$bins[-1] =~ s/\S+\-(\S+)/$1/;
	my $mid  = $bins[0] + ($bins[-1] - $bins[0])/2;
    
	return ($bins[0], $mid, $bins[-1]);
    }
    if ($self->option('min_score') || $self->option('max_score')) {
	my ($min,$max) = $self->minmax;
	my $mid  = $min + ($max - $min)/2;
	return($min,$mid,$max);
    }
    
    return (0,50,100);

}

General documentation

Sheldon McKay <mckays@cshl.edu>
Copyright (c) 2005 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.

draw	No description	Code
in_range	No description	Code
bgcolor	No description	Code
get_bins	No description	Code
keyglyph	No description	Code
example_scores	No description	Code