Ewan Birney

NAME

Bio::Graphics::Panel - Generate GD images of Bio::Seq objects

SYNOPSIS

  use Bio::Graphics;
  use Bio::DB::BioFetch;  # or some other Bio::SeqI generator

  # get a Bio::SeqI object somehow
  my $bf     = Bio::DB::BioFetch->new;
  my $cosmid = $bf->getSeq_by_id('CEF58D5');

  my @features = $seq->all_SeqFeatures;
  my @CDS      = grep {$_->primary_tag eq 'CDS'}  @features;
  my @gene     = grep {$_->primary_tag eq 'gene'} @features;
  my @tRNAs    = grep {$_->primary_tag eq 'tRNA'} @features;

  # let the drawing begin...
  my $panel = Bio::Graphics::Panel->new(
                                      -segment => $cosmid,
                                      -width  => 800
                                     );

  $panel->add_track(arrow => $cosmid,
                   -bump => 0,
                   -double=>1,
                   -tick => 2);

  $panel->add_track(transcript  => \@gene,
                   -bgcolor    =>  'blue',
                   -fgcolor    =>  'black',
                   -key        => 'Genes',
                   -bump       =>  +1,
                   -height     =>  10,
                   -label      => 1,
                   -description=> 1
                 ) ;

  $panel->add_track(transcript2  => \@CDS,
                    -bgcolor    =>  'cyan',
                    -fgcolor    =>  'black',
                    -key        => 'CDS',
                    -bump       =>  +1,
                    -height     =>  10,
                    -label      => \&cds_label,
                    -description=> \&cds_description,
                 );

  $panel->add_track(generic    => \@tRNAs,
                    -bgcolor   =>  'red',
                    -fgcolor   =>  'black',
                    -key       => 'tRNAs',
                    -bump      =>  +1,
                    -height    =>  8,
                    -label      => 1,
                   );

  my $gd = $panel->gd;
  print $gd->can('png') ? $gd->png : $gd->gif;

  # these are callbacks used to generate nice labels and descriptions for
  # the features...
  sub cds_label {
    my $feature = shift;
    my @notes;
    foreach (qw(product gene)) {
      next unless $feature->has_tag($_);
      @notes = $feature->each_tag_value($_);
      last;
    }
    $notes[0];
  }

  sub cds_description {
    my $feature = shift;
    my @notes = $feature->each_tag_value('notes')
                if $feature->has_tag('notes');
    return unless @notes;
    substr($notes[0],30) = '...' if length $notes[0] > 30;
    $notes[0];
  }

DESCRIPTION

The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, physical (contig) maps, or any other type of map in which a set of discrete ranges need to be laid out on the number line.

The module supports a drawing style in which each type of feature occupies a discrete "track" that spans the width of the display. Each track will have its own distinctive "glyph", a configurable graphical representation of the feature.

The module also supports a more flexible style in which several different feature types and their associated glyphs can occupy the same track. The choice of glyph is under run-time control.

Semantic zooming (for instance, changing the type of glyph depending on the density of features) is supported by a callback system for configuration variables. The module has built-in support for Bio::Das stylesheets, and stylesheet-driven configuration can be intermixed with semantic zooming, if desired.

You can add a key to the generated image using either of two key styles. One style places the key captions at the top of each track. The other style generates a graphical key at the bottom of the image.

Note that this modules depends on GD.

METHODS

This section describes the class and object methods for Bio::Graphics::Panel.

Typically you will begin by creating a new Bio::Graphics::Panel object, passing it the desired width of the image to generate and an origin and length describing the coordinate range to display. The Bio::Graphics::Panel->new() method has may configuration variables that allow you to control the appearance of the image.

You will then call add_track() one or more times to add sets of related features to the picture. add_track() places a new horizontal track on the image, and is likewise highly configurable. When you have added all the features you desire, you may call png() to convert the image into a PNG-format image, or boxes() to return coordinate information that can be used to create an imagemap.

CONSTRUCTORS

new() is the constructor for Bio::Graphics::Panel:

$panel = Bio::Graphics::Panel->new(@options)

The new() method creates a new panel object. The options are a set of tag/value pairs as follows:

  Option      Value                                  Default
  ------      -----                                  -------

  -offset     Base pair to place at extreme left     none
              of image, in zero-based coordinates

  -length     Length of sequence segment, in bp      none

  -start      Start of range, in 1-based             none
              coordinates.

  -stop       Stop of range, in 1-based              none
              coordinates.

  -segment    A Bio::SeqI or Das::Segment            none
              object, used to derive sequence
              range if not otherwise specified.

  -width      Desired width of image, in pixels      600

  -spacing    Spacing between tracks, in pixels      5

  -pad_top    Additional whitespace between top      0
              of image and contents, in pixels

  -pad_bottom Additional whitespace between top      0
              of image and bottom, in pixels

  -pad_left   Additional whitespace between left     0
              of image and contents, in pixels

  -pad_right  Additional whitespace between right    0
              of image and bottom, in pixels

  -bgcolor    Background color for the panel as a    white
              whole

  -key_color  Background color for the key printed   wheat
              at bottom of panel (if any)

  -key_spacing Spacing between key glyphs in the     10
               key printed at bottom of panel
               (if any)

  -key_font    Font to use in printed key            gdMediumBoldFont
               captions.

  -key_style   Whether to print key at bottom of     none
               panel ("bottom"), between each
               track ("between"), or not at all
               ("none").

  -all_callbacks Whether to invoke callbacks on      false
               the automatic "track" and "group"
               glyphs.

  -grid        Whether to draw a vertical grid in    false
               the background.  Pass a scalar true
               value to have a grid drawn at
               regular intervals (corresponding
               to the minor ticks of the arrow
               glyph).  Pass an array reference
               to draw the grid at the specified
               positions.

  -gridcolor   Color of the grid                     lightcyan

Typically you will pass new() an object that implements the Bio::RangeI interface, providing a length() method, from which the panel will derive its scale.

  $panel = Bio::Graphics::Panel->new(-segment => $sequence,
                                     -width   => 800);

new() will return undef in case of an error.

OBJECT METHODS

$track = $panel->add_track($glyph,$features,@options)

The add_track() method adds a new track to the image.

Tracks are horizontal bands which span the entire width of the panel. Each track contains a number of graphical elements called "glyphs", corresponding to a sequence feature.

There are a large number of glyph types. By default, each track will be homogeneous on a single glyph type, but you can mix several glyph types on the same track by providing a code reference to the -glyph argument. Other options passed to add_track() control the color and size of the glyphs, whether they are allowed to overlap, and other formatting attributes. The height of a track is determined from its contents and cannot be directly influenced.

The first two arguments are the glyph name and an array reference containing the list of features to display. The order of the arguments is irrelevant, allowing either of these idioms:

  $panel->add_track(arrow => \@features);
  $panel->add_track(\@features => 'arrow');

The glyph name indicates how each feature is to be rendered. A variety of glyphs are available, and the number is growing. You may omit the glyph name entirely by providing a -glyph argument among @options, as described below.

Currently, the following glyphs are available:

  Name        Description
  ----        -----------

  generic      A filled rectangle, nondirectional.

  ellipse     An oval.

  arrow       An arrow; can be unidirectional or bidirectional.
              It is also capable of displaying a scale with
              major and minor tickmarks, and can be oriented
              horizontally or vertically.

  segments    A set of filled rectangles connected by solid lines.
              Used for interrupted features, such as gapped
              alignments.

  transcript  Similar to segments, but the connecting line is
              a "hat" shape, and the direction of transcription
              is indicated by a small arrow.

  transcript2  Similar to transcript, but the direction of
              transcription is indicated by a terminal exon
              in the shape of an arrow.

  primers     Two inward pointing arrows connected by a line.
              Used for STSs.

  group       A group of related features connected by a dashed line.
              This is used internally by Panel.

  track       A group of related features not connected by a line.
              This is used internally by Panel.

If the glyph name is omitted from add_track(), the "generic" glyph will be used by default.

The @options array is a list of name/value pairs that control the attributes of the track. Some options are interpretered directly by the track. Others are passed down to the individual glyphs (see "GLYPH OPTIONS"). The following options are track-specific:

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

  -tkcolor    Track color                  white

  -glyph      Glyph class to use.         "generic"

  -stylesheet Bio::Das::Stylesheet to     none
              use to generate glyph
              classes and options.

-tkcolor controls the background color of the track as a whole.

-glyph controls the glyph type. If present, it supersedes the glyph name given in the first or second argument to add_track(). The value of -glyph may be a constant string, a hash reference, or a code reference. In the case of a constant string, that string will be used as the class name for all generated glyphs. If a hash reference is passed, then the feature's primary_tag() will be used as the key to the hash, and the value, if any, used to generate the glyph type. If a code reference is passed, then this callback will be passed each feature in turn as its single argument. The callback is expected to examine the feature and return a glyph name as its single result.

Example:

  $panel->add_track(\@exons,
                    -glyph => sub { my $feature = shift;
                                    $feature->source_tag eq 'curated'
                                          ? 'ellipse' : 'generic'; }
                    );

The -stylesheet argument is used to pass a Bio::Das stylesheet object to the panel. This stylesheet will be called to determine both the glyph and the glyph options. If both a stylesheet and direct options are provided, the latter take precedence.

If successful, add_track() returns an Bio::Graphics::Glyph object. You can use this object to add additional features or to control the appearance of the track with greater detail, or just ignore it. Tracks are added in order from the top of the image to the bottom. To add tracks to the top of the image, use unshift_track().

Adding groups of features: It is not uncommon to add a group of features which are logically connected, such as the 5' and 3' ends of EST reads. To group features into sets that remain on the same horizontal position and bump together, pass the sets as an anonymous array. For example:

  $panel->add_track(segments => [[$abc_5,$abc_3],
                                 [$xxx_5,$xxx_3],
                                 [$yyy_5,$yyy_3]]
                    );

Typical usage is:

 $panel->add_track( transcript    => \@genes,
                    -fillcolor =>  'green',
                    -fgcolor   =>  'black',
                    -bump      =>  +1,
                    -height    => 10,
                    -label     => 1);
$track = unshift_track($glyph,$features,@options)

unshift_track() works like add_track(), except that the new track is added to the top of the image rather than the bottom.

$gd = $panel->gd

The gd() method lays out the image and returns a GD::Image object containing it. You may then call the GD::Image object's png() or jpeg() methods to get the image data.

$png = $panel->png

The png() method returns the image as a PNG-format drawing, without the intermediate step of returning a GD::Image object.

$boxes = $panel->boxes
@boxes = $panel->boxes

The boxes() method returns the coordinates of each glyph, useful for constructing an image map. In a scalar context, boxes() returns an array ref. In an list context, the method returns the array directly.

Each member of the list is an anonymous array of the following format:

  [ $feature, $x1, $y1, $x2, $y2 ]

The first element is the feature object; either an Ace::Sequence::Feature, a Das::Segment::Feature, or another Bioperl Bio::SeqFeatureI object. The coordinates are the topleft and bottomright corners of the glyph, including any space allocated for labels.

GLYPH OPTIONS

Each glyph has its own specialized subset of options, but some are shared by all glyphs:

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

  -fgcolor    Foreground color             black

  -bgcolor    Background color             turquoise

  -linewidth  Width of lines drawn by      1
              glyph

  -height     Height of glyph              10

  -font       Glyph font                   gdSmallFont

  -fontcolor  Primary font color           black

  -font2color Secondary font color         turquoise

  -label      Whether to draw a label      false

  -description  Whether to draw a          false
              description

  -bump       Bump direction               0

  -connector  Type of connector to         none
              use to connect related
              features.  Options are
              "hat", "dashed" and
              "none".

  -key        Description of track for     undef
              use in key.

  -all_callbacks Whether to invoke         undef
              callbacks for autogenerated
              "track" and "group" glyphs

Specifying colors: Colors can be expressed in either of two ways: as symbolic names such as "cyan" and as HTML-style #RRGGBB triples. The symbolic names are the 140 colors defined in the Netscape/Internet Explorer color cube, and can be retrieved using the Bio::Graphics::Panel->color_names() method.

Foreground color: The -fgcolor option controls the foreground color, including the edges of boxes and the like.

Background color: The -bgcolor option controls the background used for filled boxes and other "solid" glyphs. The foreground color controls the color of lines and strings. The -tkcolor argument controls the background color of the entire track.

Track color: The -tkcolor option used to specify the background of the entire track.

Font color: The -fontcolor option controls the color of primary text, such as labels

Secondary Font color: The -font2color option controls the color of secondary text, such as descriptions.

Labels: The -label argument controls whether or not the ID of the feature should be printed next to the feature. It is accepted by all glyphs. By default, the label is printed just above the glyph and left aligned with it.

-label can be a constant string or a code reference. Values can be any of:

  -label value     Description
  ------------     -----------

    0              Don't draw a label
    1              Calculate a label based on primary tag of sequence
    "a string"     Use "a string" as the label
    code ref       Invoke the code reference to compute the label

A known bug with this naming scheme is that you can't label a feature with the string "1". To work around this, use "1 " (note the terminal space).

Descriptions: The -description argument controls whether or not a brief description of the feature should be printed next to it. By default, the description is printed just below the glyph and left-aligned with it. A value of 0 will suppress the description. A value of 1 will call the source_tag() method of the feature. A code reference will be invoked to calculate the description on the fly. Anything else will be treated as a string and used verbatim.

Connectors: A glyph can contain subglyphs, recursively. The top level glyph is the track, which contains one or more groups, which contain features, which contain subfeatures, and so forth. By default, the "group" glyph draws dotted lines between each of its subglyphs, the "segment" glyph draws a solid line between each of its subglyphs, and the "transcript" and "transcript2" glyphs draw hat-shaped lines between their subglyphs. All other glyphs do not connect their components. You can override this behavior by providing a -connector option, to explicitly set the type of connector. Valid options are "dashed", "solid", "hat" and "none".

Collision control: The -bump argument controls what happens when glyphs collide. By default, they will simply overlap (value 0). A -bump value of +1 will cause overlapping glyphs to bump downwards until there is room for them. A -bump value of -1 will cause overlapping glyphs to bump upwards. This argument can also be a code reference; see below.

Keys: The -key argument declares that the track is to be shown in a key appended to the bottom of the image. The key contains a picture of a glyph and a label describing what the glyph means. The label is specified in the argument to -key.

Options and Callbacks

Instead of providing a constant value to an option, you may subsitute a code reference. This code reference will be called every time the panel needs to configure a glyph. The callback will be called with three arguments like this:

   sub callback {
      my ($feature,$option_name,$part_no,$total_parts,$glyph) = @_;
      # do something which results in $option_value being set
      return $option_value;
   }

The five arguments are $feature, a reference to the IO::SeqFeatureI object, $option_name, the name of the option to configure, $part_no, an integer index indicating which subpart of the feature is being drawn, $total_parts, an integer indicating the total number of subfeatures in the feature, and finally $glyph, the Glyph object itself. The latter fields are useful in the common case of treating the first or last subfeature differently, such as using a different color for the terminal exon of a gene.

The callback should return a string indicating the desired value of the option. To tell the panel to use the default value for this option, return the string "*default*".

When you install a callback for a feature that contains subparts, the callback will be invoked first for the top-level feature, and then for each of its subparts (recursively). You should make sure to examine the feature's type to determine whether the option is appropriate.

Some glyphs deliberately disable this recursive feature. The "track", "group", "transcript", "transcript2" and "segments" glyphs selectively disable the -bump, -label and -description options. This is to avoid, for example, a label being attached to each exon in a transcript, or the various segments of a gapped alignment bumping each other. You can override this behavior and force your callback to be invoked by providing add_track() with a true -all_callbacks argument. In this case, you must be prepared to handle configuring options for the "group" and "track" glyphs.

ACCESSORS

The following accessor methods provide access to various attributes of the panel object. Called with no arguments, they each return the current value of the attribute. Called with a single argument, they set the attribute and return its previous value.

Note that in most cases you must change attributes prior to invoking gd(), png() or boxes(). These three methods all invoke an internal layout() method which places the tracks and the glyphs within them, and then caches the result.

   Accessor Name      Description
   -------------      -----------

   width()            Get/set width of panel
   spacing()          Get/set spacing between tracks
   key_spacing()      Get/set spacing between keys
   length()           Get/set length of segment (bp)
   pad_top()          Get/set top padding
   pad_left()         Get/set left padding
   pad_bottom()       Get/set bottom padding
   pad_right()        Get/set right padding

INTERNAL METHODS

The following methods are used internally, but may be useful for those implementing new glyph types.

@names = Bio::Graphics::Panel->color_names

Return the symbolic names of the colors recognized by the panel object. In a scalar context, returns an array reference.

@rgb = $panel->rgb($index)

Given a GD color index (between 0 and 140), returns the RGB triplet corresponding to this index. This method is only useful within a glyph's draw() routine, after the panel has allocated a GD::Image and is populating it.

$index = $panel->translate_color($color)

Given a color, returns the GD::Image index. The color may be symbolic, such as "turquoise", or a #RRGGBB triple, as in #F0E0A8. This method is only useful within a glyph's draw() routine, after the panel has allocated a GD::Image and is populating it.

$panel->set_pen($width,$color)

Changes the width and color of the GD drawing pen to the values indicated. This is called automatically by the GlyphFactory fgcolor() method. It returns the GD value gdBrushed, which should be used for drawing.

BUGS

Please report them.

SEE ALSO

Bio::Graphics::Glyph, Bio::SeqI,Bio::SeqFeatureI, Bio::Das,GD

AUTHOR

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.