SYNOPSIS

use Ace::Sequence;
use Ace::Graphics::Panel;
my $db = Ace->connect(-host=>'brie2.cshl.org',-port=>2005) or die;
my $cosmid = Ace::Sequence->new(-seq=>'Y16B4A',
-db=>$db,-start=>-15000,-end=>15000) or die;
my @transcripts = $cosmid->transcripts;
my $panel = Ace::Graphics::Panel->new(
-segment => $cosmid,
-width => 800
);
$panel->add_track(arrow => $cosmid,
-bump => 0,
-tick=>2);
$panel->add_track(transcript => \@transcripts,
-fillcolor => 'wheat',
-fgcolor => 'black',
-key => 'Curated Genes',
-bump => +1,
-height => 10,
-label => 1);
my $boxes = $panel->boxes;
print $panel->png;

DESCRIPTION

The Ace::Graphics::Panel class provides drawing and formatting services for Ace::Sequence::Feature objects or Das::Segment::Feature objects.

Typically you will begin by creating a new Ace::Graphics::Panel object, passing it the width of the visual display and the length of the segment.

You will then call add_track() one or more times to add sets of related features to the picture. 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.

Note that this modules depends on GD.

METHODS

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

CONSTRUCTORS

There is only one constructor, the new() method.

$panel = Ace::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
  ------      -----                                -------
  -length     Length of sequence segment, in bp    0
  -segment    An Ace::Sequence or Das::Segment     none
              object, used to derive length if
              not provided
  -offset     Base pair to place at extreme left   $segment->start
              of image.
  -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
  -keycolor   Background color for the key printed 'cornsilk'
              at bottom of panel (if any)
  -keyspacing Spacing between key glyphs in the    10
              key printed at bottom of panel
              (if any)

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

new() will return undef in case of an error. If the specified glyph name is not a valid one, new() will throw an exception.

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'', each corresponding to a sequence feature. There are different glyph types, but each track can only contain a single type of glyph. Options passed to the 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. Currently, the following glyphs are available:

  Name        Description
  ----        -----------
  box         A filled rectangle, nondirectional.
  ellipse     A filled ellipse, nondirectional.
  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 arrow that indicates
              the direction of transcription is the last exon
              itself.
  primers     Two inward pointing arrows connected by a line.
              Used for STSs.
  toomany     A "cloud", to indicate too many features to show
              individually.  This is a placeholder that will be
              replaced by something more clever, such as a histogram
              or density plot.
  group       A group of related features connected by a dashed line.
              This is used internally by the Track class and should
              not be called explicitly.

If the glyph name is omitted from add_track(), the ``box'' glyph will be used by default.

The @options array is a list of name/value pairs that control the attributes of the track. The options are in turn passed to the glyphs. Each glyph has its own specialized subset of options, but some are shared by all glyphs:

  Option      Description               Default
  ------      -----------               -------
  -glyph      Glyph to use              none
  -fgcolor    Foreground color          black
  -outlinecolor                         black
              Synonym for -fgcolor
  -bgcolor    Background color          white
  -fillcolor  Interior color of filled  turquoise
              images
  -linewidth  Width of lines drawn by   1
                    glyph
  -height     Height of glyph           10
  -font       Glyph font                gdSmallFont
  -label      Whether to draw a label   false
  -bump       Bump direction            0
  -connect_groups                       false
              Connect groups by a
              dashed line (see below)
  -key        Show this track in the    undef
              key

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 Ace::Graphics::Panel->color_names() method.

The background color is used for the background color of the track itself. The foreground color controls the color of lines and strings. The interior color is used for filled objects such as boxes.

The -label argument controls whether or not the ID of the feature should be printed next to the feature. It is accepted by most, but not all of the glyphs.

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.

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.

If present, the -glyph argument overrides the glyph given in the first or second argument.

add_track() returns an Ace::Graphics::Track 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().

Typical usage is:

 $panel->add_track( thistle    => \@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.

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. To connect the groups by a dashed line, pass the -connect_groups argument with a true value. For example:

  $panel->add_track(segments => [[$abc_5,$abc_3],
                                 [$xxx_5,$xxx_3],
                                 [$yyy_5,$yyy_3]],
                    -connect_groups => 1);

$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.

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
   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 = Ace::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)

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.

AUTHOR

Lincoln Stein <[email protected]>.

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.