Ubuntu Manpage: Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects

NAME

       Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects

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.

BUGS

       Please report them.

AUTHOR