SYNOPSIS

use Bio::Graphics;
use Bio::Seq;
use Bio::SeqFeature::Generic;
my $bsg = 'Bio::SeqFeature::Generic';
my $seq = Bio::Seq->new(-length=>1000);
my $whole = $bsg->new(-display_name => 'Clone82',
-start => 1,
-end => $seq->length);
my $image1 = $bsg->new(-start => 100,
-end => 300,
-display_name => 'Excretory System',
-tag=>{
image=>"http://www.flybase.org/anatomy/image-browser_files/excretory-system.gif"
}
);
my $image2 = $bsg->new(-start => 500,
-end => 800,
-display_name => 'Expression Pattern',
-tag=>{
image=>"http://www.flybase.org/anatomy/image-browser_files/embryonic-expression-pattern.gif"
}
);
my $panel = Bio::Graphics::Panel->new(-length => $seq->length,
-width => 800,
-truecolor => 1,
-key_style => 'between',
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track($whole,
-glyph => 'arrow',
-double => 1,
-tick => 2,
-label => 1,
);
$panel->add_track([$image1,$image2],
-glyph => 'image',
-label => 1,
-key => 'Example images');
binmode STDOUT;
print $panel->png;

DESCRIPTION

This glyph inserts an image into the track at the indicated feature coordinates. The image can be in PNG, JPEG, GIF or GD format, and can be either 8-bit or 24-bit (``truecolor''). The image can be located on the local filesystem or located at a remote URL (provided that you have the LWP module installed).

When working with photographic images, you may wish to have Bio::Graphics::Panel create 24-bit (truecolor) images in order to avoid running out of colors. The symptom of this is that images appear posterized. To turn on truecolor images, pass the -truecolor option to Bio::Graphics::Panel as shown in the synopsis.

OPTIONS

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 additional options are available to the ``image'' glyph:

  Option            Description                       Default
  ------            -----------                       -------
  -image            Specify the image path or URL     none
                    to use for this feature.
  -image_prefix     String to prepend to              none
                    each image path. You may prepend
                    a directory or a partial URL.
  -vertical_spacing Vertical distance from the box    20
                    that shows the physical span of
                    of the feature to the top of
                    the picture (in pixels).
  -glyph_delegate   Glyph to use for the part of      'generic'
                    the glyph that shows the physical
                    span of the feature.

Set -vertical_spacing to 0 to completely suppress the diagonal lines that connect the physical span of the feature to the image.

Specifying the Image

The path to the image can be specified in two ways. First, you can place it in the feature itself using a tag named ``image''. Second, you can specify it as a track option using a callback:

  $panel->add_track(\@features,
                    -glyph=>'image',
                    -image => sub { my $feature = shift;
                                    my $image_path = do_something();
                                    return $image }
                    );

You can of course give -image a constant string, in which case each feature will show the same image.

The image can be a file on the local operating system or a URL. However, URL fetching will only work if the LWP module is installed on your system. Otherwise the glyph will fail with an error message.

If the image is a relative path (it does not begin with a slash or a URL protocol), then the contents of -image_prefix will be prepended to it. This allows you to specify images that are relative to a particular directory or a partial URL. Example:

  $panel->add_track(\@features,
                    -glyph => 'image',
                    -image_prefix => 'http://www.flybase.org/anatomy/image-browser_files',
                   );

This specifies that each feature's ``image'' tag is to be appended to the partial FlyBase URL, thereby saving space.

Glyph Delegation

The image glyph consists of two parts: an upper part that shows the extent of the feature in base pair coordinates, and a lower part that shows the image. No scaling of the image is done; its height and width are fixed.

By default the upper part uses the ``generic'' glyph, which is a simple rectangle filled with the bgcolor and outlined with the fgcolor. To use a different glyph in the upper part, specify the -glyph_delegate option, giving the name of the glyph you wish to use. For instance, to use the ``span'' glyph:

  $panel->add_track(\@features,
                    -glyph          => 'image',
                    -glyph_delegate => 'span'
                   );

This feature does not work with all glyphs, and in particular requires a recent CVS checkout of Bio::Perl to work properly with the ``arrow'', ``span'' and ``primers'' glyphs (support for the feature did not make it into version 1.5).

AUTHOR

Lincoln Stein <[email protected]>, Todd Harris <[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.