NAME
Bio::Graphics::Glyph::image - A glyph that draws photographs & other images
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).
BUGS AND LIMITATIONS
This glyph does not work with GD::SVG. If you try to render it onto a GD::SVG panel, the image will be shown as a gray box. This will be fixed in a future version of GD::SVG.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Lincoln Stein <lstein@cshl.org>, Todd Harris <harris@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.