--- name: "Bio::Graphics::Glyph::image" section: "3pm" platform: "linux" package: "libbio-graphics-perl" version: "2.40-6" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Graphics::Glyph::image" --- # Bio::Graphics::Glyph::image(3pm) A glyph that draws photographs & other images ## 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 \, Todd Harris \ 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.