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.\" ========================================================================
.\"
.IX Title "Bio::Graphics 3pm"
.TH Bio::Graphics 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics \- Generate GD images of Bio::Seq objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\& # This script generates a PNG picture of a 10K region containing a
\& # set of red features and a set of blue features. Call it like this:
\& #         red_and_blue.pl > redblue.png
\& # you can now view the picture with your favorite image application
\&
\&
\& # This script parses a GenBank or EMBL file named on the command
\& # line and produces a PNG rendering of it.  Call it like this:
\& # render.pl my_file.embl | display \-
\&
\& use strict;
\& use Bio::Graphics;
\& use Bio::SeqFeature::Generic;
\& use Bio::SeqIO;
\&
\& my $file = shift                       or die "provide a sequence file as the argument";
\& my $io = Bio::SeqIO\->new(\-file=>$file) or die "could not create Bio::SeqIO";
\& my $seq = $io\->next_seq                or die "could not find a sequence in the file";
\&
\& my @features = $seq\->all_SeqFeatures;
\&
\& # sort features by their primary tags
\& my %sorted_features;
\& for my $f (@features) {
\&   my $tag = $f\->primary_tag;
\&   push @{$sorted_features{$tag}},$f;
\& }
\&
\& my $wholeseq = Bio::SeqFeature::Generic\->new(\-start=>1,\-end=>$seq\->length);
\&
\& my $panel = Bio::Graphics::Panel\->new(
\&                                      \-length    => $seq\->length,
\&                                      \-key_style => \*(Aqbetween\*(Aq,
\&                                      \-width     => 800,
\&                                      \-pad_left  => 10,
\&                                      \-pad_right => 10,
\&                                      );
\& $panel\->add_track($wholeseq,
\&                  \-glyph => \*(Aqarrow\*(Aq,
\&                  \-bump => 0,
\&                  \-double=>1,
\&                  \-tick => 2);
\&
\& $panel\->add_track($wholeseq,
\&                  \-glyph  => \*(Aqgeneric\*(Aq,
\&                  \-bgcolor => \*(Aqblue\*(Aq,
\&                  \-label  => 1,
\&                 );
\&
\& # general case
\& my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
\& my $idx    = 0;
\& for my $tag (sort keys %sorted_features) {
\&   my $features = $sorted_features{$tag};
\&   $panel\->add_track($features,
\&                    \-glyph    =>  \*(Aqgeneric\*(Aq,
\&                    \-bgcolor  =>  $colors[$idx++ % @colors],
\&                    \-fgcolor  => \*(Aqblack\*(Aq,
\&                    \-font2color => \*(Aqred\*(Aq,
\&                    \-key      => "${tag}s",
\&                    \-bump     => +1,
\&                    \-height   => 8,
\&                    \-label    => 1,
\&                    \-description => 1,
\&                   );
\& }
\&
\& print $panel\->png;
\& exit 0;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Please see Bio::Graphics::Panel for the full interface. Also try
the script glyph_help.pl for quick help on glyphs and their options.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Graphics::Panel,
Bio::Graphics::Glyph,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
Bio::DB::GFF::Feature,
Ace::Sequence,
\&\s-1GD\s0
glyph_help.pl
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  http://bugzilla.open\-bio.org/
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>.
.PP
Copyright (c) 2001 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.