Provided by: libbio-graphics-perl_2.40-3_all bug

NAME

       Bio::Graphics::Pictogram - generate SVG output of Pictogram display for consensus motifs

SYNOPSIS

         use Bio::Graphics::Pictogram;
         use Bio::SeqIO;

         my $sio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
         my @seq;
         while(my $seq = $sio->next_seq){
           push @seq, $seq;
         }

         my $picto = Bio::Graphics::Pictogram->new(-width=>"800",
                                                   -height=>"500",
                                                   -fontsize=>"60",
                                                   -plot_bits=>1,
                                                   -background=>{
                                                                 'A'=>0.25,
                                                                 'C'=>0.18,
                                                                 'T'=>0.32,
                                                                 'G'=>0.25},
                                                   -color=>{'A'=>'red',
                                                            'G'=>'blue',
                                                            'C'=>'green',
                                                            'T'=>'magenta'});

         my $svg = $picto->make_svg(\@seq);

         print $svg->xmlify."\n";

         #Support for Bio::Matrix::PSM::SiteMatrix now included

          use Bio::Matrix::PSM::IO;

          my $picto = Bio::Graphics::Pictogram->new(-width=>"800",
                                                   -height=>"500",
                                                   -fontsize=>"60",
                                                   -plot_bits=>1,
                                                   -background=>{
                                                                 'A'=>0.25,
                                                                 'C'=>0.18,
                                                                 'T'=>0.32,
                                                                 'G'=>0.25},
                                                   -color=>{'A'=>'red',
                                                            'G'=>'blue',
                                                            'C'=>'green',
                                                            'T'=>'magenta'});

         my $psm = $psmIO->next_psm;
         my $svg = $picto->make_svg($psm);
         print $svg->xmlify;

DESCRIPTION

       A module for generating SVG output of Pictogram display for consensus motifs.  This method
       of representation was describe by Burge and colleagues: (Burge, C.B.,Tuschl, T., Sharp,
       P.A. in The RNA world II, 525-560, CSHL press, 1999)

       This is a simple module that takes in an array of sequences (assuming equal lengths) and
       calculates relative base frequencies where the height of each letter reflects the
       frequency of each nucleotide at a given position. It can also plot the information content
       at each position scaled by the background frequencies of each nucleotide.

       It requires the SVG-2.26 or later module by Ronan Oger available at http://www.cpan.org

       Recommended viewing of the SVG is the plugin available at Adobe: http://www.adobe.com/svg

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists. Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://bugzilla.open-bio.org/

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a "_".

   new
        Title   : new
        Usage   : my $picto = Bio::Graphics::Pictogram->new(-width=>"800",
                                                   -height=>"500",
                                                   -fontsize=>"60",
                                                   -plot_bits=>1,
                                                   -background=>{
                                                                 'A'=>0.25,
                                                                 'C'=>0.18,
                                                                 'T'=>0.32,
                                                                 'G'=>0.25},
                                                   -color=>{'A'=>'red',
                                                             'G'=>'blue',
                                                             'C'=>'green',
                                                             'T'=>'magenta'});
        Function: Constructor for Pictogram Object
        Returns : L<Bio::Graphics::Pictogram>

   make_svg
        Title   : make_svg
        Usage   : $picto->make_svg();
        Function: make the SVG object
        Returns : L<SVG>
        Arguments: A fasta file or array ref of L<Bio::Seq> objects or a L<Bio::Matrix::PSM::SiteMatrixI>

   fontsize
        Title   : fontsize
        Usage   : $picto->fontsize();
        Function: get/set for fontsize
        Returns : int
        Arguments: int

   color
        Title   : color
        Usage   : $picto->color();
        Function: get/set for color
        Returns : a hash reference
        Arguments: a hash  reference

   svg_obj
        Title   : svg_obj
        Usage   : $picto->svg_obj();
        Function: get/set for svg_obj
        Returns : L<SVG>
        Arguments: L<SVG>

   plot_bits
        Title   : plot_bits
        Usage   : $picto->plot_bits();
        Function: get/set for plot_bits to indicate whether to plot
                  information content at each base position
        Returns :1/0
        Arguments: 1/0

   normalize
        Title   : normalize
        Usage   : $picto->normalize($newval)
        Function: get/set to make all columns the same height.
                  default is to scale height with information
                  content.
        Returns : value of normalize (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   background
        Title   : background
        Usage   : $picto->background();
        Function: get/set for hash reference of nucleodtide bgd frequencies
        Returns : hash reference
        Arguments: hash reference

   pwm
        Title   : pwm
        Usage   : $picto->pwm();
        Function: get/set for pwm
        Returns : int
        Arguments: int