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

- NAME
- SYNOPSIS
- DESCRIPTION
- FEEDBACK

- Mailing Lists
- Reporting Bugs

- AUTHOR - Shawn Hoon
- APPENDIX

- new
- make_svg
- fontsize
- color
- svg_obj
- plot_bits
- normalize
- background
- pwm

# 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

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