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>

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