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Bio::Graphics::Pictogram.3pm

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