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 listsReporting 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: intcolor
Title : color
Usage : $picto->color();
Function: get/set for color
Returns : a hash reference
Arguments: a hash referencesvg_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: 1/0normalize
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 referencepwm
Title : pwm
Usage : $picto->pwm();
Function: get/set for pwm
Returns : int
Arguments: int