Bio::Graphics::Pictogram man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::Graphics::PictogrUser)Contributed Perl DocumenBio::Graphics::Pictogram(3)

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

perl v5.14.1			  2011-07-22	   Bio::Graphics::Pictogram(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net