Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
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 v5.32.1			  2021-03-01	   Bio::Graphics::Pictogram(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Shawn Hoon | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Graphics::Pictogram&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help