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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
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