Bio::Graphics::Pictogram 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; 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 An example of this module may be found at: http://scooby.fugu-sg.org:9001/pictogram/index.html

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org 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