SVG::Extension(3pm) User Contributed Perl Documentation SVG::Extension(3pm)NAME
SVG::Extension - additional methods
extension
return the element object
element_decl
generate an element declaration in the DTD
attribute_decl
return generate an attribute list for an element
attlist_decl
notation_decl(%attrs)
return an extension object of type NOTATION
entity_decl(%attrs)
return an extension object of type 'ENTITY'
xmilfy
render
alias for xmlify
to_xml
alias for xmlify
serialise
alias for xmlify
serialise
alias for xmlify
getDeclName
Simply an alias for the general method for SVG::Extension objects
getExtensionName
alias to getDeclName
getDeclNames
return list of existing decl types by extracting it from the overall list of existing element types
sub getDeclNames {
getExtensionNames
alias to getDeclNames
perl v5.14.2 2012-05-29 SVG::Extension(3pm)
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Bio::Draw::Pictogram(3pm) User Contributed Perl Documentation Bio::Draw::Pictogram(3pm)NAME
Bio::Draw::Pictogram - generate SVG output of Pictogram display for consensus motifs
SYNOPSIS
use Bio::Draw::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::Draw::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."
";
#Support for Bio::Matrix::PSM::SiteMatrix now included
use Bio::Matrix::PSM::IO;
my $picto = Bio::Draw::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
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
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:
https://redmine.open-bio.org/projects/bioperl/
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::Draw::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::Draw::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 v5.14.2 2012-03-02 Bio::Draw::Pictogram(3pm)