Reference

Bio::TreeIO::svggraph(3pm)

A simple output format that converts a Tree object to an SVG output

NAME

Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output

SYNOPSIS

  use Bio::TreeIO;
  my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick');
  my $out = Bio::TreeIO->new(-file => '>output', -format => 'svggraph');
  while( my $tree = $in->next_tree ) {
      my $svg_xml = $out->write_tree($tree);
  }

DESCRIPTION

This outputs a tree as an SVG graphic using the SVG::Graph API

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 the Bioperl mailing list. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Brian OConnor

Email brian.oconnor-at-excite.com

CONTRIBUTORS

Allen Day Guillaume Rousse, Guillaume-dot-Rousse-at-inria-dot-fr

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::TreeIO::svggraph->new();
 Function: Builds a new Bio::TreeIO::svggraph object
 Returns : Bio::TreeIO::svggraph
 Args    :-width    => image width (default 1600)
          -height   => image height (default 1000)
          -margin   => margin (default 30)
          -stroke   => stroke color (default 'black')
          -stroke_width=> stroke width (default 2)
          -font_size=> font size (default '10px')
          -nomalize => undef or 'log' (default is undef)

write_tree

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Write a tree out to data stream in newick/phylip format
 Returns : none
 Args    : Bio::Tree::TreeI object

decorateRoot

 Title   : _decorateRoot
 Usage   : internal methods
 Function:
 Example :
 Returns :
 Args    :

next_tree

 Title   : next_tree
 Usage   :
 Function: Sorry not possible with this format
 Returns : none
 Args    : none

History