Bio::Tree::Draw::Cladogram(3pm) 			User Contributed Perl Documentation			   Bio::Tree::Draw::Cladogram(3pm)

NAME

       Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.

SYNOPSIS

	 use Bio::Tree::Draw::Cladogram;
	 use Bio::TreeIO;
	 my $treeio = Bio::TreeIO->new('-format' => 'newick',
				      '-file'	=> 'input.nwk');
	 my $t1 = $treeio->next_tree;
	 my $t2 = $treeio->next_tree;

	 my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree => $t1);
	 $obj1->print(-file => 'cladogram.eps');

	 if ($t2) {
	   my $obj2 = Bio::Tree::Draw::Cladogram->new(-tree => $t1, -second => $t2);
	   $obj2->print(-file => 'tanglegram.eps');
	 }

DESCRIPTION

       Bio::Tree::Draw::Cladogram is a Perl tool for drawing Bio::Tree::Tree objects in Encapsulated PostScript (EPS) format. It can be utilized
       both for displaying a single phylogenetic tree (a cladogram) and for the comparative display of two phylogenetic trees (a tanglegram) such
       as a gene tree and a species tree, a host tree and a parasite tree, two alternative trees for the same set of taxa, or two alternative
       trees for overlapping sets of taxa.

       Phylogenetic trees are drawn as rectangular cladograms, with horizontal orientation and ancestral nodes centered over their descendents.
       The font used for taxa is Courier at 10 pt. A single Bio::Tree::Tree object is drawn with ancestors to the left and taxa flushed to the
       right. Two Bio::Tree::Tree objects are drawn with the first tree oriented left-to-right and the second tree oriented right-to-left, and
       with corresponding taxa connected by straight lines in a shade of gray. Each correspondence between a $taxon1 of the first tree and a
       $taxon2 of the second tree is established by setting $taxon1->add_tag_value('connection',$taxon2). Thus, a taxon of the first tree can be
       connected to more than one taxon of the second tree, and vice versa.

       The branch from the parent to a child $node, as well as the child label, can be colored by setting $node->add_tag_value('Rcolor',$r),
       $node->add_tag_value('Gcolor',$g), and $node->add_tag_value('Bcolor',$b), where $r, $g, and $b are the desired values for red, green, and
       blue (zero for lowest, one for highest intensity).

       This is a preliminary release of Bio::Tree::Draw::Cladogram. Future improvements include an option to output phylograms instead of
       cladograms. Beware that cladograms are automatically scaled according to branch lengths, but the current release has only been tested with
       trees having unit branch lengths.

       The print method could be extended to output graphic formats other than EPS, although there are many graphics conversion programs around
       that accept EPS input. For instance, most Linux distributions include epstopdf, a Perl script that together with Ghostscript, converts EPS
       to PDF.

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.

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

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Gabriel Valiente
       Email valiente@lsi.upc.edu

       Code for coloring branches contributed by Georgii A Bazykin (gbazykin@princeton.edu).

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::Tree::Draw::Cladogram->new();
	Function: Builds a new Bio::Tree::Draw::Cladogram object
	Returns : Bio::Tree::Draw::Cladogram
	Args	: -tree => Bio::Tree::Tree object
		  -second => Bio::Tree::Tree object (optional)
		  -font => font name [string] (optional)
		  -size => font size [integer] (optional)
		  -top => top margin [integer] (optional)
		  -bottom => bottom margin [integer] (optional)
		  -left => left margin [integer] (optional)
		  -right => right margin [integer] (optional)
		  -tip => extra tip space [integer] (optional)
		  -column => extra space between cladograms [integer] (optional)
		  -compact => ignore branch lengths [boolean] (optional)
		  -ratio => horizontal to vertical ratio [integer] (optional)
		  -colors => use colors to color edges [boolean] (optional)
		  -bootstrap => draw bootstrap or internal ids [boolean]

   print
	Title	: print
	Usage	: $obj->print();
	Function: Outputs $obj in Encapsulated PostScript (EPS) format
	Returns :
	Args	: -file => filename (optional)

perl v5.14.2							    2012-03-02					   Bio::Tree::Draw::Cladogram(3pm)