Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
Bio::Tree::Draw::CladoUser(Contributed Perl DocumBio::Tree::Draw::Cladogram(3)

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

	 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');

       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

       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

   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.			- General discussion	- About	the mailing lists

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

       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

AUTHOR - Gabriel Valiente

       Code for	coloring branches contributed by Georgii A Bazykin

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

	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]

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

perl v5.24.1			  2017-07-08	 Bio::Tree::Draw::Cladogram(3)


Want to link to this manual page? Use this URL:

home | help