Bio::Tree::Draw::CladoUser(Contributed Perl DocumBio::Tree::Draw::Cladogram(3)NAMEBio::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');
}
DESCRIPTIONBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Tree::Draw::Cladogram(3)
