NAME

Bio::Phylo::Treedrawer - An object-oriented facade for drawing trees.

SYNOPSIS

 use Bio::Phylo::Treedrawer;
 use Bio::Phylo::IO;
 
 my $treedrawer = Bio::Phylo::Treedrawer->new(
    -width  => 400,
    -height => 600,
    -shape  => 'CURVY', # curvogram
    -mode   => 'CLADO', # cladogram
    -format => 'SVG'
 );
 
 my $tree = Bio::Phylo::IO->parse(
    -format => 'newick',
    -string => '((A,B),C);'
 )->first;
 
 $treedrawer->set_tree($tree);
 $treedrawer->set_padding(50);
 
 my $string = $treedrawer->draw;

DESCRIPTION

This module prepares a tree object for drawing (calculating coordinates for nodes) and calls the appropriate format-specific drawer.

METHODS

CONSTRUCTOR

new()

 Type    : Constructor
 Title   : new
 Usage   : my $treedrawer = Bio::Phylo::Treedrawer->new(
               %args 
           );
 Function: Initializes a Bio::Phylo::Treedrawer object.
 Alias   :
 Returns : A Bio::Phylo::Treedrawer object.
 Args    : none.

MUTATORS

set_format()

 Type    : Mutator
 Title   : set_format
 Usage   : $treedrawer->set_format('svg');
 Function: Sets the drawer submodule.
 Returns :
 Args    : Name of an image format (currently 
           only svg supported)

set_width()

 Type    : Mutator
 Title   : set_width
 Usage   : $treedrawer->set_width(1000);
 Function: sets the width of the drawer canvas.
 Returns :
 Args    : Integer width in pixels.

set_height()

 Type    : Mutator
 Title   : set_height
 Usage   : $treedrawer->set_height(1000);
 Function: sets the height of the canvas.
 Returns :
 Args    : Integer height in pixels.

set_mode()

 Type    : Mutator
 Title   : set_mode
 Usage   : $treedrawer->set_mode('clado');
 Function: Sets the tree mode, i.e. cladogram 
           or phylogram.
 Returns : Invocant.
 Args    : String, [clado|phylo]

set_shape()

 Type    : Mutator
 Title   : set_shape
 Usage   : $treedrawer->set_shape('rect');
 Function: Sets the tree shape, i.e. 
           rectangular, diagonal or curvy.
 Returns : Invocant.
 Args    : String, [rect|diag|curvy]

set_padding()

 Type    : Mutator
 Title   : set_padding
 Usage   : $treedrawer->set_padding(100);
 Function: Sets the canvas padding.
 Returns :
 Args    : Integer value in pixels.

set_node_radius()

 Type    : Mutator
 Title   : set_node_radius
 Usage   : $treedrawer->set_node_radius(20);
 Function: Sets the node radius in pixels.
 Returns :
 Args    : Integer value in pixels.

set_text_horiz_offset()

 Type    : Mutator
 Title   : set_text_horiz_offset
 Usage   : $treedrawer->set_text_horiz_offset(5);
 Function: Sets the distance between 
           tips and text, in pixels.
 Returns :
 Args    : Integer value in pixels.

set_text_vert_offset()

 Type    : Mutator
 Title   : set_text_vert_offset
 Usage   : $treedrawer->set_text_vert_offset(3);
 Function: Sets the text baseline 
           relative to the tips, in pixels.
 Returns :
 Args    : Integer value in pixels.

set_text_width()

 Type    : Mutator
 Title   : set_text_width
 Usage   : $treedrawer->set_text_width(150);
 Function: Sets the canvas width for 
           terminal taxon names.
 Returns :
 Args    : Integer value in pixels.

set_tree()

 Type    : Mutator
 Title   : set_tree
 Usage   : $treedrawer->set_tree($tree);
 Function: Sets the Bio::Phylo::Forest::Tree 
           object to unparse.
 Returns :
 Args    : A Bio::Phylo::Forest::Tree object.

set_scale_options()

 Type    : Mutator
 Title   : set_scale_options
 Usage   : $treedrawer->set_scale_options(
                -width => 400,
                -major => '10%', # major cross hatch interval
                -minor => '2%',  # minor cross hatch interval
                -label => 'MYA',
            );
 Function: Sets the options for time (distance) scale
 Returns :
 Args    : -width => (if a number, like 100, pixel 
                      width is assumed, if a percentage, 
                      scale width relative to longest root
                      to tip path)
           -major => ( ditto, value for major tick marks )
           -minor => ( ditto, value for minor tick marks )
           -label => ( text string displayed next to scale )

ACCESSORS

get_format()

 Type    : Mutator
 Title   : get_format
 Usage   : my $format = $treedrawer->get_format;
 Function: Gets the image format.
 Returns :
 Args    : None.

get_width()

 Type    : Mutator
 Title   : get_width
 Usage   : my $width = $treedrawer->get_width;
 Function: Gets the width of the drawer canvas.
 Returns :
 Args    : None.

get_height()

 Type    : Accessor
 Title   : get_height
 Usage   : my $height = $treedrawer->get_height;
 Function: Gets the height of the canvas.
 Returns :
 Args    : None.

get_mode()

 Type    : Accessor
 Title   : get_mode
 Usage   : my $mode = $treedrawer->get_mode('clado');
 Function: Gets the tree mode, i.e. cladogram or phylogram.
 Returns :
 Args    : None.

get_shape()

 Type    : Accessor
 Title   : get_shape
 Usage   : my $shape = $treedrawer->get_shape;
 Function: Gets the tree shape, i.e. rectangular, 
           diagonal or curvy.
 Returns :
 Args    : None.

get_padding()

 Type    : Accessor
 Title   : get_padding
 Usage   : my $padding = $treedrawer->get_padding;
 Function: Gets the canvas padding.
 Returns :
 Args    : None.

get_node_radius()

 Type    : Accessor
 Title   : get_node_radius
 Usage   : my $node_radius = $treedrawer->get_node_radius;
 Function: Gets the node radius in pixels.
 Returns : SCALAR
 Args    : None.

get_text_horiz_offset()

 Type    : Accessor
 Title   : get_text_horiz_offset
 Usage   : my $text_horiz_offset = 
           $treedrawer->get_text_horiz_offset;
 Function: Gets the distance between 
           tips and text, in pixels.
 Returns : SCALAR
 Args    : None.

get_text_vert_offset()

 Type    : Accessor
 Title   : get_text_vert_offset
 Usage   : my $text_vert_offset = 
           $treedrawer->get_text_vert_offset;
 Function: Gets the text baseline relative 
           to the tips, in pixels.
 Returns :
 Args    : None.

get_text_width()

 Type    : Accessor
 Title   : get_text_width
 Usage   : my $textwidth = 
           $treedrawer->get_text_width;
 Function: Returns the canvas width 
           for terminal taxon names.
 Returns :
 Args    : None.

get_tree()

 Type    : Accessor
 Title   : get_tree
 Usage   : my $tree = $treedrawer->get_tree;
 Function: Returns the Bio::Phylo::Forest::Tree 
           object to unparse.
 Returns : A Bio::Phylo::Forest::Tree object.
 Args    : None.

get_scale_options()

 Type    : Accessor
 Title   : get_scale_options
 Usage   : my %options = %{ 
               $treedrawer->get_scale_options  
           };
 Function: Returns the time/distance 
           scale options.
 Returns : A hash ref.
 Args    : None.

TREE DRAWING

draw()

 Type    : Unparsers
 Title   : draw
 Usage   : my $drawing = $treedrawer->draw;
 Function: Unparses a Bio::Phylo::Forest::Tree 
           object into a drawing.
 Returns : SCALAR
 Args    :

SEE ALSO

Bio::Phylo

The Bio::Phylo::Treedrawer object inherits from the Bio::Phylo object. Look there for more methods applicable to the treedrawer object.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Treedrawer.pm,v 1.8 2006/04/12 22:38:22 rvosa Exp $

AUTHOR

Rutger Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.