NAME

Bio::Phylo::Treedrawer - Visualizer of tree shapes

SYNOPSIS

use Bio::Phylo::IO 'parse';
use Bio::Phylo::Treedrawer;

my $string = '((A:1,B:2)n1:3,C:4)n2:0;';
my $tree = parse( -format => 'newick', -string => $string )->first;

my $treedrawer = Bio::Phylo::Treedrawer->new(
   -width  => 800,
   -height => 600,
   -shape  => 'CURVY', # curvogram
   -mode   => 'PHYLO', # phylogram
   -format => 'SVG'
);

$treedrawer->set_scale_options(
   -width => '100%',
   -major => '10%', # major cross hatch interval
   -minor => '2%',  # minor cross hatch interval
   -label => 'MYA',
);

$treedrawer->set_tree($tree);
print $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()

Treedrawer constructor.

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()

Sets image format.

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

set_width()

Sets image 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()

Sets image 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()

Sets tree drawing 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()

Sets tree drawing shape.

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

set_padding()

Sets image padding.

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

set_text_horiz_offset()

Sets text horizontal 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()

Sets text vertical 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()

Sets 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()

Sets tree to draw.

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()

Sets time 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
                -blocks  => '10%', # alternating blocks in light-gray
                -label   => 'MYA',
                -reverse => 1, # tips are 0
                -tmpl    => '%d', # sprintf template for major cross hatch numbers
                -font    => {
                   -face => 'Verdana',
                   -size => 11,
                }
            );
 Function: Sets the options for time (distance) scale
 Returns :
 Args    :
	-width   => 400,
	-major   => '10%', # major cross hatch interval
	-minor   => '2%',  # minor cross hatch interval
	-blocks  => '10%', # alternating blocks in light-gray
	-label   => 'MYA',
	-reverse => 1, # tips are 0
	-tmpl    => '%d', # sprintf template for major cross hatch numbers
	-font    => {
	   -face => 'Verdana',
	   -size => 11,
	}           

set_pie_colors

Sets a hash reference whose keys are (unique) names for the different segments in a likelihood pie chart, and whose values are color codes.

Type    : Mutator
Title   : set_pie_colors
Usage   : $treedrawer->set_pie_colors({ 'p1' => 'red', 'p2' => 'blue' });
Function: sets likelihood pie colors
Returns :
Args    : HASH

CASCADING MUTATORS

set_branch_width()

Sets branch width.

Type    : Mutator
Title   : set_branch_width
Usage   : $treedrawer->set_branch_width(1);
Function: sets the width of branch lines
Returns :
Args    : Integer width in pixels.

set_node_radius()

Sets 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_collapsed_clade_width()

Sets collapsed clade width.

Type    : Mutator
Title   : set_collapsed_clade_width
Usage   : $treedrawer->set_collapsed_clade_width(6);
Function: sets the width of collapsed clade triangles relative to uncollapsed tips
Returns :
Args    : Positive number

set_clade_label_width

Sets clade label width, i.e. the spacing between nested clade annotations

Type    : Mutator
Title   : set_clade_label_width
Usage   : $treedrawer->set_clade_label_width(6);
Function: sets the spacing between nested clade annotations
Returns :
Args    : Positive number

set_tip_radius()

Sets tip radius.

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

ACCESSORS

get_format()

Gets image format.

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

get_format_mime()

Gets image format as MIME type.

Type    : Accessor
Title   : get_format_mime
Usage   : print "Content-type: ", $treedrawer->get_format_mime, "\n\n";
Function: Gets the image format as MIME type.
Returns :
Args    : None.

get_width()

Gets image width.

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

get_height()

Gets image height.

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

get_mode()

Gets tree drawing 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()

Gets tree drawing shape.

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

get_padding()

Gets image padding.

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

get_text_horiz_offset()

Gets text horizontal 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()

Gets text vertical 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()

Gets 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()

Gets tree to draw.

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()

Gets time scale option.

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.

get_pie_colors

Gets a hash reference whose keys are (unique) names for the different segments in a likelihood pie chart, and whose values are color codes.

Type    : Accessor
Title   : get_pie_colors
Usage   : my %h = %{ $treedrawer->get_pie_colors() };
Function: gets likelihood pie colors
Returns :
Args    : None

get_clade_label_width

Gets clade label width, i.e. the spacing between nested clade annotations

Type    : Mutator
Title   : get_clade_label_width
Usage   : my $width = $treedrawer->get_clade_label_width();
Function: gets the spacing between nested clade annotations
Returns :
Args    : None

CASCADING ACCESSORS

get_branch_width()

Gets branch width.

Type    : Accessor
Title   : get_branch_width
Usage   : my $w = $treedrawer->get_branch_width();
Function: gets the width of branch lines
Returns :
Args    : Integer width in pixels.

get_collapsed_clade_width()

Gets collapsed clade width.

Type    : Mutator
Title   : get_collapsed_clade_width
Usage   : $w = $treedrawer->get_collapsed_clade_width();
Function: gets the width of collapsed clade triangles relative to uncollapsed tips
Returns : Positive number
Args    : None

get_node_radius()

Gets 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_tip_radius()

Gets tip radius.

Type    : Accessor
Title   : get_tip_radius
Usage   : my $tip_radius = $treedrawer->get_tip_radius;
Function: Gets the tip radius in pixels.
Returns : SCALAR
Args    : None.

TREE DRAWING

draw()

Creates tree drawing.

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

render()

Renders tree based on pre-computed node coordinates. You would typically use this method if you have passed a Bio::Phylo::Forest::DrawTree on which you have already calculated the node coordinates separately.

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

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

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 and http://rutgervos.blogspot.com.

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63