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Rutger Vos > Bio-Phylo > Bio::Phylo::Treedrawer

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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

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