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Manual Reference Pages  -  BIO::PHYLO::TREEDRAWER (3)

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NAME

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

CONTENTS

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
                -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 )
           -units => TRUE



    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_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.



    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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::TREEDRAWER (3) 2014-03-27

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