Rutger Vos > Bio-Phylo-0.55 > Bio::Phylo::Forest::DrawTree

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NAME ^

Bio::Phylo::Forest::DrawTree - Tree with extra methods for tree drawing

SYNOPSIS ^

 # see Bio::Phylo::Forest::Tree

DESCRIPTION ^

The object models a phylogenetic tree, a container of Bio::Phylo::For- est::Node objects. The tree object inherits from Bio::Phylo::Listable, so look there for more methods.

In addition, this subclass of the default tree object Bio::Phylo::Forest::Tree has getters and setters for drawing trees, e.g. font and text attributes, etc.

METHODS ^

CONSTRUCTORS

new()

Tree constructor.

 Type    : Constructor
 Title   : new
 Usage   : my $tree = Bio::Phylo::Forest::DrawTree->new;
 Function: Instantiates a Bio::Phylo::Forest::DrawTree object.
 Returns : A Bio::Phylo::Forest::DrawTree object.
 Args    : No required arguments.

MUTATORS

set_width()
 Type    : Mutator
 Title   : set_width
 Usage   : $tree->set_width($width);
 Function: Sets width
 Returns : $self
 Args    : width
set_height()
 Type    : Mutator
 Title   : set_height
 Usage   : $tree->set_height($height);
 Function: Sets height
 Returns : $self
 Args    : height
set_node_radius()
 Type    : Mutator
 Title   : set_node_radius
 Usage   : $tree->set_node_radius($node_radius);
 Function: Sets node_radius
 Returns : $self
 Args    : node_radius
set_tip_radius()
 Type    : Mutator
 Title   : set_tip_node_radius
 Usage   : $tree->set_tip_radius($node_radius);
 Function: Sets tip radius
 Returns : $self
 Args    : tip radius
set_node_colour()
 Type    : Mutator
 Title   : set_node_colour
 Usage   : $tree->set_node_colour($node_colour);
 Function: Sets node_colour
 Returns : $self
 Args    : node_colour
set_node_shape()
 Type    : Mutator
 Title   : set_node_shape
 Usage   : $tree->set_node_shape($node_shape);
 Function: Sets node_shape
 Returns : $self
 Args    : node_shape
set_node_image()
 Type    : Mutator
 Title   : set_node_image
 Usage   : $tree->set_node_image($node_image);
 Function: Sets node_image
 Returns : $self
 Args    : node_image
set_collapsed_clade_width()

Sets collapsed clade width.

 Type    : Mutator
 Title   : set_collapsed_clade_width
 Usage   : $tree->set_collapsed_clade_width(6);
 Function: sets the width of collapsed clade triangles relative to uncollapsed tips
 Returns :
 Args    : Positive number
set_branch_color()
 Type    : Mutator
 Title   : set_branch_color
 Usage   : $tree->set_branch_color($branch_color);
 Function: Sets branch_color
 Returns : $self
 Args    : branch_color
set_branch_shape()
 Type    : Mutator
 Title   : set_branch_shape
 Usage   : $tree->set_branch_shape($branch_shape);
 Function: Sets branch_shape
 Returns : $self
 Args    : branch_shape
set_branch_width()
 Type    : Mutator
 Title   : set_branch_width
 Usage   : $tree->set_branch_width($branch_width);
 Function: Sets branch width
 Returns : $self
 Args    : branch_width
set_branch_style()
 Type    : Mutator
 Title   : set_branch_style
 Usage   : $tree->set_branch_style($branch_style);
 Function: Sets branch style
 Returns : $self
 Args    : branch_style
set_font_face()
 Type    : Mutator
 Title   : set_font_face
 Usage   : $tree->set_font_face($font_face);
 Function: Sets font_face
 Returns : $self
 Args    : font face, Verdana, Arial, Serif
set_font_size()
 Type    : Mutator
 Title   : set_font_size
 Usage   : $tree->set_font_size($font_size);
 Function: Sets font_size
 Returns : $self
 Args    : Font size in pixels
set_font_style()
 Type    : Mutator
 Title   : set_font_style
 Usage   : $tree->set_font_style($font_style);
 Function: Sets font_style
 Returns : $self
 Args    : Font style, e.g. Italic
set_margin()
 Type    : Mutator
 Title   : set_margin
 Usage   : $tree->set_margin($margin);
 Function: Sets margin
 Returns : $self
 Args    : margin
set_margin_top()
 Type    : Mutator
 Title   : set_margin_top
 Usage   : $tree->set_margin_top($margin_top);
 Function: Sets margin_top
 Returns : $self
 Args    : margin_top
set_margin_bottom()
 Type    : Mutator
 Title   : set_margin_bottom
 Usage   : $tree->set_margin_bottom($margin_bottom);
 Function: Sets margin_bottom
 Returns : $self
 Args    : margin_bottom
set_margin_left()
 Type    : Mutator
 Title   : set_margin_left
 Usage   : $tree->set_margin_left($margin_left);
 Function: Sets margin_left
 Returns : $self
 Args    : margin_left
set_margin_right()
 Type    : Mutator
 Title   : set_margin_right
 Usage   : $tree->set_margin_right($margin_right);
 Function: Sets margin_right
 Returns : $self
 Args    : margin_right
set_padding()
 Type    : Mutator
 Title   : set_padding
 Usage   : $tree->set_padding($padding);
 Function: Sets padding
 Returns : $self
 Args    : padding
set_padding_top()
 Type    : Mutator
 Title   : set_padding_top
 Usage   : $tree->set_padding_top($padding_top);
 Function: Sets padding_top
 Returns : $self
 Args    : padding_top
set_padding_bottom()
 Type    : Mutator
 Title   : set_padding_bottom
 Usage   : $tree->set_padding_bottom($padding_bottom);
 Function: Sets padding_bottom
 Returns : $self
 Args    : padding_bottom
set_padding_left()
 Type    : Mutator
 Title   : set_padding_left
 Usage   : $tree->set_padding_left($padding_left);
 Function: Sets padding_left
 Returns : $self
 Args    : padding_left
set_padding_right()
 Type    : Mutator
 Title   : set_padding_right
 Usage   : $tree->set_padding_right($padding_right);
 Function: Sets padding_right
 Returns : $self
 Args    : padding_right
set_mode()
 Type    : Mutator
 Title   : set_mode
 Usage   : $tree->set_mode($mode);
 Function: Sets mode
 Returns : $self
 Args    : mode, e.g. 'CLADO' or 'PHYLO'
set_shape()
 Type    : Mutator
 Title   : set_shape
 Usage   : $tree->set_shape($shape);
 Function: Sets shape
 Returns : $self
 Args    : shape, e.g. 'RECT', 'CURVY', 'DIAG'
set_text_horiz_offset()
 Type    : Mutator
 Title   : set_text_horiz_offset
 Usage   : $tree->set_text_horiz_offset($text_horiz_offset);
 Function: Sets text_horiz_offset
 Returns : $self
 Args    : text_horiz_offset
set_text_vert_offset()
 Type    : Mutator
 Title   : set_text_vert_offset
 Usage   : $tree->set_text_vert_offset($text_vert_offset);
 Function: Sets text_vert_offset
 Returns : $self
 Args    : text_vert_offset

ACCESSORS

get_width()
 Type    : Accessor
 Title   : get_width
 Usage   : my $width = $tree->get_width();
 Function: Gets width
 Returns : width
 Args    : NONE
get_height()
 Type    : Accessor
 Title   : get_height
 Usage   : my $height = $tree->get_height();
 Function: Gets height
 Returns : height
 Args    : NONE
get_node_radius()
 Type    : Accessor
 Title   : get_node_radius
 Usage   : my $node_radius = $tree->get_node_radius();
 Function: Gets node_radius
 Returns : node_radius
 Args    : NONE
get_node_colour()
 Type    : Accessor
 Title   : get_node_colour
 Usage   : my $node_colour = $tree->get_node_colour();
 Function: Gets node_colour
 Returns : node_colour
 Args    : NONE
get_node_shape()
 Type    : Accessor
 Title   : get_node_shape
 Usage   : my $node_shape = $tree->get_node_shape();
 Function: Gets node_shape
 Returns : node_shape
 Args    : NONE
get_node_image()
 Type    : Accessor
 Title   : get_node_image
 Usage   : my $node_image = $tree->get_node_image();
 Function: Gets node_image
 Returns : node_image
 Args    : NONE
get_collapsed_clade_width()

Gets collapsed clade width.

 Type    : Mutator
 Title   : get_collapsed_clade_width
 Usage   : $w = $tree->get_collapsed_clade_width();
 Function: gets the width of collapsed clade triangles relative to uncollapsed tips
 Returns : Positive number
 Args    : None
get_branch_color()
 Type    : Accessor
 Title   : get_branch_color
 Usage   : my $branch_color = $tree->get_branch_color();
 Function: Gets branch_color
 Returns : branch_color
 Args    : NONE
get_branch_shape()
 Type    : Accessor
 Title   : get_branch_shape
 Usage   : my $branch_shape = $tree->get_branch_shape();
 Function: Gets branch_shape
 Returns : branch_shape
 Args    : NONE
get_branch_width()
 Type    : Accessor
 Title   : get_branch_width
 Usage   : my $branch_width = $tree->get_branch_width();
 Function: Gets branch_width
 Returns : branch_width
 Args    : NONE
get_branch_style()
 Type    : Accessor
 Title   : get_branch_style
 Usage   : my $branch_style = $tree->get_branch_style();
 Function: Gets branch_style
 Returns : branch_style
 Args    : NONE
get_font_face()
 Type    : Accessor
 Title   : get_font_face
 Usage   : my $font_face = $tree->get_font_face();
 Function: Gets font_face
 Returns : font_face
 Args    : NONE
get_font_size()
 Type    : Accessor
 Title   : get_font_size
 Usage   : my $font_size = $tree->get_font_size();
 Function: Gets font_size
 Returns : font_size
 Args    : NONE
get_font_style()
 Type    : Accessor
 Title   : get_font_style
 Usage   : my $font_style = $tree->get_font_style();
 Function: Gets font_style
 Returns : font_style
 Args    : NONE
get_margin()
 Type    : Accessor
 Title   : get_margin
 Usage   : my $margin = $tree->get_margin();
 Function: Gets margin
 Returns : margin
 Args    : NONE
get_margin_top()
 Type    : Accessor
 Title   : get_margin_top
 Usage   : my $margin_top = $tree->get_margin_top();
 Function: Gets margin_top
 Returns : margin_top
 Args    : NONE
get_margin_bottom()
 Type    : Accessor
 Title   : get_margin_bottom
 Usage   : my $margin_bottom = $tree->get_margin_bottom();
 Function: Gets margin_bottom
 Returns : margin_bottom
 Args    : NONE
get_margin_left()
 Type    : Accessor
 Title   : get_margin_left
 Usage   : my $margin_left = $tree->get_margin_left();
 Function: Gets margin_left
 Returns : margin_left
 Args    : NONE
get_margin_right()
 Type    : Accessor
 Title   : get_margin_right
 Usage   : my $margin_right = $tree->get_margin_right();
 Function: Gets margin_right
 Returns : margin_right
 Args    : NONE
get_padding()
 Type    : Accessor
 Title   : get_padding
 Usage   : my $padding = $tree->get_padding();
 Function: Gets padding
 Returns : padding
 Args    : NONE
get_padding_top()
 Type    : Accessor
 Title   : get_padding_top
 Usage   : my $padding_top = $tree->get_padding_top();
 Function: Gets padding_top
 Returns : padding_top
 Args    : NONE
get_padding_bottom()
 Type    : Accessor
 Title   : get_padding_bottom
 Usage   : my $padding_bottom = $tree->get_padding_bottom();
 Function: Gets padding_bottom
 Returns : padding_bottom
 Args    : NONE
get_padding_left()
 Type    : Accessor
 Title   : get_padding_left
 Usage   : my $padding_left = $tree->get_padding_left();
 Function: Gets padding_left
 Returns : padding_left
 Args    : NONE
get_padding_right()
 Type    : Accessor
 Title   : get_padding_right
 Usage   : my $padding_right = $tree->get_padding_right();
 Function: Gets padding_right
 Returns : padding_right
 Args    : NONE
get_mode()
 Type    : Accessor
 Title   : get_mode
 Usage   : my $mode = $tree->get_mode();
 Function: Gets mode
 Returns : mode
 Args    : NONE
get_shape()
 Type    : Accessor
 Title   : get_shape
 Usage   : my $shape = $tree->get_shape();
 Function: Gets shape
 Returns : shape
 Args    : NONE
get_text_horiz_offset()
 Type    : Accessor
 Title   : get_text_horiz_offset
 Usage   : my $text_horiz_offset = $tree->get_text_horiz_offset();
 Function: Gets text_horiz_offset
 Returns : text_horiz_offset
 Args    : NONE
get_text_vert_offset()
 Type    : Accessor
 Title   : get_text_vert_offset
 Usage   : my $text_vert_offset = $tree->get_text_vert_offset();
 Function: Gets text_vert_offset
 Returns : text_vert_offset
 Args    : NONE

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::Forest::Tree

This object inherits from Bio::Phylo::Forest::Tree, so methods defined there are also applicable here.

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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