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
- 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
REVISION
$Id
: DrawTree.pm 1593 2011-02-27 15:26:04Z rvos $