Bio::Phylo::Forest::DrawTreeRole - Tree with extra methods for tree drawing
# see Bio::Phylo::Forest::Tree
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.
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.
Type : Mutator Title : set_width Usage : $tree->set_width($width); Function: Sets width Returns : $self Args : width
Type : Mutator Title : set_height Usage : $tree->set_height($height); Function: Sets height Returns : $self Args : height
Type : Mutator Title : set_node_radius Usage : $tree->set_node_radius($node_radius); Function: Sets node_radius Returns : $self Args : node_radius
Type : Mutator Title : set_tip_node_radius Usage : $tree->set_tip_radius($node_radius); Function: Sets tip radius Returns : $self Args : tip radius
Type : Mutator Title : set_node_colour Usage : $tree->set_node_colour($node_colour); Function: Sets node_colour Returns : $self Args : node_colour
Type : Mutator Title : set_node_shape Usage : $tree->set_node_shape($node_shape); Function: Sets node_shape Returns : $self Args : node_shape
Type : Mutator Title : set_node_image Usage : $tree->set_node_image($node_image); Function: Sets node_image Returns : $self Args : node_image
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
Type : Mutator Title : set_branch_color Usage : $tree->set_branch_color($branch_color); Function: Sets branch_color Returns : $self Args : branch_color
Type : Mutator Title : set_branch_shape Usage : $tree->set_branch_shape($branch_shape); Function: Sets branch_shape Returns : $self Args : branch_shape
Type : Mutator Title : set_branch_width Usage : $tree->set_branch_width($branch_width); Function: Sets branch width Returns : $self Args : branch_width
Type : Mutator Title : set_branch_style Usage : $tree->set_branch_style($branch_style); Function: Sets branch style Returns : $self Args : branch_style
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
Type : Mutator Title : set_font_size Usage : $tree->set_font_size($font_size); Function: Sets font_size Returns : $self Args : Font size in pixels
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
Type : Mutator Title : set_margin Usage : $tree->set_margin($margin); Function: Sets margin Returns : $self Args : margin
Type : Mutator Title : set_margin_top Usage : $tree->set_margin_top($margin_top); Function: Sets margin_top Returns : $self Args : margin_top
Type : Mutator Title : set_margin_bottom Usage : $tree->set_margin_bottom($margin_bottom); Function: Sets margin_bottom Returns : $self Args : margin_bottom
Type : Mutator Title : set_margin_left Usage : $tree->set_margin_left($margin_left); Function: Sets margin_left Returns : $self Args : margin_left
Type : Mutator Title : set_margin_right Usage : $tree->set_margin_right($margin_right); Function: Sets margin_right Returns : $self Args : margin_right
Type : Mutator Title : set_padding Usage : $tree->set_padding($padding); Function: Sets padding Returns : $self Args : padding
Type : Mutator Title : set_padding_top Usage : $tree->set_padding_top($padding_top); Function: Sets padding_top Returns : $self Args : padding_top
Type : Mutator Title : set_padding_bottom Usage : $tree->set_padding_bottom($padding_bottom); Function: Sets padding_bottom Returns : $self Args : padding_bottom
Type : Mutator Title : set_padding_left Usage : $tree->set_padding_left($padding_left); Function: Sets padding_left Returns : $self Args : padding_left
Type : Mutator Title : set_padding_right Usage : $tree->set_padding_right($padding_right); Function: Sets padding_right Returns : $self Args : padding_right
Type : Mutator Title : set_mode Usage : $tree->set_mode($mode); Function: Sets mode Returns : $self Args : mode, e.g. 'CLADO' or 'PHYLO'
Type : Mutator Title : set_shape Usage : $tree->set_shape($shape); Function: Sets shape Returns : $self Args : shape, e.g. 'RECT', 'CURVY', 'DIAG'
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
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
Type : Accessor Title : get_width Usage : my $width = $tree->get_width(); Function: Gets width Returns : width Args : NONE
Type : Accessor Title : get_height Usage : my $height = $tree->get_height(); Function: Gets height Returns : height Args : NONE
Type : Accessor Title : get_node_radius Usage : my $node_radius = $tree->get_node_radius(); Function: Gets node_radius Returns : node_radius Args : NONE
Type : Accessor Title : get_node_colour Usage : my $node_colour = $tree->get_node_colour(); Function: Gets node_colour Returns : node_colour Args : NONE
Type : Accessor Title : get_node_shape Usage : my $node_shape = $tree->get_node_shape(); Function: Gets node_shape Returns : node_shape Args : NONE
Type : Accessor Title : get_node_image Usage : my $node_image = $tree->get_node_image(); Function: Gets node_image Returns : node_image Args : NONE
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
Type : Accessor Title : get_branch_color Usage : my $branch_color = $tree->get_branch_color(); Function: Gets branch_color Returns : branch_color Args : NONE
Type : Accessor Title : get_branch_shape Usage : my $branch_shape = $tree->get_branch_shape(); Function: Gets branch_shape Returns : branch_shape Args : NONE
Type : Accessor Title : get_branch_width Usage : my $branch_width = $tree->get_branch_width(); Function: Gets branch_width Returns : branch_width Args : NONE
Type : Accessor Title : get_branch_style Usage : my $branch_style = $tree->get_branch_style(); Function: Gets branch_style Returns : branch_style Args : NONE
Type : Accessor Title : get_font_face Usage : my $font_face = $tree->get_font_face(); Function: Gets font_face Returns : font_face Args : NONE
Type : Accessor Title : get_font_size Usage : my $font_size = $tree->get_font_size(); Function: Gets font_size Returns : font_size Args : NONE
Type : Accessor Title : get_font_style Usage : my $font_style = $tree->get_font_style(); Function: Gets font_style Returns : font_style Args : NONE
Type : Accessor Title : get_margin Usage : my $margin = $tree->get_margin(); Function: Gets margin Returns : margin Args : NONE
Type : Accessor Title : get_margin_top Usage : my $margin_top = $tree->get_margin_top(); Function: Gets margin_top Returns : margin_top Args : NONE
Type : Accessor Title : get_margin_bottom Usage : my $margin_bottom = $tree->get_margin_bottom(); Function: Gets margin_bottom Returns : margin_bottom Args : NONE
Type : Accessor Title : get_margin_left Usage : my $margin_left = $tree->get_margin_left(); Function: Gets margin_left Returns : margin_left Args : NONE
Type : Accessor Title : get_margin_right Usage : my $margin_right = $tree->get_margin_right(); Function: Gets margin_right Returns : margin_right Args : NONE
Type : Accessor Title : get_padding Usage : my $padding = $tree->get_padding(); Function: Gets padding Returns : padding Args : NONE
Type : Accessor Title : get_padding_top Usage : my $padding_top = $tree->get_padding_top(); Function: Gets padding_top Returns : padding_top Args : NONE
Type : Accessor Title : get_padding_bottom Usage : my $padding_bottom = $tree->get_padding_bottom(); Function: Gets padding_bottom Returns : padding_bottom Args : NONE
Type : Accessor Title : get_padding_left Usage : my $padding_left = $tree->get_padding_left(); Function: Gets padding_left Returns : padding_left Args : NONE
Type : Accessor Title : get_padding_right Usage : my $padding_right = $tree->get_padding_right(); Function: Gets padding_right Returns : padding_right Args : NONE
Type : Accessor Title : get_mode Usage : my $mode = $tree->get_mode(); Function: Gets mode Returns : mode Args : NONE
Type : Accessor Title : get_shape Usage : my $shape = $tree->get_shape(); Function: Gets shape Returns : shape Args : NONE
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
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
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
This object inherits from Bio::Phylo::Forest::Tree, so methods defined there are also applicable here.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.