Bio::Phylo::Treedrawer - Visualizer of tree shapes
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;
This module prepares a tree object for drawing (calculating coordinates for nodes) and calls the appropriate format-specific drawer.
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.
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
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.
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.
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]
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]
Sets image padding.
Type : Mutator Title : set_padding Usage : $treedrawer->set_padding(100); Function: Sets the canvas padding. Returns : Args : Integer value in pixels.
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.
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.
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.
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.
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, }
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
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.
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.
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
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
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.
Gets image format.
Type : Accessor Title : get_format Usage : my $format = $treedrawer->get_format; Function: Gets the image format. Returns : Args : None.
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.
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.
Gets image height.
Type : Accessor Title : get_height Usage : my $height = $treedrawer->get_height; Function: Gets the height of the canvas. Returns : Args : None.
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.
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.
Gets image padding.
Type : Accessor Title : get_padding Usage : my $padding = $treedrawer->get_padding; Function: Gets the canvas padding. Returns : Args : None.
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.
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.
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.
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.
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.
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
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
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.
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
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.
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.
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 :
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 :
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The Bio::Phylo::Treedrawer object inherits from the Bio::Phylo object. Look there for more methods applicable to the treedrawer object.
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.