| Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm) |
Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree program to draw trees
use Bio::Tools::Run::Phylo::Phylip::DrawTree; my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(); my $treeimagefile = $drawfact->run($tree);
This is a module for automating drawing of trees through Joe Felsenstein's Phylip suite.
To set parameters with option you need to pass in an array reference or a string, depending on the parameter. For example:
$treedraw->HORIZMARGINS(['2.00','2.5']);
$treedraw->ANCESTRALNODES('C');
$treedraw->TREESTYLE('PHEN');
$treedraw->USEBRANCHLENS('N');
This can be a brittle module as the menus change in PHYLIP. It should support phylip 3.6 but no guarantees.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
Email jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $obj->program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $drawfact->program_dir() Function: returns the program directory, obtained from ENV variable. Returns : string Args :
Title : new Usage : my $obj = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(); Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawTree object Returns : an instance of Bio::Tools::Run::Phylo::Phylip::DrawTree Args : The available DrawGram parameters
Title : run
Usage : my $file = $app->run($treefile);
Function: Draw a tree
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
Title : draw_tree
Usage : my $file = $app->draw_tree($treefile);
Function: This method is deprecated. Please use run method.
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to drawgram program
Example :
Returns : Bio::Tree object
Args : Name of a file the tree to draw in newick format
and a parameter string to be passed to drawgram
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for drawing program Example : Returns : filename containing tree in newick format Args : Bio::Tree::TreeI object
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for drawgram program Example : Returns : parameter string to be passed to drawgram Args : name of calling object
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
Title : outfile_name
Usage : my $outfile = $dragram->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory after a DrawTree run Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a Bio::Root::IO object Returns : Bio::Root::IO object Args : none
See Bio::Root::IO
| 2018-09-14 | perl v5.26.2 |