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Bio::PhyloNetwork::GraphViz.3pm

NAME

Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz

SYNOPSIS

   use Bio::PhyloNetwork;
   use Bio::PhyloNetwork::GraphViz;
 
   my $net=Bio::PhyloNetwork->new(
       -eNewick=>'((H1,(H1,(H2,l))),H2)t0; (some long label)H1; ("quoted label")H2;'
   );
 
   my $gv=Bio::PhyloNetwork::GraphViz->new(-net=>$net,-short_labels=>1);
 
   foreach my $u ($net->nodes()) {
       print "$u:".$gv->nodePN_to_nodeGV->{$u}."\n";
   }
 
   print $gv->as_text;
 
   open PS, "> net.ps";
   print PS $gv->as_ps;
   close PS;
 
 

DESCRIPTION

This is a module to create GraphViz objects representing phylogenetic networks.

AUTHOR

Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es

SEE ALSO

Bio::PhyloNetwork, GraphViz

APPENDIX

The rest of the documentation details each of the object methods.

new

  Title   : new
  Usage   : my $graphv = new Bio::PhyloNetwork::GraphViz();
  Function: Creates a new Bio::PhyloNetwork::GraphViz object
  Returns : Bio::PhyloNetwork::GraphViz
  Args    : -net => Bio::PhyloNetwork object
            -short_labels => boolean (optional)
 
 

Returns a Bio::PhyloNetwork::GraphViz object, which is an extension of a GraphViz object. The GraphViz object is a representation of the phylogenetic network given. The extra information the created object holds is a hash table with keys the nodes of the PhyloNetwork object and values the nodes of the GraphViz object. If the optional argument -short_labels=>1 is given, the labels of the nodes in GraphViz are shortened to a maximum of 3 letters.

nodePN_to_nodeGV

  Title   : nodePN_to_nodeGV
  Usage   : my $hashR=$graphv->nodePN_to_nodeGV()
  Function: returns (a reference to) a hash holding the translation between
            nodes of the Bio::PhyloNetwork object and nodes of the GraphViz
            object
  Returns : reference to hash
  Args    : none