[Bioperl-l] How to show branch length value in tree

Roy Chaudhuri roy.chaudhuri at gmail.com
Fri Aug 5 06:54:32 EDT 2011


In that case then you only want to add branch lengths to non-leaf nodes, 
so it would be:

for my $node ($t1->get_nodes) {
   $node->id($node->branch_length) unless $node->is_Leaf
}


On 05/08/2011 06:40, Shachi Gahoi wrote:
>
> Instead of both node id and accession, Can I replace node id with accession?
>
>
> On Thu, Aug 4, 2011 at 4:52 PM, Roy Chaudhuri <roy.chaudhuri at gmail.com
> <mailto:roy.chaudhuri at gmail.com>> wrote:
>
>     Hi Shachi,
>
>     Please keep replies on the mailing list, that way others can follow
>     the discussion.
>
>     As I mentioned, it is not possible to draw njplot-style trees with
>     labelled branches using Bio::Tree::Draw::Cladogram, it currently
>     only labels nodes (you could perhaps add branch labels as a feature
>     request on Redmine).
>
>     The code I gave overwrites the existing "leaf" node ids (the
>     accessions) with branch lengths, if you want to also keep the
>     existing labels you could try something like:
>
>
>     for my $node ($t1->get_nodes) {
>       if ($node->is_Leaf) {
>         $node->id($node->branch___length.' '.$node->id);
>       } else {
>
>         $node->id($node->branch___length)
>       }
>     }
>
>     Cheers,
>     Roy.
>
>
>     On 04/08/2011 05:36, Shachi Gahoi wrote:
>
>         Thank You so much. Now branch length is coming in tree.
>
>         But I want Accesssion number in place of node id.
>
>         I attached snapshot of tree as I want. Please tell me how can I
>         do this.
>
>
>
>
>         On Wed, Aug 3, 2011 at 7:31 PM, Roy Chaudhuri
>         <roy.chaudhuri at gmail.com <mailto:roy.chaudhuri at gmail.com>
>         <mailto:roy.chaudhuri at gmail.__com
>         <mailto:roy.chaudhuri at gmail.com>>> wrote:
>
>             Sorry, the code had a typo, it should be:
>
>
>             my $obj1 = Bio::Tree::Draw::Cladogram->____new(-bootstrap =>  1,
>                                                        -tree    =>  $t1,
>                                                        -compact =>  0);
>             for my $node ($t1->get_nodes) {
>
>                  $node->id($node->branch_____length) if defined
>         $node->branch_length;
>             }
>             $obj1->print(-file => "$dir/$stem.eps")
>
>             On 03/08/2011 14:58, Roy Chaudhuri wrote:
>
>                 Hi Shachi,
>
>                 I don't think you can draw labels on branches using
>                 Bio::Tree::Draw::Cladogram. However, it will draw node
>         labels,
>                 so you
>                 could copy the branch lengths over to the node ids:
>
>                 my $obj1 =
>         Bio::Tree::Draw::Cladogram->____new(-bootstrap =>  1,
>                                                              -tree    =>
>           $t1,
>                                                              -compact =>
>           0);
>                 for my $node ($tree->get_nodes) {
>                       $node->id($node->branch_____length) if defined
>                 $node->branch_length;
>                 }
>                 $obj1->print(-file => "$dir/$stem.eps")
>
>                 Incidentally, in your script you write the tree out to a
>         file,
>                 then read
>                 it back in using TreeIO. This is unnecessary, you can
>         use $tree
>                 directly
>                 as input to Bio::Tree::Draw::Cladogram.
>
>                 Alternatively, you could write out a newick file and use
>         non-Bioperl
>                 software such as njplot or MEGA to draw your tree with
>         labelled
>                 branch
>                 lengths.
>
>                 Cheers,
>                 Roy.
>
>                 On 03/08/2011 07:00, Shachi Gahoi wrote:
>
>                     Dear All
>
>                     I am using Bio::Tree modules for constructing and
>         drawing
>                     tree. *I am unable
>                     to show branch length value in tree.
>                     *
>                     Please tell me How can I do this, if anybody knows.
>
>                     Here is my script which i am using...and i also attached
>                     generated tree.
>
>                     Thanks in advance
>
>
>           ##############################____############################__##__##########################__####__######
>
>                     use Bio::AlignIO;
>                     use Bio::Align::ProteinStatistics;
>                     use Bio::Tree::DistanceFactory;
>                     use Bio::TreeIO;
>                     use Bio::Tree::Draw::Cladogram;
>
>                     # for a dna alignment
>                     # can also use ProteinStatistics
>
>                     my $alnio = Bio::AlignIO->new(-file => 'ADP.aln',
>                     -format=>'clustalw');
>
>                     my $dfactory =
>         Bio::Tree::DistanceFactory->____new(-method =>
>         'UPGMA');
>
>                     my $stats = Bio::Align::ProteinStatistics-____>new;
>
>                     my $treeout = Bio::TreeIO->new(-format => 'newick',
>         -file
>                     =>'>ADP1.dnd');
>
>                     while( my $aln = $alnio->next_aln )
>                     {
>                        my $mat = $stats->distance(-method => 'Kimura',
>         -align
>                       =>   $aln);
>
>                        my $tree = $dfactory->make_tree($mat);
>                        $treeout->write_tree($tree);
>                     }
>
>                     my $dir = shift || '.';
>
>                     opendir(DIR, $dir) || die $!;
>                     for my $file ( readdir(DIR) )
>                     {
>                           next unless $file =~ /(\S+)\.dnd$/;
>                           my $stem = $1;
>                           my $treeio = Bio::TreeIO->new('-format' =>
>         'newick',
>         '-file'   => "$dir/$file");
>
>                           if( my $t1 = $treeio->next_tree )
>                     {
>                               my $obj1 =
>                     Bio::Tree::Draw::Cladogram->____new(-bootstrap =>   1,
>
>         -tree
>                       =>   $t1,
>
>                     -compact =>   0);
>                               $obj1->print(-file => "$dir/$stem.eps");
>                           }
>                     }
>
>
>           ##############################____############################__##__##########################__####__##############
>
>
>
>
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>
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>
>
>
>
>
>
>         --
>         Regards,
>         Shachi
>
>
>
>
>
> --
> Regards,
> Shachi



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