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

Shachi Gahoi shachigahoimbi at gmail.com
Fri Aug 5 01:40:11 EDT 2011


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>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 <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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