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

Shachi Gahoi shachigahoimbi at gmail.com
Sat Aug 6 00:25:43 EDT 2011


Thank you so much.

Please tell me one more thing, *can I reduce branch length font?
*
On Fri, Aug 5, 2011 at 4:24 PM, Roy Chaudhuri <roy.chaudhuri at gmail.com>wrote:

> 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 <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>
>> >
>>        <mailto: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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>>        <mailto:Bioperl-l at lists.open-**bio.org<Bioperl-l at lists.open-bio.org>
>> >>
>>
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>> >
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>> >>
>>
>>
>>
>>
>>
>>
>>        --
>>        Regards,
>>        Shachi
>>
>>
>>
>>
>>
>> --
>> Regards,
>> Shachi
>>
>
>


-- 
Regards,
Shachi


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