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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Sun Aug 7 17:45:19 EDT 2011


The constructor for Bio::Tree::Draw::Cladogram lets you specify the font and size, did you try setting it there?

 Title   : new
 Usage   : my $obj = Bio::Tree::Draw::Cladogram->new();
 Function: Builds a new Bio::Tree::Draw::Cladogram object 
 Returns : Bio::Tree::Draw::Cladogram
 Args    : -tree => Bio::Tree::Tree object
           -second => Bio::Tree::Tree object (optional)
           -font => font name [string] (optional) <<<<-------------
           -size => font size [integer] (optional) <<<<-------------
           -top => top margin [integer] (optional)
           -bottom => bottom margin [integer] (optional)
           -left => left margin [integer] (optional)
           -right => right margin [integer] (optional)
           -tip => extra tip space [integer] (optional)
           -column => extra space between cladograms [integer] (optional)
           -compact => ignore branch lengths [boolean] (optional)
           -ratio => horizontal to vertical ratio [integer] (optional)
           -colors => use colors to color edges [boolean] (optional)
           -bootstrap => draw bootstrap or internal ids [boolean]



--Russell



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Shachi Gahoi
> Sent: Saturday, 6 August 2011 4:26 p.m.
> To: Roy Chaudhuri
> Cc: bioperl-l List
> Subject: Re: [Bioperl-l] How to show branch length value in tree
> 
> 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");
> >>                          }
> >>                    }
> >>
> >>
> >>
> ##############################**____##########################**
> >> ##__##__######################**####__####__##############
> >>
> >>
> >>
> >>
> >>
> ______________________________**_____________________
> >>                    Bioperl-l mailing list
> >>        Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-**
> >> bio.org <Bioperl-l at lists.open-bio.org>>
> >>        <mailto:Bioperl-l at lists.open-_**_bio.org<Bioperl-
> l at lists.open-__bio.org>
> >>        <mailto:Bioperl-l at lists.open-**bio.org<Bioperl-l at lists.open-
> bio.org>
> >> >>
> >>
> >>        http://lists.open-bio.org/____**mailman/listinfo/bioperl-
> l<http://lists.open-bio.org/____mailman/listinfo/bioperl-l>
> >>        <http://lists.open-bio.org/__**mailman/listinfo/bioperl-
> l<http://lists.open-bio.org/__mailman/listinfo/bioperl-l>
> >> >
> >>        <http://lists.open-bio.org/__**mailman/listinfo/bioperl-
> l<http://lists.open-bio.org/__mailman/listinfo/bioperl-l>
> >>        <http://lists.open-bio.org/**mailman/listinfo/bioperl-
> l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> >> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>        --
> >>        Regards,
> >>        Shachi
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Regards,
> >> Shachi
> >>
> >
> >
> 
> 
> --
> Regards,
> Shachi
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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