[Bioperl-l] How to show branch length value in tree
Smithies, Russell
Russell.Smithies at agresearch.co.nz
Sun Aug 7 21:45:19 UTC 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");
> >> }
> >> }
> >>
> >>
> >>
> ##############################**____##########################**
> >> ##__##__######################**####__####__##############
> >>
> >>
> >>
> >>
> >>
> ______________________________**_____________________
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> >> 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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