Does anyone know how I can convert a phylip tree format file in text format to a PNG image programmically in perl?
Tree file:
(
B:6.0,
(
A:5.0,
C:3.0,
E:4.0)
:5.0,
D:11.0);
I have tried using the Bio::Tree::Tree
module but it writes incorrect nodes into an SVG file.
This code produces SVG output on STDOUT
(I'm not qualified to comment on whether the correct nodes are displayed):
use v5.16; # sets strict and warnings
use Bio::Phylo::Forest;
use Bio::Phylo::Treedrawer;
my $string = '(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);';
my $forest
= Bio::Phylo::IO->parse( -format => 'newick', -string => $string )->first;
my $treedrawer = Bio::Phylo::Treedrawer->new(
-width => 800,
-height => 600,
-shape => 'CURVY', # curvogram
-mode => 'PHYLO', # phylogram
-format => 'SVG'
);
$treedrawer->set_scale_options(
-width => '100%',
-major => '10%', # major cross hatch interval
-minor => '2%', # minor cross hatch interval
-label => 'MYA',
);
$treedrawer->set_tree($forest);
$treedrawer->set_format('Svg');
print $treedrawer->draw;
To produce a PNG image I used the script to direct the SVG output to a file and converted it to PNG with ImageMagick's convert
utility. It looks like this:
There are facilities for directly creating PNG images with Bio::Phylo::Treedrawer
as well. To have Bio::Phylo::Treedrawer
output PNG images you can modify the object's properties using: $treedrawer->set_format('Png');
However on my system I get a warning when using the PNG image format:
WARN Bio::Phylo::Treedrawer::Abstract::_draw_legend [Bio/Phylo/Treedrawer/Abstract.pm: 106] - Bio::Phylo::Treedrawer::Png can't draw a legend
. I don't think this is a bug. The message would probably be better put as:
Bio::Phylo::Treedrawer::Png does not support drawing a legend
If the SVG output from Bio::Phylo::Treedrawer
is preferable to that of Bio::Tree::Tree
then you may want to just use that as your data format. You can convert your output file with either an image editor or a perl module that can convert your SVG data to PNG as part of the script.