Bio::Graphics::DrawTransmembrane(3pm) User Contributed Perl Documentation Bio::Graphics::DrawTransmembrane(3pm)
NAME
Bio::Graphics::DrawTransmembrane - draw a cartoon of an Alpha-helical transmembrane protein.
SYNOPSIS
use Bio::Graphics::DrawTransmembrane;
my @topology = (20,45,59,70,86,109,145,168,194,220);
## Simple use - -topology is the only option that is required
my $im = Bio::Graphics::DrawTransmembrane->new(
-title => 'This is a cartoon displaying transmembrane helices.',
-topology => @topology);
## More advanced use
my %labels = (5 => '5 - Sulphation Site',
21 => '1st Helix',
47 => '40 - Mutation',
60 => 'Voltage Sensor',
72 => '72 - Mutation 2',
73 => '73 - Mutation 3',
138 => '138 - Glycosylation Site',
170 => '170 - Phosphorylation Site',
200 => 'Last Helix');
my $im = Bio::Graphics::DrawTransmembrane->new(-n_terminal=> 'out',
-topology => @topology,
-bold_helices=> 1,
-labels=> \%labels,
-text_offset=> -15,
-outside_label=>'Lumen',
-inside_label=>'Cytoplasm',
-membrane_label=>'Membrane',
-vertical_padding=> 155);
## Parse Tmhmm data
use Bio::Tools::Tmhmm;
my $im = Bio::Graphics::DrawTransmembrane->new(
-title=>'Let's parse some Tmhmm output...',
-bold_helices=> 1);
open(FILE, 'tmhmm.out');
my $parser = new Bio::Tools::Tmhmm(-fh => *FILE );
while(my $tmhmm_feat = $parser->next_result ) {
## Load features into DrawTransmembrane object
$im->add_tmhmm_feat($tmhmm_feat);
}
close FILE;
## Now write the image to a .png file
open(OUTPUT, ">output.png");
binmode OUTPUT;
print OUTPUT $im->png;
close OUTPUT;
DESCRIPTION
A module to draw a cartoon of an alpha-helical transmembrane protein. It uses GD and allows the image to be written to a .png file.
The options are a set of tag/value pairs as follows:
Option Value Default
------ ----- -------
-topology Array containing transmembrane helix none
boundaries. This is the only option that
is required
-topology_string Alternative to -topology, provide a string none
containing the topology data in the form
A.11,31;B.41,59;C.86,107;D.145,166
-n_terminal Location of the N-terminal of the sequence, out
either 'in' or 'out'
-title Title to add to the image none
-inside_label Label for the inside of the membrane Cytoplasmic
-outside_label Label for the outside of the membrane Extracellular
-membrane_label Label for the membrane Plasma Membrane
-colour_scheme Colour scheme to use. Current choices are blue
blue, yellow, red, green, pink or white.
-labels Label loops and helices using data from a none
hash, e.g.
%labels = (138 => 'Glycosylation Site',
190 => 'Binding Site');
The hash key must be numeric, ranges are
not allowed.
-bold_helices Draws black boxes round helices 1
-bold_labels Draws black boxes round labels 0
-text_offset Shift the text labeling the loops. Use a 0
negative value to shift it left, a positive
value to shift it right
-helix_height Transmembrane helix height 130
-helix_width Transmembrane helix width 50
-loop_width Loop width 20
-vertical_padding Vertical padding 140
-horizontal_padding Horizontal Padding 150
-membrane_offset Offest between helix end and membrane 6
-short_loop_height Height of short loops 90
-medium_loop_height Height of medium loops 120
-long_loop_height Height of long loops 150
-short_loop_limit Length in residues below which a loop is 15
classed as short
-long_loop_limit Length in residues above which a loop is 30
classed as long
-loop_heights Explicitly set heights of each loop, e.g.
%loop_heights = (1 => 45,
2 => 220,
3 => 50,
4 => 220,
9 => 70);
The key corresponds to the loop number. Both
key and value must be numeric. If you use
-loop_height and there is a defined height
for the current loop then other height values
will be overridden
-n_terminal_height Height of N-terminal 150
-c_terminal_height Height of C-terminal 80
-n_terminal_offset Shift the N-terminal left by this amount 0
-c_terminal_offset Shift the C-terminal right by this amount 0
-helix_label Change the 'S' label on each helix. Only 1 S
character is allowed
-show_labels Display text labels on
-draw_cytosol Show the cytosol false
-draw_bilayer Show the membrane true
-draw_loops Show the loops true
-draw_terminai Show the terminai true
-draw_helices Show the helices true
-dontsort Don't automatically sort the topology array 0
-ttf_font Path to TTF font, e.g. none
/usr/share/fonts/msttcorefonts/arial.ttf
-ttf_font_size Default size for TTF font. Use 7-9 with 8
Arial for best results
Height, width, padding and other numerical values can gernerally be left alone. They are useful if your labels consists of a lot of text as
this may lead to them overlapping. In this case try increasing the loop_width or helix_width options. -text_offset is also very useful for
avoiding overlapping.
AUTHOR
Tim Nugent <timnugent@gmail.com>
perl v5.14.2 2012-02-20 Bio::Graphics::DrawTransmembrane(3pm)