Linux Certif

Toute la documentation sur la certification Linux LPI

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>