--- name: "Bio::Align::Graphics" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.2-3" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Align::Graphics" --- # Bio::Align::Graphics(3pm) Graphic Rendering of Bio::Align::AlignI Objects ## NAME Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects ## SYNOPSIS ``` use Bio::Align::Graphics; #Get an AlignI object, usually by using Bio::AlignIO my $file=shift @ARGV; my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw'); my $aln=$in->next_aln(); #Create a new Graphics object my $print_align = new Bio::Align::Graphics(align => $aln); #Draw the alignment $print_align->draw(); ``` ## DESCRIPTION Bio::Align::Graphics is a module designed to create image files out of Bio::Align::AlignI objects. An alignment may be manipulated with various formatting and highlighting options. An example: ``` #!/usr/bin/perl -w use Bio::AlignIO; use Bio::Align::Graphics; use strict; #Get an alignment file my $file = shift @ARGV; #Create an AlignI object using AlignIO my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw'); #Read the alignment my $aln=$in->next_aln(); #Create some domains for highlighting my @domain_start = ( 25 , 50, 80 ); my @domain_end = ( 40 , 60 , 100 ); my @domain_color = ( 'red' , 'cyan' , 'green' ); #Create Labels for the domains my @dml = ("CARD", "Proline Rich", "Transmembrane"); my @dml_start = (25, 50, 80); my @dml_end = (40, 60, 100); my @dml_color = ("lightpink", "lightblue", "lightgreen"); #Create individual labels my %labels = ( 145 => "Hep-c target"); my $print_align = new Bio::Align::Graphics( align => $aln, pad_bottom => 5, domain_start => \@domain_start, domain_end => \@domain_end, dm_color => \@domain_color, dm_labels => \@dml, dm_label_start => \@dml_start, dm_label_end => \@dml_end, dm_label_color => \@dml_color, labels => \%labels, out_format => "png"); $print_align->draw(); ``` ## METHODS This section describes the class and object methods for Bio::Align::Graphics. Typically you will begin by creating a Bio::Align::Graphics object, passing it an alignment object created using Bio::AlignIO. The Bio::Align::Graphics-\>*new()* method has a number of configuration variables that allow you to control the appearance of the final image. You will then call the *draw()* method to output the final image. ## CONSTRUCTORS *new()* is the constructor for Bio::Align::Graphics: - $print\_align = Bio::Align::Graphics-\>new(@options) The *new()* method creates a new graphics object. The options are a set of tag/value pairs as follows: ``` Option Value Default ------ ----- ------- align Bio::AlignI object None, must be supplied to draw an alignment output Filename to print image to STDOUT out_format png, jpeg, gif, gd png font Size of font, ranging from 1 to 5 2 and equal to the standard GD fonts ranging from gdTinyFont to gdGiantFont x_label Draws a scale numbering alignment true bases along top of image, every x bases are numbered, where x is the block_size option y_label Draws sequence ids of alignment true along left side of image bg_color Background color of the image white font_color Color of the font used for drawing black the alignment characters x_label_color Color of the font used for drawing red the base scale characters y_label_color Color of the font used for drawing blue the sequence id characters p_color Colors protein bases according to false a coloring scheme proposed by W.R. Taylor(Protein Engineering, vol 10 no 7, 1997), only works with protein alignments pad_top Additional whitespace characters 5 between top of image and x-label pad_bottom Additional whitespace characters 5 between bottom of image and alignment pad_left Additional whitespace characters 5 between left side of image and y-label pad_right Additional whitespace characters 5 between right side of image and alignment x_label_space Additional whitespace characters 1 between x_label and alignment y_label_space Additional whitespace characters 1 between y_label and alignment reference Characters which are identical to false the reference sequence are replaced with the match character reference_id Sequence id of the sequence to use First sequence as the reference supplied in alignment match_char Character to replace identical bases . in aligned sequences block_size Number of bases to group together 10 when printing alignment, groups are separated by whitespace block_space Amount of character whitespace to 2 separate groups of bases by labels A hash containing labels to be none printed beneath the alignment, where the keys are the bases to print the values at dm_start An array containing start bases none for highlighting of segments of the alignment, paired with dm_end option dm_end An array containing end bases none for highlighting of segments of the alignment, paired with dm_start options dm_color An array containing colors for silver highlighting segments of bases denoted by the coordinates located in the dm_start and dm_end options dml_start An array containing start bases none for addition of domain labels underneath the alignment, paired with dml_end dml_end An array containing end bases none for addition of domain labels underneath the alignment, paired with dml_start dml_color An array containing colors for silver the domain labels denoted by the coordinates located in the dml_start and dml_end options dm_labels An array containing labels to be none printed underneath specified domains, each label should correspond with the base position located in the dml_start option show_nonsynonymous Boolean value to turn option false on or off. If 0 (or undef), option is off. If 1 (or non-0), option is on. Only valid for nucleotide alignments. Output images are wider with this option on. ``` Note that all arrays and hashes must be passed by reference. ## OBJECT METHODS - $draw\_align-\>*draw()*; The *draw()* method draws the image with the options that were specified with *new()*. - $draw\_align-\>*width()*; Get the width of the image created with *new()*, in pixels. - $draw\_align-\>*height()*; Get the height of the image created with *new()*, in pixels. - $draw\_align-\>*aln\_length()*; Get the length of the alignment submitted to *new()*. - $draw\_align-\>*aln\_format()*; Get the format of the alignment submitted to *new()*. - $draw\_align-\>*no\_sequences()*; Get the number of sequences in the alignment submitted to *new()*. ## AUTHORS AND CONTRIBUTORS William McCaig, \ Mikhail Bekarev, \ Yoezen Hernandez, \ Weigang Qiu (Corresponding Developer), \ ## COPYRIGHT AND LICENSE Copyright (C) 2006-2008 by William McCaig This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.3 or, at your option, any later version of Perl 5 you may have available. ## SEE ALSO Bio::Align::AlignI, Bio::AlignIO, GD, GD::Simple