Mercurial > repos > dereeper > roary_plots

comparison Roary/contrib/roary2svg/roary2svg.pl @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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-1:000000000000 0:c47a5f61bc9f
1 #!/usr/bin/env perl
2 # From Torsten Seemann commit f46312e9df539c56b058f0ef25479d7297ceec89
3 # https://raw.githubusercontent.com/tseemann/nullarbor/master/bin/roary2svg.pl
4 use warnings;
5 use strict;
6 use Data::Dumper;
7 use List::Util qw(min max sum);
8 use List::MoreUtils qw(uniq all any);
9 use Text::CSV;
10 use SVG;
11
12 use constant FONT_ASPECT => 0.8;
13
14 my(@Options, $verbose, $taxacol, $width, $height, $acconly,
15 $consensus, $border, $colour, $sepcolour);
16 setOptions();
17
18 # read gene_presence_absence.csv from stdin
19 # "Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences","Avg sequences per isolate","Genome Fragment","Order within Fragment","Accessory Fragment","Accessory Order with Fragment","QC","SRR2352235","SRR2352236","SRR2352237","SRR2352238","SRR2352239","SRR2352240","SRR2352241","SRR2352242","SRR2352243","SRR2352244","SRR2352245","SRR2352246","SRR2352247","SRR2352248","SRR2352249","SRR2352250","SRR2352251","SRR2352252"
20 my $csv = Text::CSV->new() or die $!;
21 my $count=0;
22 my @matrix;
23 my @id;
24 my $N;
25 my $C=0;
26 my @tally; # genes per taxon
27 my @is_core; # boolean for this cluster being core
28
29 while (my $row = $csv->getline(\*ARGV) ) {
30 if ($count == 0) {
31 @id = splice @$row, $taxacol;
32 $N = scalar(@id);
33 print STDERR "Found $N taxa: @id\n";
34 }
35 else {
36 my @present = map { $row->[$taxacol+$_] ? 1 : 0 } (0 .. $N-1);
37 my $num_present = sum(@present);
38 $is_core[$count] = ($num_present == $N);
39 next if $acconly and $is_core[$count];
40 # next if $panonly and all { $_==1 } @present;
41 push @{ $matrix[$_] }, $present[$_] for (0 .. $N-1);
42 $tally[$_] += $present[$_] for (0 .. $N-1);
43 $C++;
44 }
45 $count++;
46 }
47 print STDERR "Found $C clusters.\n";
48
49 my $real_height = $height*($N+1);
50 my $svg = SVG->new(width=>$width, height=>$real_height);
51 my $dy = $height;
52 my $fontsize = 0.75 * $dy;
53
54 my $lchars = max( map { length($_) } @id );
55 my $llen = $fontsize * (1 + $lchars) * FONT_ASPECT;
56
57 my $rchars = max( map { length("$_") } @tally);
58 my $rlen = $fontsize * (1 + $rchars) * FONT_ASPECT;
59
60 my $width2 = $width - $llen - $rlen;
61 my $dx = $width2 / $C;
62 my $font_style = { 'font-family'=>'sans-serif', 'fill'=>'black', 'font-size'=>$fontsize };
63
64 print STDERR "Box = $dx x $dy px\n";
65 print STDERR "Left label = $lchars chr x $fontsize px\n";
66 print STDERR "Right label = $rchars chr x $fontsize px\n";
67
68 for my $j (0 .. $N-1) {
69 for my $i (0 .. $C-1) {
70 # print STDERR "$j $i $matrix[$j][$i]\n";
71 if ($matrix[$j][$i]) {
72 # box for each present gene
73 $svg->rectangle(
74 'x' => $llen+$i*$dx, 'y' => $j*$dy, 'width' => $dx, 'height' => $dy-1,
75 'style' => { fill=>$colour, opacity=>($is_core[$i] ? 1 : 0.75) },
76 );
77 }
78 }
79 # taxon label for each row
80 $svg->text( x=>$fontsize, y=>($j+0.75)*$dy, -cdata=>$id[$j], style=>$font_style );
81 # number of genes for each row
82 $svg->text( x=>$llen+$width2+$fontsize, y=>($j+0.75)*$dy, -cdata=>$tally[$j], style=>$font_style );
83 # separator line
84 my $ypos = ($j+1)*$dy;
85 $svg->line( x1=>0, y1=>$ypos, x2=>$width, y2=>$ypos, style=>{stroke=>$sepcolour});
86 }
87
88 # bottom label
89 my $bottom_text = "$N taxa, $C clusters";
90 $bottom_text .= $acconly ? " (accessory only)" : " (core + accessory)";
91 $svg->text( x=>$llen, y=>($N+0.75)*$dy, -cdata=>$bottom_text, style=>$font_style );
92
93 # border
94 if ($border) {
95 $svg->rectangle(
96 'x' => 0, 'y' => 0, 'width' => $width, 'height' => $real_height,
97 'style' => { stroke=>$sepcolour, fill=>'none' },
98 );
99 }
100
101 print STDERR "Writing SVG file\n";
102 print STDOUT $svg->xmlify;
103
104 print STDERR "Done.\n";
105
106 #----------------------------------------------------------------------
107 # Option setting routines
108
109 sub setOptions {
110 use Getopt::Long;
111
112 @Options = (
113 {OPT=>"help", VAR=>\&usage, DESC=>"This help"},
114 {OPT=>"verbose!", VAR=>\$verbose, DEFAULT=>0, DESC=>"Verbose output"},
115 {OPT=>"width=i", VAR=>\$width, DEFAULT=>1024, DESC=>"Canvas width"},
116 {OPT=>"height=i", VAR=>\$height, DEFAULT=>20, DESC=>"Row height"},
117 {OPT=>"taxacolumn=i", VAR=>\$taxacol, DEFAULT=>14, DESC=>"Column in gpa.csv where taxa begin"},
118 {OPT=>"colour=s", VAR=>\$colour, DEFAULT=>'DimGray', DESC=>"Colour of core cells"},
119 {OPT=>"sepcolour=s", VAR=>\$sepcolour, DEFAULT=>'LightGray', DESC=>"Colour of horizontal separators/borders"},
120 {OPT=>"acconly!", VAR=>\$acconly, DEFAULT=>0, DESC=>"Only draw accessory (non-core) genes"},
121 # {OPT=>"consensus!", VAR=>\$consensus, DEFAULT=>0, DESC=>"Add consensus row"},
122 {OPT=>"border!", VAR=>\$border, DEFAULT=>0, DESC=>"Add outline border"},
123 );
124
125 (!@ARGV) && (usage());
126
127 &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();
128
129 # Now setup default values.
130 foreach (@Options) {
131 if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
132 ${$_->{VAR}} = $_->{DEFAULT};
133 }
134 }
135 }
136
137 sub usage {
138 print "Usage: $0 [options] gene_presence_absence.csv > pan_genome.svg\n";
139 foreach (@Options) {
140 printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
141 defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
142 }
143 exit(1);
144 }
145
146 #----------------------------------------------------------------------
147