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