根据SNPs展示基因的haplotypes

介绍：使用基因区域的SNP，绘制不同群体中基因的haplotypes

输入文件格式：

Index   R210    R077    R207    R204    R005    R038    R208    18Q0087 R205    R206    R065    R217    R216    R068    18Q0164 R089    R081    R153    18Q0050
ICF32654        CC      CC      CC      CC      NA      NA      CC      CC      CC      CC      NA      CC      CC      CC      CC      CG      CC      CC
ICF29002        GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG
ICF28260        GG      GG      GG      GG      GG      NA      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG
DCF15177        CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CG      CC      CC      CC      CC
DCF16046        CC      CC      CC      CC      CC      CG      CC      CG      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC
ICF48804        GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      GG      CG      GG      GG      GG      GG      GG      GG
DCF2829 CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC
DCF3113 CC      CC      CC      CC      NA      NA      CC      CC      CC      NA      CC      CC      CC      CC      CC      CC      CC      CC      CC
DCF37409        GG      GG      GG      GG      CC      NA      CC      CC      GG      CC      CC      GG      CG      CC      CC      CC      CC      CC
DCF23525        CC      CC      CC      CG      NA      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC      CC
ICF49621        GG      GG      GG      GG      GG      CG      GG      GG      GG      GG      GG      CG      GG      GG      GG      GG      GG      GG

脚本：plot_haplotypes.pl

#!/usr/bin/perl -w
use strict;
use SVG;

my $in0 = $ARGV[0]; ##- pos genotype
my $out = $ARGV[1];

my $width = 575;
my $height = 300;

my $svg = SVG->new(width => $width, height => $height);
my $xstart = 30;
my $ystart = 20;

my @color = ("#d9d6c3", "#fe4365", "#014d67", "#563624");  ##- NA:CC:GG:CG


my $high = 5;
my $widLen = 1;

   $svg -> rect(x => $xstart+480, y => 10, width => $widLen, height => $high, stroke => '#dbcfca', fill => $color[0], 'stroke-opacity' => 1, 'fill-opacity' => 1, 'stroke-width' => 0.1);
   $svg -> text(x => $xstart+480, y => 7, 'font-family' => 'Arial', 'font-size' => 5, 'font-weight' => 'normal', stroke => 'black', 'stroke-width' => 0.2, 'text-anchor' => 'middle', -cdata => "NA");
   
   $svg -> rect(x => $xstart+490, y => 10, width => $widLen, height => $high, stroke => '#dbcfca', fill => $color[1], 'stroke-opacity' => 1, 'fill-opacity' => 1, 'stroke-width' => 0.1);
   $svg -> text(x => $xstart+490, y => 7, 'font-family' => 'Arial', 'font-size' => 5, 'font-weight' => 'normal', stroke => 'black', 'stroke-width' => 0.2, 'text-anchor' => 'middle', -cdata => "CC");
   
   $svg -> rect(x => $xstart+500, y => 10, width => $widLen, height => $high, stroke => '#dbcfca', fill => $color[2], 'stroke-opacity' => 1, 'fill-opacity' => 1, 'stroke-width' => 0.1);
   $svg -> text(x => $xstart+500, y => 7, 'font-family' => 'Arial', 'font-size' => 5, 'font-weight' => 'normal', stroke => 'black', 'stroke-width' => 0.2, 'text-anchor' => 'middle', -cdata => "GG");

   $svg -> rect(x => $xstart+510, y => 10, width => $widLen, height => $high, stroke => '#dbcfca', fill => $color[3], 'stroke-opacity' => 1, 'fill-opacity' => 1, 'stroke-width' => 0.1);
   $svg -> text(x => $xstart+510, y => 7, 'font-family' => 'Arial', 'font-size' => 5, 'font-weight' => 'normal', stroke => 'black', 'stroke-width' => 0.2, 'text-anchor' => 'middle', -cdata => "CG");



my $count = 0;
open IN0, $in0;
<IN0>;
while(<IN0>){
  chomp;
  my @temp = split(/\t/, $_);
  $svg -> text(x => 15, y => $ystart+$high*$count+4, 'font-family' => 'Arial', 'font-size' => 3, 'font-weight' => 'normal', stroke => 'black', 'stroke-width' => 0.2, 'text-anchor' => 'middle', -cdata => "$temp[0]");
  for(my $m=1; $m<=$#temp; $m++){
      my $color = "white";
         $color = $color[0], if($temp[$m] eq "NA"); 
         $color = $color[1], if($temp[$m] eq "CC");
         $color = $color[2], if($temp[$m] eq "GG");
         $color = $color[3], if($temp[$m] eq "CG");
         $svg -> rect(x => $xstart+$widLen*($m-1), y => $ystart+$high*$count, width => $widLen, height => $high,
                        stroke => '#dbcfca', fill => $color, 'stroke-opacity' => 1, 'fill-opacity' => 1, 'stroke-width' => 0.1);
  }
  $count += 1;
}
close IN0;

open OUT,">$out.svg";
print OUT $svg->xmlify;
system ("/10t/caix/bin/distributing_svg_4.74/svg2xxx_release/svg2xxx  $out.svg -t png -dpi 500");

结果图展示

image.png