tools/genotyping/pl/plot.pl

   1 #!/usr/bin/perl -w
   2 use strict;
   3 use SVG;
   4 unless(@ARGV)
   5 {
   6         die "perl $0 <chrlen file><input file><out file><chr><width><proportion>\n";
   7 }
   8 my $chrlen;
   9 open IN,"$ARGV[0]" or die "The chrlen file can't open:$!\n";
  10 while(<IN>)
  11 {
  12         chomp;
  13         my @temp=split;
  14         if($temp[0]=~/$ARGV[3]/i)
  15         {
  16                 $chrlen=$temp[1];
  17         }
  18 }
  19 close IN;
  20 open CIN,"$ARGV[1]" or die "The input file can't open:$!\n";
  21
  22 my $temp='#';
  23 while ($temp =~ /^#/) {
  24         $temp=<CIN>;
  25 }
  26 chomp $temp;
  27 #chomp(my $temp=<CIN>);
  28
  29 my @name=split /\s+/,$temp;
  30 #shift @name;
  31 my $samnum=@name;
  32 #print "@name\n$samnum\n";
  33 #ast;
  34 my $side=100;
  35 my $width=$chrlen/$ARGV[5]+$side*3;
  36 my $height=$samnum*$ARGV[4]+200;
  37 my $svg=SVG->new('width',$width,'height',$height);
  38 $svg->rect('x',0,'y',0,'width',$width,'height',$height,'stroke','white','fill','white');
  39
  40 my %ReFormatGT=(0=>1, 1=>2, 0.5=>3,'NA'=>0, 'N'=>-1);
  41 my %FormatGT=(1=>0, 2=>1, 3=>0.5, 0=>'NA', -1=>'N');
  42 #my @color=("#2A2F7F","#68BE4A","#8C63A4","#B6292B","#FCDAD5");
  43 my %Color=(
  44         1  => '#CC0000',
  45         3  => '#1100CC',
  46         2  => '#008800',
  47         0  => '#CCCCCC',
  48         -1 => '#000022',
  49 );
  50 #my @label=("9311","pair64","no_decide","het","no_cov");
  51 my @Label=( [1,'9311'],[2,'PA64'],[3,'Hete'],[0,'N/A'],[-1,'N Zone'] );
  52 pop @Label;
  53 my $i=0;
  54 foreach(@Label) {
  55         my ($id,$label)=@$_;
  56         $svg->line('x1',$side,'y1',$side/2+$ARGV[4]*$i*2,'x2',$side+20,'y2',$side/2+$ARGV[4]*$i*2,'stroke',$Color{$id},'stroke-width',$ARGV[4]);
  57         $svg->text('x',$side+25,'y',$side/2+$ARGV[4]*$i*2+3,'font-family','Arial','stroke-width',0.3,'font-size',12,'-cdata',$label);
  58         ++$i;
  59 }
  60 #plot left
  61 $svg->line('x1',$side,'y1',$side,'x2',$side,'y2',$height-100,'stroke','black','stroke-width',1);
  62 foreach(1..int(($height-200)/($ARGV[4]*20)))
  63 {
  64         $svg->line('x1',$side,'y1',$height-100-20*$_*$ARGV[4],'x2',$side-5,'y2',$height-100-20*$_*$ARGV[4],'stroke','black','stroke-width',0.7);
  65         $svg->text('x',$side-30,'y',$height-100-20*$_*$ARGV[4]+5,'font-family','Arial','stroke-width',0.3,'font-size',14,'-cdata',20*$_);
  66 }
  67 my $sit=($height-200)/2+100+30;
  68 $svg->text('x',50,'y',$sit,'font-family','Arial','stroke-width',0.5,'font-size',16,'-cdata','Individuals','transform',"rotate(270,50,$sit)");
  69 #plot down
  70 $svg->line('x1',$side,'y1',$height-100,'x2',$width-$side*2,'y2',$height-100,'stroke','black','stroke-width',1);
  71 my $par=int($chrlen/5000000);
  72 my $len=int($chrlen/($ARGV[5]*$par));
  73 foreach(0..$par)
  74 {
  75         $svg->line('x1',$side+$_*$len,'y1',$height-100,'x2',$side+$_*$len,'y2',$height-100+5,'stroke','black','stroke-width',0.7);
  76         $svg->text('x',$side+$_*$len-5,'y',$height-100+20,'font-family','Arial','stroke-width',0.3,'font-size',14,'-cdata',5*$_);
  77 }
  78 $svg->text('x',($width-$side*3)/2+$side,'y',$height-100+50,'font-family','Arial','stroke-width',0.5,'font-size',16,'-cdata','Position(Mb)');
  79 #plot right
  80 $svg->line('x1',$width-200,'y1',$side,'x2',$width-200,'y2',$height-100,'stroke','black','stroke-width',1);
  81 my $m=0;
  82 foreach my $sam(1..$samnum)
  83 {
  84         $svg->line('x1',$width-2*$side,'y1',$height-$side-$ARGV[4]*$sam+$ARGV[4]/2,'x2',$width-2*$side+$ARGV[4]*4,'y2',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2,'stroke','black','stroke-width',0.7);
  85         if($sam%2==1)
  86         {
  87          $svg->line('x1',$width-2*$side+$ARGV[4]*4,'y1',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2,'x2',$width-2*$side+$ARGV[4]*14,'y2',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2,'stroke','black','stroke-width',0.7);
  88         $svg->text('x',$width-2*$side+$ARGV[4]*15,'y',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2+$ARGV[4]/2+2,'font-family','Arial','stroke-width',0.5,'font-size',10,'-cdata',$name[$sam-1]);
  89         }
  90         else
  91         {
  92                 $svg->line('x1',$width-2*$side+$ARGV[4]*4,'y1',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2,'x2',$width-2*$side+$ARGV[4]*6,'y2',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2,'stroke','black','stroke-width',0.7);
  93         $svg->text('x',$width-2*$side+$ARGV[4]*6,'y',$height-$side-$ARGV[4]*$sam-$ARGV[4]*2+$ARGV[4]/2+2,'font-family','Arial','stroke-width',0.5,'font-size',10,'-cdata',$name[$sam-1]);
  94         }
  95 }
  96 #plot up
  97 $svg->line('x1',$side,'y1',$side,'x2',$width-200,'y2',$side,'stroke','black','stroke-width',1);
  98 #plot data
  99 #chomp(my $line=<CIN>);
 100 #my @last=split /\s+/,$line;
 101 #my @color=("#2A2F7F","#00A06B");
 102 my $mark=0;
 103 my @new;
 104 my @last;
 105 my @start;
 106 while(<CIN>)
 107 {
 108         next if /^#/;
 109         chomp;
 110         my @now=split;
 111         if($mark==0)
 112         {
 113                 @last=@now;
 114                 foreach my $sam(1..$samnum)
 115                 {
 116                         $start[$sam]=1;
 117                 }
 118                 $start[0]="seat";
 119         }
 120         foreach my $sam(1..$samnum)
 121         {
 122                 if($last[$sam] ne $now[$sam])
 123                 {
 124                         my $n=$last[$sam];
 125                         my $x1=$side+$start[$sam]/$ARGV[5];
 126                         my $y1=$height-$side-$ARGV[4]*$sam+$ARGV[4]/2;
 127                         my $x2=$now[0]/$ARGV[5]+$side;
 128                         my $y2=$y1;
 129                         my $colr=$Color{$ReFormatGT{$n}};
 130 #               print "$x1\t$y1\n";
 131 =pod
 132                         if($n eq 0.5)
 133                         {
 134                                 $colr=$color[3];
 135                         }
 136                         elsif($n eq "NA")
 137                         {
 138                                 $colr=$color[4];
 139                         }
 140                         else
 141                         {
 142                                 $colr=$color[$n];
 143                         }
 144 =cut
 145                         $svg->line('x1',$x1,'y1',$y1,'x2',$x2,'y2',$y2,'stroke',$colr,'stroke-width',$ARGV[4]);# unless $n =~ /^N/;
 146                         $last[$sam]=$now[$sam];
 147                         $start[$sam]=$now[0];
 148                 }
 149         }
 150 #       print "@last\n";
 151 #       last;
 152         $mark=1;
 153         @new=@now;
 154 }
 155 foreach my $sam(1..$samnum)
 156 {
 157         if($last[$sam] eq $new[$sam])
 158         {
 159                 my $n=$last[$sam];
 160                 my $x1=$side+$start[$sam]/$ARGV[5];
 161                 my $y1=$height-$side-$ARGV[4]*$sam+$ARGV[4]/2;
 162                 my $x2=$new[0]/$ARGV[5]+$side;
 163                 my $y2=$y1;
 164 #               print "$x1\t$y1\n";
 165                 my $colr=$Color{$ReFormatGT{$n}};
 166                 $svg->line('x1',$x1,'y1',$y1,'x2',$x2,'y2',$y2,'stroke',$colr,'stroke-width',$ARGV[4]);# unless $n =~ /^N/;
 167         }
 168 }
 169
 170 open(OUT,">$ARGV[2]")or die;
 171 print OUT $svg->xmlify();
 172 close OUT;
 173
 174 __END__
 175 /nas/RD_09C/resequencing/user/zhangxm/soft/zijiao/new_selfing.pl
 176 perl /nas/RD_09C/resequencing/user/zhangxm/soft/zijiao/new_selfing.pl /nas/RD_09C/resequencing/Genome/Rice/Genome_9311/chr.nfo /panfs/POPULATION/PROJECT/Rice_RIL/chongqiong_RIL/data/Chr01.out.new /panfs/POPULATION/PROJECT/Rice_RIL/chongqiong_RIL/pic/Chr01.out.new.svg Chr01 5 40000
 177 cat ../9311/chrorder |while read a; do ./plot.pl ../9311/chr.nfo ril.$a.rgt ril.$a.r.svg $a 6 40000; done
 178 find . -name '*.?1.svg'|perl -lane '$a=$_;s/\.svg$/\.png/;system "convert $a $_"'