Mercurial > repos > big-tiandm > sirna_plant
diff sRNA_plot.pl @ 19:e0884a4b996b draft
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| author | big-tiandm |
|---|---|
| date | Wed, 05 Nov 2014 01:17:26 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sRNA_plot.pl Wed Nov 05 01:17:26 2014 -0500 @@ -0,0 +1,411 @@ +#!/usr/bin/perl -w +#========================================================================================== +# Date: +# Title: +# Comment: Program to plot gene structure +# Input: 1. +# 2. +# 3. +# Output: output file of gene structure graph by html or svg formt +# Test Usage: +#======================================================================================== +#use strict; +my $version=1.00; +use SVG; +use Getopt::Long; +my %opt; +GetOptions(\%opt,"g=s","l=s","span=s","c=s","o=s","out=s","cen:s","mark=s","h"); +if (!( defined $opt{o}) || defined $opt{h}) { +&usage; +} +my $span=$opt{span}; +#my $sample_cloumn=$opt{n}; +my $mark=$opt{mark}; +my @mark=split/\#/,$mark; +my $genelist=$opt{g}; +#===============================Define Attribute========================================== +my %attribute=( + canvas=>{ + 'width'=>1500, + 'height'=>1800 + }, + text=>{ + 'stroke'=>"#000000", + 'fill'=>"none", + 'stroke-width'=>0.5 + }, + line=>{ + 'stroke'=>"black", + 'stroke-width'=>1 + }, + csv=>{ + 'stroke'=>"red", + 'stroke-width'=>0.5 + }, + exon=>{ + 'stroke'=>"black", + 'stroke-width'=>1 + }, + intron=>{ + 'stroke'=>"black", + 'stroke-width'=>1.5 + }, + font=>{ + 'fill'=>"#000000", + 'font-size'=>12, + 'font-size2'=>10, + #'font-weight'=>'bold', + 'font-family'=>"Arial" + #'font-family'=>"ArialNarrow-bold" + }, + rect=>{ + 'fill'=>"lightgreen", + 'stroke'=>"black", + 'stroke-width'=>0.5 + }, + readwidth=>0.5 +); +#############################s#define start coordinate and scale +open(TXT,">$opt{out}"); +open(LENGTH,"$opt{l}")||die"cannot open the file $opt{l}"; +my %length; +while (my $aline=<LENGTH>) { + chomp $aline; + next if($aline=~/^\#/); + my @temp=split/\t/,$aline; + $temp[0]=~s/^c/C/; + $length{$temp[0]}=$temp[1]; +} +close LENGTH; +#--------------------------------------------------------------- +open(GENE,"$opt{g}")||die"cannot open the file $opt{g}"; +my %genelist; +while (my $aline=<GENE>) { + chomp $aline;#LOC_Os01g01280 Chr1 133291 134685 + + next if($aline=~/^\#/); + my @temp=split/\t/,$aline; + if ($temp[1]=~/^Chr(\d)$/) { + $temp[1]="Chr0$1"; + } + push @{$genelist{$temp[1]}},[$temp[0],$temp[2],$temp[3]]; + +} +close GENE; +#my %have_gene; +#foreach my $chr (sort keys %genelist) { +# my @genelist=sort{$a->[1] <=> $b->[1]}@{$genelist{$chr}}; +# my $start=$genelist[0][1]; +# my $end=$genelist[0][2]; +# for (my $i=0;$i<@genelist ;$i++) { +# if ($gene) { +# } +# } +#} + +my %gene_desity; +foreach my $chr (sort keys %genelist) { + my @genelist=sort{$a->[1] <=> $b->[1]}@{$genelist{$chr}}; + for (my $i=0;$i<@genelist ;$i++) { + my $start=int($genelist[$i][1]/$span); + my $end=int($genelist[$i][2]/$span); + #my @t_rpkm=split/\t/,$target_rpkm{$genelist[$i][0]}; + if ($start==$end) { + $gene_desity{$chr}[$start]++; + } + else{ + for (my $k=$start;$k<=$end ;$k++) { + $gene_desity{$chr}[$k]++; + } + } + } +} +#------------------------------------------region_gene_number------------------------- +my $max_gene_number=0; +my $total=0; +foreach my $chr (sort keys %genelist) { + for (my $i=0;$i<@{$gene_desity{$chr}} ;$i++) { + if (!(defined($gene_desity{$chr}[$i]))) { + $gene_desity{$chr}[$i]=0; + } + if ($gene_desity{$chr}[$i]>$max_gene_number) { + $max_gene_number=$gene_desity{$chr}[$i]; + #print "$gene_desity{$chr}[$i]\n"; + } + #print TXT "$i\t$gene_desity[$i]\n"; + $total+=$gene_desity{$chr}[$i]; + #print "$chr\t$i\t$gene_desity{$chr}[$i]\n"; + } +} +#print "Gene max:$max_gene_number\ntotal:$total\n"; + +#--------------------------------------------------------------- +my %centromere; +if (defined($opt{cen})) { + open CEN,"$opt{cen}"; + while (my $aline=<CEN>) { + chomp $aline; + next if($aline=~/^\#/); + my @temp=split/\t/,$aline; + $temp[0]=~s/^c/C/; + $centromere{$temp[0]}[0]=$temp[1]; + $centromere{$temp[0]}[1]=$temp[2]; + } + close CEN; +} + +#--------------------------------------------------------------- +my $max_length=0; +foreach my $chr (keys %length) { + if ($max_length<$length{$chr}) { + $max_length=$length{$chr}; + } + print "$chr\n"; +} +#====================================cluster data======================================= +open(CLUSTER,"$opt{c}")||die"cannot open the file $opt{c}"; +my %cluster; +my %cluster_density; +#my @sample=qw(39B3 3PA3 3LC3); +my @cluster_non_add; +while (my $aline=<CLUSTER>) { + next if($aline=~/^\#/); + chomp $aline;##Chr MajorLength Percent end 19B1 + my @temp=split/\t/,$aline; + my @ID=split/\:/,$temp[0]; + my @posi=split/\-/,$ID[1]; + my @all_rpkm=@temp; + shift @all_rpkm; + shift @all_rpkm; + shift @all_rpkm; +# for (my $s=0;$s<@all_rpkm ;$s++) {#log transfer +# $all_rpkm[$s]=log2($all_rpkm[$s]); +# } + push @{$cluster{$ID[0]}},[$temp[0],$posi[0],$posi[1],@all_rpkm];#ID start end rpkm(19B1,1PA1,1LC1); +} +close CLUSTER; +my %max_cluster; +my $chr_number=0; +print "@mark\n$mark\n"; +foreach my $chr (sort keys %cluster) { + for (my $i=0;$i<@mark ;$i++) { + $max_cluster{$chr}[$i]=0; + } + $chr_number++; +} +foreach my $chr (sort keys %cluster) { + @{$cluster{$chr}}=sort{$a->[1] <=> $b->[1]}@{$cluster{$chr}}; + for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) { + for (my $s=0;$s<@mark;$s++) { + if ($cluster{$chr}[$i][3+$s]>$max_cluster{$chr}) { + $max_cluster{$chr}[$s]=$cluster{$chr}[$i][3+$s]; + } + } + } + +} +foreach my $chr (sort keys %max_cluster) { + for (my $s=0; $s<@mark;$s++) { + # print "$max_cluster{$chr}[$s]\n"; + } +} +#--------------------------------------------------------------------------------------- +foreach my $chr(keys %cluster) { + for(my $i=0;$i<$#{$cluster{$chr}};$i++) { + my $start=int($cluster{$chr}[$i][1]/$span); + my $end=int($cluster{$chr}[$i][2]/$span); + if ($start==$end) { + for (my $s=0;$s<@mark ;$s++) { + $cluster_density{$chr}[$start][$s]+=$cluster{$chr}[$i][3+$s]; + } + + } + else{ + for (my $m=$start;$m<=$end ;$m++) { + for (my $s=0;$s<@mark ;$s++) { + $cluster_density{$chr}[$m][$s]+=$cluster{$chr}[$i][3+$s]; + } + } + } + } +} +my %max_cluster_density; +my $max_all_density=0; +foreach my $chr (sort keys %cluster) {# + for (my $s=0;$s<@mark ;$s++) { + for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) { + $max_cluster_density{$chr}[$s]=0; + } + } + +} +foreach my $chr (sort keys %cluster_density) { + print "$#{$cluster_density{$chr}}\n"; + for (my $k=0;$k<$#{$cluster_density{$chr}} ;$k++) { + print TXT "$chr\t$k"; + for (my $s=0;$s<@mark;$s++) { + if (!(defined($cluster_density{$chr}[$k][$s]))) { + $cluster_density{$chr}[$k][$s]=0; + } + if ($cluster_density{$chr}[$k][$s]>$max_cluster_density{$chr}[$s]) { + $max_cluster_density{$chr}[$s]=$cluster_density{$chr}[$k][$s]; + } + if ($cluster_density{$chr}[$k][$s]>$max_all_density) { + $max_all_density=$cluster_density{$chr}[$k][$s]; + } + print TXT "\t$cluster_density{$chr}[$k][$s]"; + } + print TXT "\n"; + } +} +print "max density: $max_all_density\n"; +#-------------------------------------------------------------------- +my $top_margin=30; +my $tail_margin=30; +my $XOFFSET=50; +my $YOFFSET=60; +my $chr_length=600; +my $Xscale=$chr_length/$max_length;#定义X轴比例尺 1:1000 x轴的坐标长度都要按照此比例尺换算 +#my $high_cov=$high_cov9B1=0.5;#定义峰图最高峰 +#my $Yscale=1/$high_cov;#定义Y轴比例尺 1:60 y轴的坐标长度都要按照此比例尺换算 +#========================================New canvas============================ +#### Starting #### +#新建画布 +my $width=1000; +my $heigth=100+130*$chr_number; +my $svg=SVG->new(width=>$width, height=>$heigth); +#画图起始点 +my $canvas_start_x=$XOFFSET; +my $canvas_end_x=$XOFFSET+$max_length*$Xscale;#按照比例尺 画线 +my $canvas_start_y=$YOFFSET; +my $canvas_end_y=$YOFFSET; +my $chr_heigth=$heigth-$YOFFSET-$tail_margin; +print "chr number:$chr_number\n"; +my $one_chr_heigth=$chr_heigth/$chr_number; +my $Yscale=($one_chr_heigth-15)/$max_all_density; +#my $chr_width=$YOFFSET; +#my $chr_start_y; +#my $chr_end_y; +#my $Yscale=0.01; +#=======================================title of the graph=============================== +#my $span_k=$span/1000; +#$svg->text('x',$width/2,'y',$YOFFSET-20,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',"Clusters rpkm/"."$span_k"."kb Distribution"); +#=======================================the top max chr line============================= +$svg->line(id=>'l1',x1=>$canvas_start_x,y1=>$canvas_start_y,x2=>$canvas_end_x,y2=>$canvas_end_y,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'}); +$long_scale=int ($max_length/10);#十等分 大刻度 +#大坐标刻度 +for ($i=0;$i<=10;$i++) { + my $long_x_start=$XOFFSET+$long_scale*$i*$Xscale; + my $long_x_end=$long_x_start; + my $long_y_start=$YOFFSET; + my $long_y_end=$YOFFSET-5; + $svg->line('x1',$long_x_start,'y1',$long_y_start,'x2',$long_x_end,'y2',$long_y_end,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'}); + my $Bscale=$long_scale*$i; + my $cdata=int ($Bscale/1000000); + $svg->text('x',$long_x_start,'y',$long_y_start-10,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$cdata."M"); +} +#========================================================================================= +my $cc=1; +foreach my $chr (sort keys %length) { + my $chr_end_x=$XOFFSET+$length{$chr}*$Xscale; + my $chr_start_x=$XOFFSET; + my $chr_start_y=$YOFFSET+$cc*$one_chr_heigth; + my $chr_end_y=$chr_start_y; + #$chr_start_y+=$chr_width; + #$chr_end_y+=$chr_width; +# for (my $i=0;$i<@{$gene_desity{$chr}};$i++) { +# print "$chr\t$i\t$gene_desity{$chr}[$i]\n"; +# my $red=$gene_desity{$chr}[$i]/$max_gene_number*255; +# my $green=$gene_desity{$chr}[$i]/$max_gene_number*255; +# print "$red\t$green\t0\n"; +# $svg->rect('x',$chr_start_x+$i*$span*$Xscale,'y',$chr_start_y,'width',$span*$Xscale,'height',8,'stroke',"rgb($red,$green,0)",'stroke-width',0.1,'fill',"rgb($red,$green,0)"); +# } + + $svg->line(x1=>$chr_start_x,y1=>$chr_start_y,x2=>$chr_end_x,y2=>$chr_end_y,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'}); + $svg->text('x',$XOFFSET-40,'y',$chr_start_y,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$chr); + my $m_length=$length{$chr}%1000000; + $svg->text('x',$chr_end_x+20,'y',$chr_start_y,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$m_length."M"); + + + if (defined($centromere{$chr}[0])) { + $svg->rect('x',$XOFFSET+$centromere{$chr}[0]*$Xscale,'y',$chr_start_y-2,'width',($centromere{$chr}[1]-$centromere{$chr}[0]+1)*$Xscale,'height',5,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue"); + } + for (my $s=0;$s<@mark ;$s++) { + for (my $i=0;$i<$#{$cluster_density{$chr}}-1 ;$i++) { + #if ($cluster_density{$chr}[$i]*$Yscale>40) { + #$cluster_density{$chr}[$i]=40/$Yscale; + #$svg->rect('x',$XOFFSET+$i*$span*$Xscale,'y',$chr_start_y-45,'width',$span*$Xscale,'height',5,'stroke',"green",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green"); + #} + #print "$i\t$cluster_density{$chr}[$i][$s]\t$cluster_density{$chr}[$i+1][$s]\n"; + my $cluster_density_start_x=$XOFFSET+$i*$span*$Xscale; + my $cluster_density_end_x=$XOFFSET+($i+1)*$span*$Xscale; + my $cluster_density_start_y=$chr_start_y-$cluster_density{$chr}[$i][$s]*$Yscale; + my $cluster_density_end_y=$chr_start_y-$cluster_density{$chr}[$i+1][$s]*$Yscale; + my $c_red=($s+1)/@mark*255; + $svg->line('x1',$cluster_density_start_x,'y1',$cluster_density_start_y,'x2',$cluster_density_end_x,'y2',$cluster_density_end_y,'stroke',"rgb($c_red,125,0)",'stroke-width',0.3); + } + + } + #=======Y axis + $svg->line(x1=>$chr_start_x,y1=>$chr_start_y,x2=>$chr_start_x,y2=>$chr_start_y-$one_chr_heigth+15,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'}); + #=======Y axis ===>3 xiaoge + my $s10=1; + my $e10=0; + my $chr_max=$max_all_density; + while ($chr_max>10) { + $chr_max=int($chr_max/10); + $s10=$s10*10; + $e10++; + } + $chr_max=$chr_max/2; + #print "*****$max_all_density\t$chr_max\t$s10\n"; + for (my $i=1;$i<3 ;$i++) { + my $y1=$chr_start_y-$chr_max*$s10*$Yscale*$i; + my $xiaoge_Y=$chr_max*$i; + $svg->line('x1',$chr_start_x,'y1',$y1,'x2',$chr_start_x+3,'y2',$y1,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'}); + $svg->text('x',$chr_start_x-26,'y',$y1+4,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',8,'font-family',$attribute{font}{'font-family'},'-cdata',$xiaoge_Y."e".$e10); + } + $cc++; +} + +for (my $s=0;$s<@mark ;$s++) { + my $c_red=($s+1)/@mark*255; + print "**$c_red\n"; + $svg->line('x1',$canvas_end_x+100,'y1',$YOFFSET+$s*20+30,'x2',$canvas_end_x+130,'y2',$YOFFSET+$s*20+30,'stroke',"rgb($c_red,125,0)",'stroke-width',1); + $svg->text('x',$canvas_end_x+150,'y',$YOFFSET+$s*20+5+30,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',$mark[$s]); +} +# +# +if (defined($opt{cen})) { + $svg->rect('x',$canvas_end_x+100,'y',$YOFFSET+@mark*20+30,'width',30,'height',5,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue"); + $svg->text('x',$canvas_end_x+150,'y',$YOFFSET+@mark*20+30+5,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',"centromere"); +} + +close TXT; + +open (OUT,">$opt{o}"); +print OUT $svg->xmlify(); + +sub log2 { + my $n = shift; + return log($n)/log(2); +} + +sub usage{ +print <<"USAGE"; +Version $version +Usage: +$0 +options: +-g genelist +-span +-n sample cloumn +-mark sample name +-o output graph file name with html or svg extension +-c cluster file input +-out txt output +-l length of chr +-cen centromere +-h help +USAGE +exit(1); +} \ No newline at end of file