Mercurial > repos > big-tiandm > sirna_plant
view chr_plot.pl @ 33:09fefe8db1d0 draft default tip
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| author | big-tiandm |
|---|---|
| date | Sat, 15 Nov 2014 01:33:45 -0500 |
| parents | 07745c0958dd |
| children |
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#!/usr/bin/perl -w #========================================================================================== # Date: # Title: # Comment: Program to plot gene structure # Input: 1. input file of Gene region annotation which format like GenePred # 2. input file of Transcripts region annotation which format like GenePred # 3. input file of gene snp detail info # 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","chro=s","mark=s","span=s","te=s","t=s","cen=s","c=s","o=s","out=s","h"); if (!(defined $opt{g} and defined $opt{c} and defined $opt{l} and defined $opt{chro} and defined $opt{mark} and defined $opt{o}) || defined $opt{h}) { &usage; } my $span=$opt{span}; #===============================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 my $length=$opt{"l"};#11 #my @target_e_value=qw(1.78 1.83 1.92 2.00 1.92 2.00 1.93 2.11 2.05 2.03 1.92 1.91 1.54 1.72 1.67); my $chr=$opt{"chro"}; my $start=1; my $XOFFSET=50; my $YOFFSET=60; #my $length=$end-$start+1; my $Xscale=600/$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============================ #--------------------------------------------------------------- if (defined($opt{cen})) { open(CEN,"$opt{cen}")||die"cannot open the file $opt{cen}"; my %centromere; while (my $aline=<CEN>) { chomp $aline; next if($aline=~/^\#/); my @temp=split/\t/,$aline; $centromere{$temp[0]}[0]=$temp[1]; $centromere{$temp[0]}[1]=$temp[2]; } close CEN; } #### Starting #### #新建画布 my $svg=SVG->new(); #画图起始点 my $canvas_start_x=$XOFFSET; my $canvas_end_x=$XOFFSET+$length*$Xscale;#按照比例尺 画线 my $canvas_start_y=$YOFFSET; my $canvas_end_y=$YOFFSET; #Draw a straight line between two points start(x1,y1) and end(x2,y2). #location attribute $svg->line(id=>'l1',x1=>$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'}); $long_scale=int ($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 $Bscale=$start+$long_scale*$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',$cdata."M"); } if (defined($opt{cen})) { $svg->rect('x',$XOFFSET+$centromere{$chr2}[0]*$Xscale,'y',$YOFFSET-2,'width',($centromere{$chr2}[1]-$centromere{$chr2}[0]+1)*$Xscale,'height',5,'stroke',"black",'stroke-width',"5",'fill',"black"); $svg->rect('x',$XOFFSET+$length*$Xscale+15,'y',$YOFFSET+20,'width',10,'height',5,'stroke',"black",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"black"); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$YOFFSET+20+5,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"Centromere"); } $svg->text('x',$XOFFSET+$length*$Xscale*0.42,'y',$YOFFSET-30,'stroke',"black",'stroke-width',1,'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',$chr); #====================================================MAIN PROGRAM======================== #===========================================gene list data================================ #open (TXT,">$opt{out}"); #open(TE,"$opt{te}")||die"cannot open the file $opt{te}"; #my %te; #while (my $aline=<TE>) { # chomp $aline; # my @temp=split/\t/,$aline; # if ($temp[2] eq "Y") { # $te{$temp[0]}=1; # } #} #close TE; #===================================Exp gene list data ================================= #open(TARGET,"$opt{t}")||die"cannot open the file $opt{t}"; #my %target_e; #my %target_rpkm; #while (my $aline=<TARGET>) { # chomp $aline;##Gene 19B1 1PA1 1LC1 29B2 2PA2 2LC2 39B3 3PA3 3LC3 93-4C PA-4C LY-4C 9343 PA43 LY43 19B1_VS_1LC1 19B1_VS_1PA1 1PA1_VS_1LC1 29B2_VS_2LC2 29B2_VS_2PA2 2PA2_VS_2LC2 39B3_VS_3LC3 39B3_VS_3PA3 3PA3_VS_3LC3 934C_LY4C 934C_PA4C PA4C_LY4C 9343_VS_LY43 9343_VS_PA43 PA43_VS_LY43 mpv_1 fold_1 mpv_2 fold_2 mpv_3 fold_3 mpv_4_B fold_4_B mpv_leaf fold_lead # next if($aline=~/^\#/); # my @temp=split/\t/,$aline; # $target_rpkm{$temp[0]}="$temp[7]\t$temp[8]\t$temp[9]"; # if ($temp[7]>$target_e_value[6]||$temp[8]>$target_e_value[7]||$temp[9]>$target_e_value[8]) { # $target_e{$temp[0]}="$temp[7]\t$temp[8]\t$temp[9]"; # } #} #close TARGET; #==================================================================================== my @genelist; #my @te_genelist; my @target_e; open(GENE,"$opt{g}")||die"cannot open the file $opt{g}"; while (my $aline=<GENE>) { chomp $aline;#LOC_Os01g01280 Chr1 133291 134685 + my @temp=split/\t/,$aline; #my $te; if ($temp[1]=~/^Chr(\d)$/) { $temp[1]="Chr0$1"; } next if($temp[1] ne $chr); #push @genelist,[$temp[0],$temp[3],$temp[4]]; push @genelist,[$temp[0],$temp[2],$temp[3]]; # if ($te{$temp[0]}) { # push @te_genelist,[$temp[0],$temp[3],$temp[4]]; # } # else{ # push @genelist,[$temp[0],$temp[3],$temp[4]]; # } # if ($target_e{$temp[0]}) { # push @target_e,[$temp[0],$temp[3],$temp[4]]; # } } close GENE; my @gene_desity; #my @region_target_rpkm; @genelist=sort{$a->[1] <=> $b->[1]}@genelist; for (my $i=0;$i<@genelist ;$i++) { # if ($genelist[$i][1]>($num1+1)*$span) { # $num1++; # } # if ($genelist[$i][1]>$num1*$span&&$genelist[$i][1]<=($num1+1)*$span) { # $gene_desity[$num1]++; # # } 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) { $gene_desity[$start]++; #for (my $rs=0;$rs<3 ;$rs++) { #print TXT "$rs\t$i\t$genelist[$i][0]\t$target_rpkm{$genelist[$i][0]}\n"; #$region_target_rpkm[$start][$rs]+=$t_rpkm[$rs]; #} #$target_rpkm_desity[$start][0]+=$temp[0]; #$target_rpkm_desity[$start][1]+=$temp[1]; #$target_rpkm_desity[$start][2]+=$temp[2]; } else{ for (my $k=$start;$k<=$end ;$k++) { $gene_desity[$k]++; #for (my $rs=0;$rs<3 ;$rs++) { #$region_target_rpkm[$k][$rs]+=$t_rpkm[$rs]; #} #$target_rpkm_desity[$k][0]+=$temp[0]; #$target_rpkm_desity[$k][1]+=$temp[1]; #$target_rpkm_desity[$k][2]+=$temp[2]; } } } #------------------------------------------region_gene_number------------------------- my $max_gene_number=0; my $total=0; for (my $i=0;$i<@gene_desity ;$i++) { if (!(defined($gene_desity[$i]))) { $gene_desity[$i]=0; } if ($gene_desity[$i]>$max_gene_number) { $max_gene_number=$gene_desity[$i]; } #print TXT "$i\t$gene_desity[$i]\n"; $total+=$gene_desity[$i]; } print "Gene max:$max_gene_number\ntotal:$total\n"; my $abc=@genelist; #my $cba=@te_genelist; print "aaaaaa:$abc\n"; #print "bbbbbb:$cba\n"; #---------------------------------------------region_gene_rpkm------------------------ #my $max_region_gene_rpkm=0; #my @max_region_gene_rpkm=qw(0 0 0); #my @total_region_gene_rpkm=qw(0 0 0); #for (my $i=0;$i<@region_target_rpkm ;$i++) { # for (my $s=0; $s<3;$s++) { # # if (!(defined($region_target_rpkm[$i][$s]))) { # $region_target_rpkm[$i][$s]=0; # } # $total_region_gene_rpkm[$s]+=$region_target_rpkm[$i][$s]; # if ($max_region_gene_rpkm<$region_target_rpkm[$i][$s]) { # $max_region_gene_rpkm=$region_target_rpkm[$i][$s]; # } # if ($max_region_gene_rpkm[$s]<$region_target_rpkm[$i][$s]) { # $max_region_gene_rpkm[$s]=$region_target_rpkm[$i][$s]; # } # } #} #my @ave_region_gene_rpkm=qw(0 0 0); #my $max_ave_rpkm=0; #for (my $i=0;$i<3;$i++) { # $ave_region_gene_rpkm[$i]=$total_region_gene_rpkm[$i]/($#region_target_rpkm+1); # if ($max_ave_rpkm<$ave_region_gene_rpkm[$i]) { # $max_ave_rpkm=$ave_region_gene_rpkm[$i]; # } #} # #print "***max region gene rpkm :$max_region_gene_rpkm\n\n"; #print "@max_region_gene_rpkm\n"; #if ($max_region_gene_rpkm>10*$max_ave_rpkm) { # $max_region_gene_rpkm=10*$max_ave_rpkm; #} #my @max_region_rpkm; #---------------------------------------------------------------------------------- #my @te_gene_desity; #@te_genelist=sort{$a->[1] <=> $b->[1]}@te_genelist; ##my $num2=0; #for (my $i=0;$i<@te_genelist ;$i++) { ## if ($te_genelist[$i][1]>($num2+1)*$span) { ## $num2=int($te_genelist[$i][1]/$span); ## } ## if ($te_genelist[$i][1]>$num2*$span&&$te_genelist[$i][1]<=($num2+1)*$span) { ## $te_gene_desity[$num2]++; ## } # my $start=int($te_genelist[$i][1]/$span); # my $end=int($te_genelist[$i][2]/$span); # if ($start==$end) { # $te_gene_desity[$start]++; # } # else{ # for (my $k=$start;$k<=$end ;$k++) { # $te_gene_desity[$k]++; # } # } #} #$max_te_gene_number=0; #$total=0; #for (my $i=0;$i<@te_gene_desity ;$i++) { # if (!(defined($te_gene_desity[$i]))) { # $te_gene_desity[$i]=0; # } # if ($te_gene_desity[$i]>$max_te_gene_number) { # $max_te_gene_number=$te_gene_desity[$i]; # } # print TXT "$i\t$te_gene_desity[$i]\n"; # $total+=$te_gene_desity[$i]; #} # #print "TE gene max:$max_te_gene_number\ntotal:$total\n"; #------------------------------------------------------- #my @target_e_desity; #@target_e=sort{$a->[1] <=> $b->[1]}@target_e; #for (my $i=0;$i<@target_e ;$i++) { # my $start=int($target_e[$i][1]/$span); # my $end=int($target_e[$i][2]/$span); # if ($start==$end) { # $target_e_desity[$start]++; # } # else{ # for (my $k=$start;$k<=$end ;$k++) { # $target_e_desity[$k]++; # } # } #} #my $max_target_e_number=0; #$total=0; #for (my $i=0;$i<@target_e_desity ;$i++) { # if (!(defined($target_e_desity[$i]))) { # $target_e_desity[$i]=0; # } # if ($target_e_desity[$i]>$max_target_e_number) { # $max_target_e_number=$target_e_desity[$i]; # } # print TXT "$i\t$target_e_desity[$i]\n"; # $total+=$target_e_desity[$i]; #} # #print "Target max:$max_target_e_number\ntotal:$total\n"; #====================================cluster data======================================= open(CLUSTER,"$opt{c}")||die"cannot open the file $opt{c}"; my $mark="$opt{mark}"; my @sample=split/\#/,$mark; my $sample_num=@sample; my @cluster; my @cluster_density; my @max_cluster_read=(0)x$sample_num; while (my $aline=<CLUSTER>) { next if($aline=~/^\#/); chomp $aline;##ID chr strand start end 19B1 #clusterID major_length percent sample1 sample2 sample3 #Chr01:192429-192452 24nt 1.00 0.00 97222.22 0.00 my @temp=split/\t/,$aline; my @id=split/\:/,$temp[0]; my @posit=split/\-/,$id[1]; next if($id[0] ne $chr);#Chr.01 chr04 push @cluster,[$id[0],$posit[0],$posit[1],@temp[3..3+$sample_num+1]]; #push @cluster,[$temp[0],$temp[3],$temp[4],$temp[11],$temp[12],$temp[13]];#ID start end rpkm(19B1,1PA1,1LC1); for (my $i=0;$i<@sample ;$i++) { if($temp[3+$i]>$max_cluster_read[$i]){ $max_cluster_read[$i]=$temp[3+$i]; } } } close CLUSTER; @cluster=sort{$a->[1] <=> $b->[1]}@cluster; for(my $i=0;$i<$#cluster;$i++) { my $start=int($cluster[$i][1]/$span); my $end=int($cluster[$i][2]/$span); if ($start==$end) { for (my $j=0;$j<$sample_num ;$j++) { $cluster_density[$start][$j]+=$cluster[$i][$j+$sample_num]; } } else{ for (my $m=$start;$m<=$end ;$m++) { for (my $j=0;$j<$sample_num ;$j++) { $cluster_density[$m][$j]+=$cluster[$i][$j+$sample_num]; } } } } my @max_cluster_density=(0)x$sample_num; my @total_cluster_density=(0)x$sample_num; my $max_cluster_density=0; for (my $i=0;$i<@sample;$i++) { for (my $k=0;$k<$#cluster_density ;$k++) { if (!(defined($cluster_density[$k][$i]))) { $cluster_density[$k][$i]=0; } $total_cluster_density[$i]+=$cluster_density[$k][$i]; if ($cluster_density[$k][$i]>$max_cluster_density[$i]) { $max_cluster_density[$i]=$cluster_density[$k][$i]; } if ($cluster_density[$k][$i]>$max_cluster_density) { $max_cluster_density=$cluster_density[$k][$i]; } } } my @ave_cluster_density=(0)x$sample_num; my $max_ave=0; for (my $i=0;$i<@sample;$i++) { $ave_cluster_density[$i]=$total_cluster_density[$i]/($#cluster_density+1); if ($max_ave<$ave_cluster_density[$i]) { $max_ave=$ave_cluster_density[$i]; } } print "max cluster reads:@max_cluster_read\n"; print "max cluster density:@max_cluster_density\n"; if ($max_cluster_density>10*$max_ave) { $max_cluster_density=10*$max_ave; } #===================================== plot gene desity ================================= #===row my $Y1scale=5; my $y1_gene_density=$YOFFSET+$max_gene_number*$Y1scale+10; for (my $i=0;$i<@gene_desity-1 ;$i++) { my $density_start_x=$XOFFSET+$i*$span*$Xscale; my $density_start_y=$y1_gene_density-$gene_desity[$i]*$Y1scale; my $density_end_x=$XOFFSET+($i+1)*$span*$Xscale; my $density_end_y=$y1_gene_density-$gene_desity[$i+1]*$Y1scale; my $heigth=$gene_desity[$i]/$max_gene_number; $svg->rect('x',$density_start_x,'y',$density_start_y,'width',$span*$Xscale,'height',$y1_gene_density-$density_start_y,'stroke',"read",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green"); #$svg->line('x1',$density_start_x,'y1',$density_start_y,'x2',$density_end_x,'y2',$density_end_y,'stroke',"red",'stroke-width',$attribute{csv}{'stroke-width'}); } $svg->line('x1',$XOFFSET,'y1',$y1_gene_density,'x2',$XOFFSET+$length*$Xscale,'y2',$y1_gene_density,'stroke',"black",'stroke-width',"black"); #====clomun $svg->line('x1',$XOFFSET,'y1',$y1_gene_density,'x2',$XOFFSET,'y2',$y1_gene_density-$max_gene_number*$Y1scale,'stroke',"black",'stroke-width',"black"); $svg->text('x',$XOFFSET-15,'y',$y1_gene_density,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',"0");#min gene number $svg->text('x',$XOFFSET-20,'y',$y1_gene_density-$max_gene_number*$Y1scale,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_gene_number);#max gene number #========================================================================================= #=============================plot TE gene desity========================================= #===row =cut my $Y2scale=$Y1scale; my $y2_te_gene_density=$y1_gene_density; for (my $i=0;$i<@te_gene_desity-1 ;$i++) { my $te_density_start_x=$XOFFSET+$i*$span*$Xscale; my $te_density_start_y=$y2_te_gene_density+$te_gene_desity[$i]*$Y2scale; my $te_density_end_x=$XOFFSET+($i+1)*$span*$Xscale; my $te_density_end_y=$y2_te_gene_density+$te_gene_desity[$i+1]*$Y2scale; #my $te_heigth=$te_gene_desity[$i]/$max_gene_number; $svg->rect('x',$te_density_start_x,'y',$y2_te_gene_density,'width',$span*$Xscale,'height',$te_density_start_y-$y2_te_gene_density,'stroke',"read",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green"); #$svg->line('x1',$density_start_x,'y1',$density_start_y,'x2',$density_end_x,'y2',$density_end_y,'stroke',"red",'stroke-width',$attribute{csv}{'stroke-width'}); } #column $svg->line('x1',$XOFFSET,'y1',$y2_te_gene_density,'x2',$XOFFSET,'y2',$y2_te_gene_density+$max_te_gene_number*$Y2scale,'stroke',"black",'stroke-width',"black"); $svg->text('x',$XOFFSET-20,'y',$y2_te_gene_density+$max_te_gene_number*$Y2scale,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_te_gene_number);#min gene number =cut #=======================gene density txt================================================== my $md=$span/1000; #$svg->text('x',$XOFFSET-30,'y',$YOFFSET+10,'width',"698",'height',"298",'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',"Number per \\30 kb","rotate","90",'writing-mode',"tb-rl"); $svg->rect('x',$XOFFSET+$length*$Xscale+15,'y',$y1_gene_density-$max_gene_number*$Y1scale*0.7,'width',10,'height',5,'stroke',"green",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green"); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y1_gene_density-$max_gene_number*$Y1scale*0.7+5,'stroke',"green",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"Genes"); #$svg->rect('x',$XOFFSET+$length*$Xscale+15,'y',$y1_gene_density-$max_gene_number*$Y1scale*0.7+20,'width',10,'height',5,'stroke',"green",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green"); #$svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y1_gene_density-$max_gene_number*$Y1scale*0.7+20+5,'stroke',"green",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"TE Genes"); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y1_gene_density-$max_gene_number*$Y1scale*0.7+20,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"genes number \/ $md kb"); #========================================================================================= #=============================plot exp gene desity========================================= =cut my $y3_target_e_density=$y2_te_gene_density+$max_te_gene_number*$Y2scale+$max_target_e_number*$Y2scale+20; #my $Y3scale=$Y1scale; for (my $i=0;$i<@target_e_desity-1 ;$i++) { my $target_e_density_start_x=$XOFFSET+$i*$span*$Xscale; my $target_e_density_start_y=$y3_target_e_density-$target_e_desity[$i]*$Y2scale; my $target_e_density_end_x=$XOFFSET+($i+1)*$span*$Xscale; my $target_e_density_end_y=$y3_target_e_density-$target_e_desity[$i+1]*$Y2scale; $svg->rect('x',$target_e_density_start_x,'y',$target_e_density_start_y,'width',$span*$Xscale,'height',$y3_target_e_density-$target_e_density_start_y,'stroke',"read",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red"); } $svg->line('x1',$XOFFSET,'y1',$y3_target_e_density,'x2',$XOFFSET+$length*$Xscale,'y2',$y3_target_e_density,'stroke',"black",'stroke-width',"black"); #column $svg->line('x1',$XOFFSET,'y1',$y3_target_e_density,'x2',$XOFFSET,'y2',$y3_target_e_density-$max_te_gene_number*$Y2scale,'stroke',"black",'stroke-width',"black"); $svg->text('x',$XOFFSET-15,'y',$y3_target_e_density,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',0);#max gene number $svg->text('x',$XOFFSET-20,'y',$y3_target_e_density-$max_te_gene_number*$Y2scale+10,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_target_e_number);#max gene number #=========================================exp gene indensity txt========================== $svg->rect('x',$XOFFSET+$length*$Xscale+15,'y',$y3_target_e_density-$max_target_e_number*$Y2scale*0.7,'width',10,'height',5,'stroke',"red",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red"); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y3_target_e_density-$max_target_e_number*$Y2scale*0.7+5,'stroke',"red",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"Exp Genes"); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y3_target_e_density-$max_target_e_number*$Y2scale*0.7+20,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"genes number \/ 50kb"); #calculate the different =cut #======================================================================================== my $Y3scale=0.04/$max_cluster_density*2500; #my $y3_cluster_density=$y2_te_gene_density+$max_te_gene_number*5+$max_cluster_density*$Y3scale+10; my $y3_cluster_density=$y1_gene_density+20; my $y3_total=$y1_gene_density+10; my @cluster_color=qw(fuchsia violet tomato); for (my $s=0;$s<3 ;$s++) { $y3_total=$y3_total+$max_cluster_density*$Y3scale+5; $svg->line('x1',$XOFFSET,'y1',$y3_total,'x2',$XOFFSET+$length*$Xscale,'y2',$y3_total,'stroke',"black",'stroke-width',$attribute{csv}{'stroke-width'}); $svg->line('x1',$XOFFSET,'y1',$y3_total,'x2',$XOFFSET,'y2',$y3_total-$max_cluster_density*$Y3scale,'stroke',"black",'stroke-width',$attribute{csv}{'stroke-width'}); $svg->text('x',$XOFFSET-15,'y',$y3_total,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',"0");#min gene number if ($max_cluster_density[$s]>$max_cluster_density) { $svg->text('x',$XOFFSET-40,'y',$y3_total-$max_cluster_density*$Y3scale+10,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_cluster_density[$s]);#max gene number } else{ $svg->text('x',$XOFFSET-40,'y',$y3_total-$max_cluster_density[$s]*$Y3scale+10,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_cluster_density[$s]);#max gene number } for (my $i=0;$i<$#cluster_density ;$i++) { my $cluster_density_start_x=$XOFFSET+$i*$span*$Xscale; my $cluster_density_end_x=$XOFFSET+($i+1)*$span*$Xscale; if ($cluster_density[$i][$s]>$max_cluster_density) { $cluster_density[$i][$s]=$max_cluster_density; } if ($cluster_density[$i+1][$s]>$max_cluster_density) { $cluster_density[$i+1][$s]=$max_cluster_density; } my $cluster_density_start_y=$y3_total-$cluster_density[$i][$s]*$Y3scale; my $cluster_density_end_y=$y3_total-$cluster_density[$i+1][$s]*$Y3scale; $svg->line('x1',$cluster_density_start_x,'y1',$cluster_density_start_y,'x2',$cluster_density_end_x,'y2',$cluster_density_end_y,'stroke',$cluster_color[$s],'stroke-width',$attribute{csv}{'stroke-width'}); } } for (my $s=0;$s<@sample ;$s++) { $svg->line('x1',$XOFFSET+$length*$Xscale+10,'y1',$y3_cluster_density+($y3_total-$y3_cluster_density)*0.3+30*$s,'x2',$XOFFSET+$length*$Xscale+30,'y2',$y3_cluster_density+($y3_total-$y3_cluster_density)*0.3+30*$s,'stroke',$cluster_color[$s],'stroke-width',$attribute{csv}{'stroke-width'}); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y3_cluster_density+($y3_total-$y3_cluster_density)*0.3+30*$s+5,'stroke',$cluster_color[$s],'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"Small RNAs ".$sample[$s]); } $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y3_cluster_density+($y3_total-$y3_cluster_density)*0.3+30*3-5,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"indensity of sRNA \/ $md kb"); #===================================plot region target gene rpkm================ =cut my $y4_region_gene_rpkm_1=$y3_total+10; my $y4_region_gene_rpkm=$y4_region_gene_rpkm_1; my $Y4scale=0.1/$max_region_gene_rpkm*1000; my @cluster_color_t=qw(blue slateblue steelblue); for (my $s=0;$s<3 ;$s++) { $y4_region_gene_rpkm+=$max_region_gene_rpkm*$Y4scale+5; $svg->line('x1',$XOFFSET,'y1',$y4_region_gene_rpkm,'x2',$XOFFSET+$length*$Xscale,'y2',$y4_region_gene_rpkm,'stroke',"black",'stroke-width',$attribute{csv}{'stroke-width'}); $svg->line('x1',$XOFFSET,'y1',$y4_region_gene_rpkm,'x2',$XOFFSET,'y2',$y4_region_gene_rpkm-$max_region_gene_rpkm*$Y4scale,'stroke',"black",'stroke-width',$attribute{csv}{'stroke-width'}); $svg->text('x',$XOFFSET-15,'y',$y4_region_gene_rpkm,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',"0");#min gene number if ($max_region_gene_rpkm[$s]>$max_region_gene_rpkm) { $svg->text('x',$XOFFSET-40,'y',$y4_region_gene_rpkm-$max_region_gene_rpkm*$Y4scale+10,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_region_gene_rpkm[$s]);#max gene number } else{ $svg->text('x',$XOFFSET-40,'y',$y4_region_gene_rpkm-$max_region_gene_rpkm[$s]*$Y4scale+10,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size2'},'font-family',$attribute{font}{'font-family'},'-cdata',$max_region_gene_rpkm[$s]);#max gene number } for (my $i=0;$i<$#region_target_rpkm ;$i++) { my $region_target_rpkm_start_x=$XOFFSET+$i*$span*$Xscale; my $region_target_rpkm_end_x=$XOFFSET+($i+1)*$span*$Xscale; if ($region_target_rpkm[$i][$s]>$max_region_gene_rpkm) { $region_target_rpkm[$i][$s]=$max_region_gene_rpkm; } if ($region_target_rpkm[$i+1][$s]>$max_region_gene_rpkm) { $region_target_rpkm[$i+1][$s]=$max_region_gene_rpkm; } my $region_target_rpkm_start_y=$y4_region_gene_rpkm-$region_target_rpkm[$i][$s]*$Y4scale; my $region_target_rpkm_end_y=$y4_region_gene_rpkm-$region_target_rpkm[$i+1][$s]*$Y4scale; $svg->line('x1',$region_target_rpkm_start_x,'y1',$region_target_rpkm_start_y,'x2',$region_target_rpkm_end_x,'y2',$region_target_rpkm_end_y,'stroke',$cluster_color_t[$s],'stroke-width',$attribute{csv}{'stroke-width'}); } } for (my $s=0;$s<3 ;$s++) { $svg->line('x1',$XOFFSET+$length*$Xscale+10,'y1',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y4_region_gene_rpkm_1)*0.3+30*$s,'x2',$XOFFSET+$length*$Xscale+30,'y2',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y4_region_gene_rpkm_1)*0.3+30*$s,'stroke',$cluster_color_t[$s],'stroke-width',$attribute{csv}{'stroke-width'}); $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y4_region_gene_rpkm_1)*0.3+30*$s+5,'stroke',$cluster_color_t[$s],'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"Target Genes ".$sample[$s]); } $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y4_region_gene_rpkm_1)*0.3+30*3-5,'stroke',"black",'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',"indensity of genes \/ 50kb"); =cut #for (my $s=0;$s<3 ;$s++) { # $svg->line('x1',$XOFFSET+$length*$Xscale+10,'y1',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y3_cluster_density)*0.3+30*$s,'x2',$XOFFSET+$length*$Xscale+30,'y2',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y3_cluster_density)*0.3+30*$s,'stroke',$cluster_color[$s],'stroke-width',$attribute{csv}{'stroke-width'}); # $svg->text('x',$XOFFSET+$length*$Xscale+35,'y',$y4_region_gene_rpkm_1+($y4_region_gene_rpkm-$y3_cluster_density)*0.3+30*$s+5,'stroke',$cluster_color[$s],'stroke-width',$attribute{text}{'stroke-width'},'font-size',$attribute{font}{'font-size'},'font-family',$attribute{font}{'font-family'},'-cdata',$sample[$s]); #} #========================================================================================= #sub ExpG_number { # #} #sub ExpCluster_number{ # #} #======================================================================================== open (OUT,">$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: -l centromere length -chro -mark \# -g input file of Gene region annotation which format like GenePred -span -c cluster file input -o svg output -h help USAGE exit(1); }