diff sRNA_plot.pl @ 23:cad6a1dfb174 draft

Uploaded
author big-tiandm
date Wed, 05 Nov 2014 21:11:49 -0500
parents e0884a4b996b
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRNA_plot.pl	Wed Nov 05 21:11:49 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