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1 package Rcall;
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2
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3 use strict;
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4 use warnings;
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5 use Statistics::R;
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6
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7 use Exporter;
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8 our @ISA = qw(Exporter);
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9 our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );
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10
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11 sub histogram
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12 {
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13 my ($size_hashR, $out_png, $size) = @_;
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14 my (@abs, @ord);
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15 my $i = 0;
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16 foreach my $k (sort {$a <=> $b} keys %{$size_hashR})
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17 {
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18 my $percentage = 0;
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19 $percentage = $size_hashR->{$k} * 100 / $size if $size != 0;
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20 $abs[$i] = $k ; $ord[$i] = $percentage; $i++;
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21 }
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22 my $abs = join (",", @abs );
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23 my $ord = join (",", @ord );
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24 if (scalar(@abs) != 0)
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25 {
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26
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27 my $R = Statistics::R->new();
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28 $R->startR;
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29 $R->send(
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30 qq`library(ggplot2)
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31 percentage = c($ord)
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32 size =c($abs)
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33 min = min(size)
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34 max = max(size)
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35 dat = data.frame(size,percentage)
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36 png(filename=\"$out_png\", width = 800, height = 480)
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37 c = ggplot(dat,aes(size,percentage))
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38 c + geom_bar(stat="identity") + scale_x_continuous(breaks=min:max)+theme( axis.text.x = element_text(angle=90, hjust=0.5, size=20), axis.text.y = element_text( size=20 ), axis.title.x = element_text( size=25, face="bold"), axis.title.y = element_text( size=25, face="bold") )
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39 dev.off()`);
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40 $R->stopR();
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41
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42 }
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43 }
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44
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45 sub bg_to_png
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46 {
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47 my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;
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48 my $R = Statistics::R->new();
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49 $R->startR;
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50 $R->send(
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51 qq`library('Sushi')
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52 fai =read.table("$fai")
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53 if ( file.info("$bgP")\$size !=0 )
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54 {
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55 bgP = read.table("$bgP")
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56 } else { bgP = data.frame(factor(),integer()) }
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57
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58 if ( file.info("$bgM")\$size !=0 )
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59 {
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60 bgM = read.table("$bgM")
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61 } else { bgM = data.frame(factor(),integer()) }
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62
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63 f_both = function(chr,end) {
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64 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
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65 par(mfrow=c(2,1),mar=c(1,10,1,3))
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66 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
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67 axis(side=2,las=2,tcl=.2)
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68 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
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69 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
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70 labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
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71 axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
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72 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
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73 dev.off()
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74 }
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75
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76 f_plus = function(chr,end) {
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77 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
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78 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
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79 labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
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80 axis(side=2,las=2,tcl=.2)
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81 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
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82 dev.off()
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83 }
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84
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85 f_minus = function(chr,end) {
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86 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
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87 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
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88 labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
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89 axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
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90 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
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91 dev.off()
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92 }
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93
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94 fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ]
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95 mapply( f_both, fai_b\$V1, fai_b\$V2)
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96
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97 fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ]
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98 mapply( f_plus, fai_p\$V1, fai_p\$V2)
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99
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100 fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ]
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101 mapply( f_minus, fai_m\$V1, fai_m\$V2) `);
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102
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103 $R->stopR();
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104 }
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105
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106 sub pie_chart
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107 {
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108 my $dir = shift;
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109 my $in = $dir.'repartition.txt';
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110 my $out = $dir.'pie_chart.png';
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111
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112 my $R = Statistics::R->new();
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113 $R->startR;
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114 $R->send(
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115 qq`
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116 library(plotrix)
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117 library(RColorBrewer)
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118 R =read.table("$in",header=T)
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119 values = round(R\$percentage)
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120 keys = R\$type
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121 lab = paste(values, "%", sep="")
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122 png("$out")
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123 colors <- brewer.pal(7,"Paired")
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124 pie(values, col=colors, labels=lab, clockwise=TRUE)
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125 legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3)
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126 par(mai = c(0,0,0,0))
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127 layout(c(1,2),heights=c(0.3,1))
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128 plot.new()
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129 legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3)
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130 pie(values, col=colors, labels=lab, clockwise=TRUE)
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131 dev.off()`
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132 );
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133 $R->stopR();
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134 }
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135
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136 1;
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