Mercurial > repos > romaingred > pirna_pipeline

comparison bin/Rcall.pm @ 0:198009598544 draft

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author romaingred
date Wed, 11 Oct 2017 09:57:58 -0400
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children ee6b4b2072a9
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-1:000000000000 0:198009598544
1 package Rcall;
2
3 use strict;
4 use warnings;
5 use Statistics::R;
6
7 use Exporter;
8 our @ISA = qw(Exporter);
9 our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );
10
11 sub histogram
12 {
13 my ($size_hashR, $out_png, $size) = @_;
14 my (@abs, @ord);
15 my $i = 0;
16 foreach my $k (sort {$a <=> $b} keys %{$size_hashR})
17 {
18 my $percentage = $size_hashR->{$k} * 100 / $size;
19 $abs[$i] = $k ; $ord[$i] = $percentage; $i++;
20 }
21 my $abs = join (",", @abs );
22 my $ord = join (",", @ord );
23 if (scalar(@abs) != 0)
24 {
25
26 my $R = Statistics::R->new();
27 $R->startR;
28 $R->send(
29 qq`library(ggplot2)
30 percentage = c($ord)
31 size =c($abs)
32 min = min(size)
33 max = max(size)
34 dat = data.frame(size,percentage)
35 png(filename=\"$out_png\", width = 800, height = 480)
36 c = ggplot(dat,aes(size,percentage))
37 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") )
38 dev.off()`);
39 $R->stopR();
40
41 }
42 }
43
44 sub bg_to_png
45 {
46 my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;
47 my $R = Statistics::R->new();
48 $R->startR;
49 $R->send(
50 qq`library('Sushi')
51 fai =read.table("$fai")
52 bgP = read.table("$bgP")
53 bgM = read.table("$bgM")
54 fun = function(chr,end) {
55 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
56 par(mfrow=c(2,1),mar=c(1,10,1,3))
57 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
58 axis(side=2,las=2,tcl=.2)
59 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
60 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
61 labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
62 axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
63 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
64 dev.off()
65 }
66 mapply( fun, fai\$V1, fai\$V2)`);
67 $R->stopR();
68 }
69
70 sub pie_chart
71 {
72 my $dir = shift;
73 my $in = $dir.'repartition.txt';
74 my $out = $dir.'pie_chart.png';
75
76 my $R = Statistics::R->new();
77 $R->startR;
78 $R->send(
79 qq`
80 library(plotrix)
81 library(RColorBrewer)
82 R =read.table("$in",header=T)
83 values = round(R\$percentage)
84 keys = R\$type
85 lab = paste(values, "%", sep="")
86 png("$out")
87 colors <- brewer.pal(7,"Paired")
88 pie(values, col=colors, labels=lab, clockwise=TRUE)
89 legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3)
90 par(mai = c(0,0,0,0))
91 layout(c(1,2),heights=c(0.3,1))
92 plot.new()
93 legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3)
94 pie(values, col=colors, labels=lab, clockwise=TRUE)
95 dev.off()`
96 );
97 $R->stopR();
98 }
99
100 1;