Mercurial > repos > brasset_jensen > srnapipe

annotate bin/Rcall.pm @ 61:9185ca0a7b43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated package according to recommendations.
author pierre.pouchin
date Wed, 16 Jan 2019 08:18:13 -0500
parents 4bc00caa60b4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
61
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
1 package Rcall;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
2
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
3 use strict;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
4 use warnings;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
5 use Statistics::R;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
6
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
7 use Exporter;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
8 our @ISA = qw(Exporter);
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
9 our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
10
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
11 sub histogram
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
12 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
13 my ($size_hashR, $out_png, $size) = @_;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
14 my (@abs, @ord);
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
15 my $i = 0;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
16 foreach my $k (sort {$a <=> $b} keys %{$size_hashR})
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
17 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
18 my $percentage = 0;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
19 $percentage = $size_hashR->{$k} * 100 / $size if $size != 0;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
20 $abs[$i] = $k ; $ord[$i] = $percentage; $i++;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
21 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
22 my $abs = join (",", @abs );
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
23 my $ord = join (",", @ord );
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
24 if (scalar(@abs) != 0)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
25 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
26
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
27 my $R = Statistics::R->new();
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
28 $R->startR;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
29 $R->send(
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
30 qq`library(ggplot2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
31 percentage = c($ord)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
32 size =c($abs)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
33 min = min(size)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
34 max = max(size)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
35 dat = data.frame(size,percentage)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
36 png(filename=\"$out_png\", width = 640, height = 640)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
37 c = ggplot(dat,aes(size,percentage))
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
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") )
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
39 dev.off()`);
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
40 $R->stopR();
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
41
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
42 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
43 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
44
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
45 sub bg_to_png
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
46 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
47 my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
48 my $R = Statistics::R->new();
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
49 $R->startR;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
50 $R->send(
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
51 qq`library('Sushi')
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
52 fai =read.table("$fai")
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
53 if ( file.info("$bgP")\$size !=0 )
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
54 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
55 bgP = read.table("$bgP")
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
56 } else { bgP = data.frame(factor(),integer()) }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
57
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
58 if ( file.info("$bgM")\$size !=0 )
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
59 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
60 bgM = read.table("$bgM")
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
61 } else { bgM = data.frame(factor(),integer()) }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
62
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
63 f_both = function(chr,end) {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
64 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
65 par(mfrow=c(2,1),mar=c(1,10,1,3))
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
66 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
67 axis(side=2,las=2,tcl=.2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
68 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
69 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
70 labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
71 axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
72 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
73 dev.off()
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
74 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
75
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
76 f_plus = function(chr,end) {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
77 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
78 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
79 labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
80 axis(side=2,las=2,tcl=.2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
81 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
82 dev.off()
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
83 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
84
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
85 f_minus = function(chr,end) {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
86 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
87 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
88 labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
89 axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
90 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
91 dev.off()
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
92 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
93
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
94 fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ]
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
95 mapply( f_both, fai_b\$V1, fai_b\$V2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
96
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
97 fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ]
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
98 mapply( f_plus, fai_p\$V1, fai_p\$V2)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
99
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
100 fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ]
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
101 mapply( f_minus, fai_m\$V1, fai_m\$V2) `);
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
102
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
103 $R->stopR();
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
104 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
105
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
106 sub pie_chart
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
107 {
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
108 my $dir = shift;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
109 my $in = $dir.'repartition.txt';
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
110 my $out = $dir.'pie_chart.png';
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
111
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
112 my $R = Statistics::R->new();
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
113 $R->startR;
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
114 $R->send(
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
115 qq`
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
116 library(plotrix)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
117 library(RColorBrewer)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
118 R =read.table("$in",header=T)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
119 values = round(R\$percentage)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
120 keys = R\$type
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
121 lab = paste(values, "%", sep="")
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
122 png("$out")
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
123 colors <- brewer.pal(7,"Paired")
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
124 pie(values, col=colors, labels=lab, clockwise=TRUE)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
125 legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
126 par(mai = c(0,0,0,0))
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
127 layout(c(1,2),heights=c(0.3,1))
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
128 plot.new()
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
129 legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
130 pie(values, col=colors, labels=lab, clockwise=TRUE)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
131 dev.off()`
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
132 );
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
133 $R->stopR();
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
134 }
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
135
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents: 40
diff changeset
136 1;