annotate bin/Rcall.pm @ 15:6d9f127da28f draft

Uploaded
author brasset_jensen
date Fri, 26 Jan 2018 08:08:42 -0500
parents 1df6aaac800e
children 4bc00caa60b4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
1 package Rcall;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
2
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
3 use strict;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
4 use warnings;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
5 use Statistics::R;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
6
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
7 use Exporter;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
8 our @ISA = qw(Exporter);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
9 our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
10
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
11 sub histogram
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
12 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
13 my ($size_hashR, $out_png, $size) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
14 my (@abs, @ord);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
15 my $i = 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
16 foreach my $k (sort {$a <=> $b} keys %{$size_hashR})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
17 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
18 my $percentage = 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
19 $percentage = $size_hashR->{$k} * 100 / $size if $size != 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
20 $abs[$i] = $k ; $ord[$i] = $percentage; $i++;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
21 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
22 my $abs = join (",", @abs );
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
23 my $ord = join (",", @ord );
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
24 if (scalar(@abs) != 0)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
25 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
26
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
27 my $R = Statistics::R->new();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
28 $R->startR;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
29 $R->send(
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
30 qq`library(ggplot2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
31 percentage = c($ord)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
32 size =c($abs)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
33 min = min(size)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
34 max = max(size)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
35 dat = data.frame(size,percentage)
15
6d9f127da28f Uploaded
brasset_jensen
parents: 1
diff changeset
36 png(filename=\"$out_png\", width = 640, height = 640)
1
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
37 c = ggplot(dat,aes(size,percentage))
1df6aaac800e Deleted selected files
brasset_jensen
parents:
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") )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
39 dev.off()`);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
40 $R->stopR();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
41
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
42 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
43 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
44
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
45 sub bg_to_png
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
46 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
47 my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
48 my $R = Statistics::R->new();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
49 $R->startR;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
50 $R->send(
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
51 qq`library('Sushi')
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
52 fai =read.table("$fai")
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
53 if ( file.info("$bgP")\$size !=0 )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
54 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
55 bgP = read.table("$bgP")
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
56 } else { bgP = data.frame(factor(),integer()) }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
57
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
58 if ( file.info("$bgM")\$size !=0 )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
59 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
60 bgM = read.table("$bgM")
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
61 } else { bgM = data.frame(factor(),integer()) }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
62
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
63 f_both = function(chr,end) {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
64 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
65 par(mfrow=c(2,1),mar=c(1,10,1,3))
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
66 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
67 axis(side=2,las=2,tcl=.2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
68 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
69 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
70 labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
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)]))
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
72 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
73 dev.off()
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
74 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
75
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
76 f_plus = function(chr,end) {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
77 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
78 plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
79 labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
80 axis(side=2,las=2,tcl=.2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
81 mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
82 dev.off()
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
83 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
84
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
85 f_minus = function(chr,end) {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
86 jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
87 plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
88 labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
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)]))
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
90 mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
91 dev.off()
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
92 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
93
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
94 fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ]
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
95 mapply( f_both, fai_b\$V1, fai_b\$V2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
96
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
97 fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ]
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
98 mapply( f_plus, fai_p\$V1, fai_p\$V2)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
99
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
100 fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ]
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
101 mapply( f_minus, fai_m\$V1, fai_m\$V2) `);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
102
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
103 $R->stopR();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
104 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
105
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
106 sub pie_chart
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
107 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
108 my $dir = shift;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
109 my $in = $dir.'repartition.txt';
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
110 my $out = $dir.'pie_chart.png';
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
111
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
112 my $R = Statistics::R->new();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
113 $R->startR;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
114 $R->send(
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
115 qq`
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
116 library(plotrix)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
117 library(RColorBrewer)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
118 R =read.table("$in",header=T)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
119 values = round(R\$percentage)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
120 keys = R\$type
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
121 lab = paste(values, "%", sep="")
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
122 png("$out")
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
123 colors <- brewer.pal(7,"Paired")
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
124 pie(values, col=colors, labels=lab, clockwise=TRUE)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
125 legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
126 par(mai = c(0,0,0,0))
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
127 layout(c(1,2),heights=c(0.3,1))
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
128 plot.new()
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
129 legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
130 pie(values, col=colors, labels=lab, clockwise=TRUE)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
131 dev.off()`
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
132 );
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
133 $R->stopR();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
134 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
135
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
136 1;