annotate bin/Rcall.pm @ 30:a8a6e346893f draft

Uploaded

package Rcall;

use strict;
use warnings;
use Statistics::R;

use Exporter;
our @ISA = qw(Exporter);
our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );

sub histogram
{
  my ($size_hashR, $out_png, $size)  = @_;
  my (@abs, @ord);
  my $i = 0;
  foreach my $k (sort {$a <=> $b} keys %{$size_hashR})
  {
    my $percentage = 0;
    $percentage = $size_hashR->{$k} * 100 / $size if $size != 0;
    $abs[$i] = $k ; $ord[$i] = $percentage; $i++;
  }
  my $abs = join (",", @abs );
  my $ord = join (",", @ord );
  if (scalar(@abs) != 0)
  {

    my $R = Statistics::R->new();
    $R->startR;
    $R->send(
      qq`library(ggplot2)
      percentage = c($ord)
      size =c($abs)
      min = min(size) 
      max = max(size) 
      dat = data.frame(size,percentage)
      png(filename=\"$out_png\", width = 800, height = 480)
      c = ggplot(dat,aes(size,percentage))
      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") )
      dev.off()`);
    $R->stopR();

  }
}

sub bg_to_png
{
  my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;
  my $R = Statistics::R->new();
  $R->startR;
  $R->send( 
  qq`library('Sushi')
  fai =read.table("$fai")
  if ( file.info("$bgP")\$size !=0 )
  {
    bgP = read.table("$bgP")
  } else { bgP = data.frame(factor(),integer()) }

  if ( file.info("$bgM")\$size !=0 )
  {
    bgM = read.table("$bgM")
  } else { bgM = data.frame(factor(),integer()) }

  f_both = function(chr,end) {
    jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
    par(mfrow=c(2,1),mar=c(1,10,1,3))
    plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50,  color=SushiColors(2)(2)[1])
    axis(side=2,las=2,tcl=.2)
    mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
    plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])    
    labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0,  chromline = 0.5,  scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
    axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
    mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
    dev.off() 
  }

  f_plus = function(chr,end) {
    jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
    plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50,  color=SushiColors(2)(2)[1])
    labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0,  chromline = 0.5,  scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
    axis(side=2,las=2,tcl=.2)
    mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)
    dev.off()
  }

  f_minus = function(chr,end) {
    jpeg( paste0("$dir",as.character(chr),".png"), quality=100)
    plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])    
    labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0,  chromline = 0.5,  scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)
    axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))
    mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)
    dev.off()
  }

  fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ]
  mapply( f_both, fai_b\$V1, fai_b\$V2)

  fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ]
  mapply( f_plus, fai_p\$V1, fai_p\$V2)

  fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ]
  mapply( f_minus, fai_m\$V1, fai_m\$V2) `);

  $R->stopR();
}

sub pie_chart
{
  my $dir = shift;
  my $in = $dir.'repartition.txt';
  my $out = $dir.'pie_chart.png';

  my $R = Statistics::R->new();
  $R->startR;
  $R->send(
  qq`
  library(plotrix)
  library(RColorBrewer)
  R =read.table("$in",header=T)
  values = round(R\$percentage)
  keys = R\$type
  lab = paste(values, "%", sep="")
  png("$out")
  colors <- brewer.pal(7,"Paired")
  pie(values, col=colors, labels=lab, clockwise=TRUE)
  legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3)
  par(mai = c(0,0,0,0))
  layout(c(1,2),heights=c(0.3,1))
  plot.new()
  legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3)
  pie(values, col=colors, labels=lab, clockwise=TRUE)
  dev.off()`
  );
  $R->stopR();
}

1;