--- a/bin/Rcall.pm	Wed Oct 24 07:40:20 2018 -0400
+++ b/bin/Rcall.pm	Wed Jan 16 08:18:13 2019 -0500
@@ -1,136 +1,136 @@
-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 = 640, height = 640)
-      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()`
-  );
-  $R->stopR();
-}
-
-1;
+package Rcall;
+
+use strict;
+use warnings;
+use Statistics::R;
+
+use Exporter;
+our @ISA = qw(Exporter);
+our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );
+
+sub histogram
+{
+    my ($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 = 640, height = 640)
+            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;