diff snpEff_2_1a/scripts/qqplot.pl @ 0:f8eaa3f8194b default tip

Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/scripts/qqplot.pl	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/perl
+#-------------------------------------------------------------------------------
+#
+# Plot a QQ plot (using R) 
+# Data is feed as a 1 column of numbers 
+#
+# Note: Any line that does not match a numeric regular expression, is filtered out).
+#
+#														Pablo Cingolani
+#-------------------------------------------------------------------------------
+
+#-------------------------------------------------------------------------------
+# Main
+#-------------------------------------------------------------------------------
+
+# Parse command line option (file base name)
+$base = 'QQ-plot';
+if( $ARGV[0] ne '' )	{ $base = $ARGV[0]; }
+
+$pngFile = "$base.png";
+$txtFile = "$base.txt";
+
+# Read STDIN and create an R vector
+open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n";
+print TXT "x\n";
+for( $ln = 0 ; $l = <STDIN> ; ) {
+	chomp $l;
+
+	# Does the string contain exactly one number? (can be float)
+	if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; }
+}
+close TXT;
+
+#---
+# Create an R program, save QQ-plot as PNG image
+#---
+
+open R, "| R --vanilla --slave " or die "Cannot open R program\n";
+print R <<EOF;
+
+qqplot <- function( x, title ) {
+	keep <- (x > 0) & (x <= 1) & ( ! is.na(x) );
+	x <- x[keep]
+	s <- sort(x);
+	ly <- -log10(s);
+
+	n <- length(s);
+	lx <- -log10( (1:n) / (n+1) )
+	
+	# Show auto range
+	#par( mfrow=c(2,1) );
+	#plot( lx, ly, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" );
+	#abline( 0 , 1 , col='red');
+
+	# Show full range in both plots
+	range <- c(0 , max(lx, ly) );
+	plot( lx, ly, xlim=range, ylim=range, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" );
+	abline( 0 , 1 , col='red');
+}
+
+png('$pngFile', width = 1024, height = 1024);
+
+data <- read.csv("$txtFile", sep='\t', header = TRUE);
+qqplot( data\$x, "$base" );
+
+dev.off();
+quit( save='no' )
+EOF
+
+close R;
+
+#---
+# Show figure
+#---
+
+$os = `uname`;
+$show = "eog"; 
+if( $os =~ "Darwin" )	{ $show = "open"; }
+`$show $pngFile`;
+