diff snpEff_2_1a/scripts/smoothScatter.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/smoothScatter.pl	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,82 @@
+#!/usr/bin/perl
+#-------------------------------------------------------------------------------
+#
+# Plot a smooth scatter plot
+# Data is feed as two 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 = 'smoothScatter';
+if( $ARGV[0] ne '' )	{ $base = $ARGV[0]; }
+
+$pngFile = "$base.png";
+$txtFile = "$base.txt";
+
+# Read STDIN and create an R table
+open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n";
+print TXT "x\ty\n";
+for( $ln = 0 ; $l = <STDIN> ; ) {
+	chomp $l;
+	($x, $y) = split /\t/, $l;
+
+	# Does the string contain exactly one number? (can be float)
+	if(( $x =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) && ( $y =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ )) { print TXT "$x\t$y\n"; }
+}
+close TXT;
+
+#---
+# Create an R program, save histogram plot as PNG image
+#---
+
+open R, "| R --vanilla --slave " or die "Cannot open R program\n";
+print R <<EOF;
+
+smoothLowess <- function( x, y, title, q=1.0 ) {
+	# Show only this part of the data
+	xmin <- quantile( x, 1-q )
+	xmax <- quantile( x, q )
+
+	ymin <- quantile( y, 1-q )
+	ymax <- quantile( y, q )
+
+	keep <- (x >= xmin) & (x <= xmax) & (y >= ymin) & (y <= ymax);
+    qx <- x[ keep ]
+    qy <- y[ keep ]
+
+	smoothScatter(qx, qy, main=title, ylab='Y (column 2)', xlab='X (column 1)');
+	lines( lowess(qx,qy), col='orange' );
+}
+
+png('$pngFile', width = 1024, height = 1024);
+par( mfrow=c(2,1) );
+
+data <- read.csv("$txtFile", sep='\\t', header = TRUE);
+x <- data\$x
+y <- data\$y
+
+smoothLowess(x, y, "Smooth scatter plot and Lowess", 1.0);
+smoothLowess(x, y, "Smooth scatter plot and Lowess: Quantile [2% - 98%]", 0.98);
+
+dev.off();
+quit( save='no' )
+EOF
+
+close R;
+
+#---
+# Show figure
+#---
+
+$os = `uname`;
+$show = "eog"; 
+if( $os =~ "Darwin" )	{ $show = "open"; }
+`$show $pngFile`;
+