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#!/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 "$l\n"; }
}
close TXT;
#---
# Create an R program, save QQ-plot as PNG image
#---
open R, "| R --vanilla --slave " or die "Cannot open R program\n";
print R <<EOF;
qqplot <- function( x, titleStr ) {
keep <- (x > 0) & (x <= 1) & ( ! is.na(x) );
x <- x[keep]
s <- sort(x);
ly <- -log10(s);
n <- length(s);
lx <- -log10( (1:n) / (n+1) )
# Show auto range
#par( mfrow=c(2,1) );
#plot( lx, ly, main=titleStr, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" );
#abline( 0 , 1 , col='red');
# Show full range in both plots
range <- c(0 , max(lx, ly) );
plot( lx, ly, xlim=range, ylim=range, main=titleStr, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" );
abline( 0 , 1 , col='red');
# Calculate inflation
ones <- rep(1, length(lx) )
X <- cbind(ones, lx)
fit <- lm.fit(x=X, y=ly)
abline( fit\$coefficients[1], fit\$coefficients[2], col='green')
title( sub=paste("Inflation:", fit\$coefficients[2], " Offset:", fit\$coefficients[1]) )
}
png('$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 &`;
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