# Function for creating .pdf files with plots of per-locus linkage scores
# for the optimal ordered subset for each covariate.  This function
# requires output from FLOSS version 1.4.1 or later.  For comparison, 
# each graph also plots the per-locus linkage scores for the set of all families.
#
# The plot for covariate "XXX" is written to file "XXX.pdf".  To run this script
#
# 1. Save this script to your computer.
# 2. Start R (available for download from the web at www.r-project.org).
# 3. At the R prompt enter: 
#
#       source("<pathname>") 
#
#    where <pathname> is the full pathname for this script (see step 1).
# 4. At the R prompt enter: 
#
#       plt2pdf("<pathname>") 
#
#    where <pathname> is the full pathname of the FLOSS ".plt" file.
#
plt2pdf <- function(filename) {

    d <- read.table(filename, header=TRUE);
    for (j in 3:dim(d)[2]) {
        cov.name <- names(d)[j];
        pdf(paste(cov.name, ".pdf", sep=""));
        x <- c(d[,1], d[,1]);
        y <- c(d[,2], d[,j]);
        plot(x, y, pch=20, main=paste(cov.name, " vs.  all families"), xlab="Position", ylab="Linkage Score");
        lines(d[, c(1,2)], lty=2);
        lines(d[, c(1,j)], lty=1);
        grid();
        dev.off();
    }
}