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#! /usr/bin/perl
#
# Given a list file with 3-tuples for each series to plot
# create a pdf of a ROC curve.
#
# Format of list file:
# <series_name> <root> <color>
#
# <root>/<root>.em<key>.xy, <root>/<root>.em<key>.mer and <root>/<root>.time must exist.
#
# <key> is the second command line argument.
#
# Usage: perl rmark-Rroc.pl <listfile> <key: E-value multiplier (often 1)> <name for pdf> <1/0 yes/no draw error-bars> <plot title>
# Example usage:
# > perl rmark-Rroc.pl -R rmark-2.list 1 rmark-2.pdf 0 RMARK3_results
use Getopt::Std;
getopts('RPLM:');
if (defined $opt_R) { $replace_underscores = 1; }
if (defined $opt_P) { $paper_mode = 1; }
if (defined $opt_L) { $lty_mode = 1; }
if (defined $opt_M) { $perMb_mode = 1; $numMb = $opt_M; }
my $usage = "Usage: perl rmark-Rroc.pl [OPTIONS] <listfile> <key (e.g. 1E04)> <pdfname> <1/0 yes/no draw error-bars> <plot title>\n";
$usage .= "\nFormat of list file:\n\t<series_name> <root> <color/linetype>\n\n";
$usage .= "\nExample:\n\tinf1p02-df r2-i1p02 green\n\n";
$usage .= "<root>/<root>.em$key.xy, <root>/<root>.em$key.mer and <root>/<root>.time must exist\n\n";
$usage .= "Options:\n\t";
$usage .= "-R : replace underscores in <list file> with spaces\n\t";
$usage .= "-P : run in 'paper' mode, create a smaller PDF for a Bioinformatics Applications Note\n\t";
$usage .= "-L : list file includes line types instead of colors\n\t";
$usage .= "-M <f> : modify X-axis to FPs/query/Mb for a database of <f> Mb\n\n";
if(scalar(@ARGV) != 5) { printf("$usage"); exit(1); }
($listfile, $key, $pdf, $do_errorbars, $main) = @ARGV;
$n = 0;
if($do_errorbars && $lty_mode) { die "ERROR -L is incompatible with error bars"; }
if($replace_underscores) { $main =~ s/\_/ /g; }
@R = ();
$xlabel = "errors per query";
$ylabel = "fractional coverage of positives";
#push(@R, "xlimit<-c(0.001,20)\n");
if($perMb_mode) {
push(@R, "xlimit<-c(0.001,1.0)\n");
}
push(@R, "ylimit<-c(0,1)\n");
if($paper_mode) {
push(@R, "postscript(\"$pdf\", height=5.5, width=9.3)\n");
}
else {
push(@R, "pdf(\"$pdf\", height=8.5, width=11)\n");
}
open(LIST, $listfile) || die "ERROR, could not open $listfile";
@nametimemerA = ();
while(<LIST>) {
chomp $_;
if(m/\S+/) {
@fields = split(' ', $_, 3);
if(scalar(@fields) != 3) { die "ERROR, format of $listfile invalid"; }
($name, $root, $color_or_lty) = @fields;
$n++;
@xA = ();
@yA = ();
@dy1A = ();
@dy2A = ();
$xyfile = $root . ".em" . $key . ".xy";
$merfile = $root . ".em" . $key . ".mer";
$sumfile = $root . ".sum";
$timefile = $root . ".time";
$sumfile = $root . ".em" . $key . ".sum";
if(! -e $xyfile) {
$xyfile = $root . "/" . $xyfile;
if(! -e $xyfile) {
die "ERROR, $xyfile does not exist";
}
}
if(! -e $merfile) {
$merfile = $root . "/" . $merfile;
if(! -e $merfile) {
die "ERROR, $merfile does not exist";
}
}
if(! -e $sumfile) {
$sumfile = $root . "/" . $sumfile;
if(! -e $sumfile) {
die "ERROR, $sumfile does not exist";
}
}
if(! -e $timefile) {
$timefile = $root . "/" . $timefile;
if(! -e $timefile) {
die "ERROR, $timefile does not exist";
}
}
# process time file
open(TIME, $timefile) || die "ERROR, could not open time file $timefile";
while($line = <TIME>) {
chomp $line;
if($line =~ s/^total\s+//) {
$line =~ s/\s+.+$//;
$time = $line;
}
}
close(TIME);
# process mer file
open(MER, $merfile) || die "ERROR, could not open mer file $merfile";
while($mer = <MER>) {
if($mer =~ s/^\s*\*summary\*\s+//) {
$mer =~ s/\s+$//;
#$legstring = sprintf("\"%-25s %-10s MER: %4d\"", $name, $time . "h", $mer);
#push(@nametimemerA, $legstring);
#push(@nametimemerA, "\"" . $name . " " . $time . "h MER: " . $mer . "\"");
}
}
close(MER);
# process sum file
open(SUM, $sumfile) || die "ERROR, could not open sum file $sumfile";
$sum = <SUM>;
chomp $sum;
$summer = $sum;
($sumname, $trash1, $trash2, $summer, $sumfn, $sumfp, $summerthr, $trash3, $trash4, $trash5, $time) = split(/\s+/, $sum);
$legstring = sprintf("\"%-25s %-10s MER: %5.1f\"", $name, $time, $summer);
push(@nametimemerA, $legstring);
close(SUM);
if($lty_mode) {
push(@ltyA, "$color_or_lty");
$col_or_lty_str = "lty=$color_or_lty";
}
else {
push(@colorA, "\"$color_or_lty\"");
$col_or_lty_str = "col=\"$color_or_lty\"";
}
open(XY, $xyfile) || die "ERROR, could not open xy file $root.xy";
while(<XY>) {
if(/(\S+)\s+(\S+)\s+(\S+)\s+(\S+)/) {
($x, $y, $dy1, $dy2) = ($1, $2, $3, $4);
if($perMb_mode) { $x /= $numMb; }
push(@xA, $x);
push(@yA, $y);
push(@dy1A, $y + $dy1);
push(@dy2A, $y - $dy2);
$have_errorbars = 1;
}
elsif(/(\S+)\s+(\S+)/) {
if($perMb_mode) { $x /= $numMb; }
($x, $y) = ($1, $2, $3, $4);
push(@xA, $x);
push(@yA, $y);
if($do_errorbars) { die "ERROR, confidence intervals not read, but you want error bars"; }
$have_errorbars = 0;
}
}
push(@R, "x" . $n . "<-c" . return_vec_line(\@xA) . "\n");
push(@R, "y" . $n . "<-c" . return_vec_line(\@yA) . "\n");
if($have_errorbars) {
push(@R, "dy1" . $n . "<-c" . return_vec_line(\@dy1A) . "\n");
push(@R, "dy2" . $n . "<-c" . return_vec_line(\@dy2A) . "\n");
}
if($n == 1) {
push(@R, "plot(x$n, y$n, type=\"l\", lwd=2, log=\"x\", ylim=ylimit, $col_or_lty_str, main=\"$main\", xlab=\"$xlabel\", ylab=\"$ylabel\")\n");
if($paper_mode) {
push(@R, "points(x$n, y$n, type=\"p\", $col_or_lty_str)\n");
}
}
else {
push(@R, "points(x$n, y$n, type=\"l\", lwd=2, $col_or_lty_str)\n");
if($paper_mode) {
push(@R, "points(x$n, y$n, type=\"p\", $col_or_lty_str)\n");
}
}
if($do_errorbars) {
push(@R, "points(x$n, dy1$n, type=\"l\", lty=2, lwd=0.4, $col_or_lty_str)\n");
push(@R, "points(x$n, dy2$n, type=\"l\", lty=2, lwd=0.4, $col_or_lty_str)\n");
}
if($paper_mode) {
push(@R, "axis(2, labels=FALSE, at=c(0.2,0.4,0.6,0.8,1.0))\n");
push(@R, "axis(4, labels=FALSE, at=c(0.2,0.4,0.6,0.8,1.0))\n");
}
else {
push(@R, "axis(2, labels=FALSE, at=c(0.05,0.10,0.15,0.20,0.25,0.30,0.35,0.40,0.45,0.50,0.55,0.60,0.65,0.70,0.75,0.80,0.85,0.90,0.95,1.0))\n");
push(@R, "axis(4, labels=FALSE, at=c(0.05,0.10,0.15,0.20,0.25,0.30,0.35,0.40,0.45,0.50,0.55,0.60,0.65,0.70,0.75,0.80,0.85,0.90,0.95,1.0))\n");
}
close(XY);
}
}
close(LIST);
if($lty_mode) {
if($perMb_mode) {
push(@R, "legend(0.05, 0.25, c" . return_vec_line(\@nametimemerA) . ", cex=0.8, lty=c" . return_vec_line(\@ltyA) . ")\n");
}
else {
push(@R, "legend(0.5, 0.25, c" . return_vec_line(\@nametimemerA) . ", cex=0.8, lty=c" . return_vec_line(\@ltyA) . ")\n");
}
}
else {
push(@R, "legend(0.5, 0.25, c" . return_vec_line(\@nametimemerA) . ", lty=1, cex=0.8, col=c" . return_vec_line(\@colorA) . ", text.col=c" . return_vec_line(\@colorA) . ")\n");
}
push(@R, "dev.off()\n");
$Rinput = join("", @R);
open(OUT, ">rmark-Rroc.tmp") || die "ERROR, couldn't open rmark-Rroc.tmp for writing";
print OUT $Rinput;
close(OUT);
$status = system("cat rmark-Rroc.tmp | R --vanilla");
if ($status != 0) { die "FAILED: cat rmark-Rroc.tmp | R --vanilla"; }
#unlink "rmark-Rroc.tmp";
sub return_vec_line
{
($arr_ref) = $_[0];
$return_line = "(";
for($i = 0; $i < (scalar(@{$arr_ref})-1); $i++) { $return_line .= $arr_ref->[$i] . ", "; }
$return_line .= $arr_ref->[(scalar(@{$arr_ref}-1))] . ")";
return $return_line;
}
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