/usr/bin/R_mds is in seer 1.1.4-1build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | #!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Long;
my $usage_message = <<USAGE;
Usage: R_mds -d <distances.csv> -p <pheno_file>
Projects distance matrix into lower number of dimensions
Requires R and rhdf5 to be installed, see github wiki for more details
NB ensure order in dist matrix and pheno file is the same!
Options
Required
-d, --dist Distance matrix output by kmds/mash
-p, --pheno Phenotype file used by seer
Optional
-o, --output Output prefix (default 'all_structure')
--pc Number of dimensions to project into (default 10)
--no_hdf5 Write output as csv, use if seer compiled with 'NO_HDF5'
-R R executable (default 'which R')
-h, --help Displays this message
USAGE
my $tmp_file_name = "mds_tmp.Rscript";
#****************************************************************************************#
#* Main *#
#****************************************************************************************#
#* gets input parameters
my ($distance_file, $pheno, $output_prefix, $dimensions, ,$no_hdf5, $R_exec, $help);
GetOptions ("dist|d=s" => \$distance_file,
"pheno|p=s" => \$pheno,
"output|o=s" => \$output_prefix,
"no_hdf5" => \$no_hdf5,
"pc=i" => \$dimensions,
"R=s" => \$R_exec,
"help|h" => \$help
) or die($usage_message);
if (defined($help) || !defined($distance_file) || !defined($pheno))
{
print $usage_message;
}
else
{
# Set defaults
if (!defined($dimensions))
{
$dimensions = 10;
}
if (!defined($R_exec))
{
$R_exec = `which R`;
chomp $R_exec;
}
if (!defined($output_prefix))
{
$output_prefix = "all_structure";
}
# Check number of samples matches, write .samples if ok
open(PHENO, $pheno) || die("Could not open pheno file $pheno: $!\n");
my @samples;
while (my $line_in = <PHENO>)
{
chomp $line_in;
my @fields = split(/\t/, $line_in);
push(@samples, $fields[0]);
}
open(DIST, $distance_file) || die("Could not open distance file $distance_file: $!\n");
my $dist_line = <DIST>;
my @dist_cols = split(",", $dist_line);
if(scalar(@dist_cols) != scalar(@samples))
{
die("Number of samples in $pheno does not match those in $distance_file\n");
}
my $dist_rows = 1;
while (my $line_in = <DIST>)
{
$dist_rows++;
}
if($dist_rows != scalar(@dist_cols))
{
die("Distance matrix $distance_file is not square\n");
}
close DIST;
open(SAMPLES, ">$output_prefix.samples") || die("Could not write to $output_prefix.samples\n");
foreach my $sample (@samples)
{
print SAMPLES $sample . "\n";
}
close SAMPLES;
#****************************************************************************************#
#* Rscript *#
#****************************************************************************************#
my $Rscript;
if ($no_hdf5)
{
$Rscript = <<RSCRIPT;
distances <- read.csv("$distance_file", header=FALSE, stringsAsFactors=FALSE)
projection <- cmdscale(distances, k = $dimensions, eig = T)
covariates <- projection[["points"]]
for (i in 1:$dimensions)
{
covariates[,i] <- covariates[,i]/max(abs(covariates[,i]))
}
write.table(covariates, file="$output_prefix", quote=F, sep=",", row.names=F, col.names=F)
pdf("scree_plot.pdf")
plot(projection[[2]][1:30], type='l', xlab="Dimensions", ylab="Eigenvalue", main="Scree plot")
dev.off()
RSCRIPT
}
else
{
$Rscript = <<RSCRIPT;
library(rhdf5)
distances <- read.csv("$distance_file", header=FALSE, stringsAsFactors=FALSE)
projection <- cmdscale(distances, k = $dimensions, eig = T)
covariates <- projection[["points"]]
for (i in 1:$dimensions)
{
covariates[,i] <- covariates[,i]/max(abs(covariates[,i]))
}
h5createFile("$output_prefix")
h5write(covariates,"$output_prefix","dataset")
H5close()
pdf("scree_plot.pdf")
plot(projection[[2]][1:30], type='l', xlab="Dimensions", ylab="Eigenvalue", main="Scree plot")
dev.off()
RSCRIPT
}
open(RSCRIPT, ">$tmp_file_name") || die("Could not open $tmp_file_name: $!\n");
print RSCRIPT $Rscript;
close(RSCRIPT);
print STDERR "Running projection\n";
my $R_command = "$R_exec CMD BATCH --no-save --no-restore $tmp_file_name";
system($R_command);
unlink($tmp_file_name, "$tmp_file_name.Rout");
}
exit(0);
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