xbin/catCompare.pl at main · mocksu/xbin · GitHub

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
#!/usr/bin/perl -w
sub printUsage() {
    print "Categorical comparison of the specified fields of different files\n\n";
    print "Usage: ~ [-o 'opColumns.pl op'] <title> <in1.csv> <fld1> <label1> <in2.csv> <fld2> <label2> ... <inN.csv> <fldN> <labelN> <out.html>\n";
    exit(1);
}

use Getopt::Std;
my(%options);
getopts("o:", \%options);
my($op) = "";

if(exists $options{"o"}) {
    $op = $options{"o"};
}

if(scalar(@ARGV) < 8) {
    printUsage();
}

my $title = shift @ARGV;
my $out = pop @ARGV;

if(scalar(@ARGV) % 3 != 0) {
    printUsage();
}

use Flat;
use math;

my(@inFiles, @flds, @labels);

while(scalar(@ARGV) > 0) {
    my $inFile = shift @ARGV;
    my $fldName = shift @ARGV;

    if($op) {
	Util::run("opColumns.pl $inFile '$op' $fldName OP_$fldName $inFile.op", 1);
	  $inFile = "$inFile.op";
	  $fldName = "OP_$fldName";
      }

    my $in = Flat->new1($inFile);
    my $fld = $in->getFieldIndex($fldName);
    my $label = shift @ARGV;

    push @inFiles, $in;
    push @flds, $fld;
    push @labels, $label;
}

open OUT, ">>$out" or die $!;
print OUT "<html><title>Categorical Comparison of $title @labels</title></html>\n";
print OUT "<body>\n";

### compare and output results

# compare all-together
for(my($i) = 0; $i < scalar(@inFiles); $i++) {
    # box plot
}

# compare pair wise
print OUT "<h3>Categorical Comparison of $title</h3>\n";
print OUT "<table border=1>\n";
print OUT "<tr><th>Field</th><th>Value</th><th>Count (Total)</th><th>Pct</th><th>Pct Ratio</th></tr>\n";

my(%val2count); # categorical data for chi-square test

for(my($i) = 0; $i < scalar(@inFiles) - 1; $i++) {
    my(@arr1) = $inFiles[$i]->getFieldValues($flds[$i]);
    my(%val2count1);
    map {$val2count1{$_}++;} @arr1;
    my($sum1) = math::util::getSum(values %val2count1);
    my @keys1 = keys %val2count1;
    %{$val2count{$i}} = %val2count1;

    # category comparison
    for(my($j) = $i + 1; $j < scalar(@inFiles); $j++) {
	print "Comparing ", $inFiles[$i]->getFileName(), " with ", $inFiles[$j]->getFileName(), "\n";
	my(@arr2) = $inFiles[$j]->getFieldValues($flds[$j]);
	my(%val2count2);
	map {$val2count2{$_}++;} @arr2;
	my($sum2) = math::util::getSum(values %val2count2);
	my @keys2 = keys %val2count2;
	my @keys12 = @keys1;
	push @keys12, @keys2;
	@keys12 = math::util::getUniqueElements(@keys12);
	%{$val2count{$j}} = %val2count2;

	foreach $val (sort @keys12) {
	    my $ratio;

	    if(exists $val2count2{$val}) {
		print "val2count1{$val} = $val2count1{$val}, sum1 = $sum1, val2count2{$val} = $val2count2{$val}, sum2 = $sum2\n";
		$ratio = $val2count1{$val}/$sum1 / ($val2count2{$val}/$sum2);
	    }
	    elsif(exists $val2count1{$val}) {
		$ratio = "$val2count1{$val}/0";
	    }
	    else {
		$ratio = "0/0";
	    }

	    print OUT "<tr><td>$labels[$i]</td><td>$val</td><td>$val2count1{$val} ($sum1)</td><td>", $val2count1{$val}/$sum1, "</td><td rowspan=2>", $ratio, "</td></tr>\n",
	    "<tr><td>$labels[$j]</td><td>$val</td><td>$val2count2{$val} ($sum2)</td><td>", $val2count2{$val}/$sum2, "</td></tr>\n";
	}

#	print OUT "<tr><td colspan=2>Sum</td><td colspan=2>$sum1</td><td colspan=4>$sum2</td><td></td></tr>\n";
    }
}

my(%catValCounts);
foreach $i (keys %val2count) {
    map {$catValCounts{$_}++; } keys %{$val2count{$i}};
}

my(@catVals) = keys %catValCounts;

my(@catData); # categorical data for chi-square analysis
foreach $i (keys %val2count) {
    for(my($j) = 0; $j < scalar(@catVals); $j++) {
	if(exists $val2count{$i}{$catVals[$j]}) {
	    $catData[$i][$j] = $val2count{$i}{$catVals[$j]};
	}
	else {
	    $catData[$i][$j] = 0;
	}
    }
}

my $chisq = math::util::getChiSquare([@catData], "$out.r");
print OUT "<tr><td>chi-squared</td><td>X-squared = $chisq->[0]</td><td>df = $chisq->[1]</td><td colspan=2>p-value $chisq->[2]</td></tr>\n";
print OUT "</table><p>\n";
#print OUT "</body>\n";
#print OUT "</html>\n";

close OUT;