"."![](https://chart.googleapis.com/chart?".
"cht=bvs".
"&chxt=x,y".
"&chm=N,000000,0,-1,11".
"&chxl=0:|$fmt_xaxis".
"&chd=t:$fmt_yaxis".
"&chxr=1,0," . max(array_values($array)).
"&chds=0," . max(array_values($array)).
"&chbh=25,15,4".
"&chs=1000x200)
";
}
//-------------------function of plot need filename---------------
function plot($filename) {
$chromosome = chromosome_count($filename);
$fmt_xaxis = join("|",array_keys($chromosome));
$fmt_yaxis = join(",",array_values($chromosome));
//cht (chart type), chd (data), and chs (chart size)
//print max(array_values($chromosome));
print "
"."![](https://chart.googleapis.com/chart?".
"cht=bvs".
"&chxt=x,y".
"&chm=N,000000,0,-1,11".
"&chxl=0:|$fmt_xaxis".
"&chd=t:$fmt_yaxis".
"&chxr=1,0," . max(array_values($chromosome)).
"&chds=0," . max(array_values($chromosome)).
"&chbh=25,15,4".
"&chs=1000x200)
";
}
//--------------------function of plot_percentage---------------
function plot_percentage($filename,$filename1) {
$percentage = chromosome_count($filename);
$chromosome1 = chromosome_count($filename1);
foreach(array_keys($percentage) as $key) {
if($chromosome1[$key] == 0) {
$percentage[$key] = 0;
} else {
$percentage[$key] = round(100 * $percentage[$key] / $chromosome1[$key], 2);
}
}
$fmt_xaxis = join("|",array_keys($percentage));
$fmt_yaxis = join(",",array_values($percentage));
//cht (chart type), chd (data), and chs (chart size)
//print max(array_values($chromosome));
//print "
Overlap Percentage on each Chr:";
print "
"."![](https://chart.googleapis.com/chart?".
"cht=bvs".
"&chxt=x,y".
"&chm=N*p0*,000000,0,-1,11".
"&chxl=0:|$fmt_xaxis".
"&chd=t:$fmt_yaxis".
"&chxr=1,0," . max(array_values($percentage)).
"&chds=0," . max(array_values($percentage)).
"&chbh=25,15,4".
"&chs=1000x200)
";
}
//--------------------function of chromosome_count-------------------
function chromosome_count($filename) {
$chromosome = array(
"chr1"=>0,"chr2"=>0,"chr3"=>0,
"chr4"=>0,"chr5"=>0,"chr6"=>0,
"chr7"=>0,"chr8"=>0,"chr9"=>0,
"chr10"=>0,"chr11"=>0,"chr12"=>0,
"chr13"=>0,"chr14"=>0,"chr15"=>0,
"chr16"=>0,"chr17"=>0,"chr18"=>0,
"chr19"=>0,"chr20"=>0,"chr21"=>0,
"chr22"=>0,"chrX"=>0,"chrY"=>0
);
$file = fopen($filename, "r") or exit("Unable to open file!");
while(!feof($file)) {
$line = fgets($file) . "
";
$chr = explode(" ",$line);
$chr = $chr[0];
if(in_array($chr, array_keys($chromosome))) {
$chromosome[$chr]++;
}
}
fclose($file);
return $chromosome;
}
//--------------------function of repeats length-------------------
function repeats_length($filename) {
$chromosome = chromosome_count($filename);
$lengths = array(
"chr1"=>0,"chr2"=>0,"chr3"=>0,
"chr4"=>0,"chr5"=>0,"chr6"=>0,
"chr7"=>0,"chr8"=>0,"chr9"=>0,
"chr10"=>0,"chr11"=>0,"chr12"=>0,
"chr13"=>0,"chr14"=>0,"chr15"=>0,
"chr16"=>0,"chr17"=>0,"chr18"=>0,
"chr19"=>0,"chr20"=>0,"chr21"=>0,
"chr22"=>0,"chrX"=>0,"chrY"=>0
);
$file = fopen($filename,"r") or exit("Unable to open file!");
while(!feof($file)) {
$line = fgets($file). "
";
//$chr = explode(" ",$line);
$chr = explode("\t",$line);
$chr1 = $chr[0];
$length = (int)$chr[2] - (int)$chr[1] + 1;
$lengths[$chr1] = $lengths[$chr1] + $length;
}
foreach(array_keys($lengths) as $key) {
if($chromosome[$key] == 0) {
$lengths[$key] = 0;
} else {
$lengths[$key] = $lengths[$key]/$chromosome[$key];
}
}
fclose($file);
return $lengths;
}
//-----------------------For the overlapped counts and percentage ---//
function print_counts_percentage($chromosome, $chromosome1) { // $chromosome is after bedtool, $chromosome1 is before bedtool
$total = 0; // $total for overlaps
$total1 = 0; // $total1 for whole counts in .narrowPeak
print "
chromosomes: numbers of overlaps(Site counts, Percentage)";
foreach ($chromosome as $key => $value) {
if($chromosome1[$key] == 0) {
$per = 0;
} else {
$per = round(100 * $value / $chromosome1[$key], 2);
}
print "
$key : $value ($chromosome1[$key], $per%)";
$total += $value;
$total1 += $chromosome1[$key];
}
print "
Total overlaps: $total($total1, ".round(100*$total/$total1,2)."%)";
}
?>