DrYak/make_local_report.pl

## make_local_report.pl
#!/usr/bin/env perl


use strict;
use Encode;

my $path = 'support';

my $report_html = <<'END_MESSAGE';
<!DOCTYPE html>
<meta charset="utf-8">
<title>Stacked-to-Grouped Bars</title>
<link rel="stylesheet" type="text/css" href="./inspector.css">
<script src="https://d3js.org/d3.v5.min.js"></script>
<body>
<form id=form name=form>
  <label style="margin-right:0.5em;"><input type=radio name=radio value="stacked" onchange="chrt.update(form.radio.value);" checked> Stacked</label>
  <label style="margin-right:0.5em;"><input type=radio name=radio value="grouped" onchange="chrt.update(form.radio.value);"> Grouped</label>
  <label style="margin-right:0.5em;">Palette <select name=palette onChange="chrt.recolor(form.palette.value);"><option value="blue" selected>Blues</option><option value="ryb" selected>RdYlBu</option><option value="spectral" selected>Spectral</option><option value="rainbow">Less Angry Rainbow</option><option value="set3">Discrete Set3</option><option value="paired">Discrete Paired</option></select></label>
</form>
<div style="position: absolute;
 overflow: hidden;
 top: 0;
 right: 0;
 z-index: 9999;
"><button onclick="filterselector.toggle()
">Filter:</button> <br/><svg id="scatter_filter"></div>
<svg id="stackedSVG" width=975 height=700 viewBox="0,0,975,700"></svg>
<script>
function selector() {
  // set the dimensions and margins of the graph
  const margin = {top: 10, right: 30, bottom: 30, left: 60},
    width = 460 - margin.left - margin.right,
    height = 400 - margin.top - margin.bottom;

  // append the svg object to the body of the page
  const svg = d3.select("#scatter_filter")
    .attr("cursor", "crosshair")
     .on("click", function() {
       var p = d3.mouse(this)
;
       updatefilter(x.invert(p[0] - margin.left), y.invert(p[1], margin.top));
    })
    .attr("width", width + margin.left + margin.right)
    .attr("height", height + margin.top + margin.bottom)
    .attr("overflow", "hidden")
  .append("g")
    .attr("transform",
          `translate(${margin.left},${margin.top})`);

  //Read the data
  const data = @PS_SCATTER@;

  // Add X axis
  const x = d3.scaleLinear()
    .domain([0, 1.2])
    .range([ 0, width ]);
  svg.append("g")
    .attr("transform", `translate(0,${height})`)
    .call(d3.axisBottom(x));

  // Add Y axis
  const y = d3.scaleLog()
    .domain([0.01, 10000])
    .range([ height, 0 ])
    .base(10);
  svg.append("g")
    .call(d3.axisLeft(y));

  // Add dots
  svg.append('g')
   .selectAll("dot")
    .data(data)
    .enter()
    .append("circle")
      .attr("cx", d => x(d[0])  )
      .attr("cy", d => y(d[1])  )
      .attr("r", 1.5)
      .style("fill", "#69b3a2")
;

  // Add selector
  const filterselector = svg
    .append('g')
      .style("fill", "#69b3a2")
      .style("opacity", ".2")
     .append("rect")
      .attr("y", 0);


  function updatefilter(p, s) {
    const fx = x(p);
    const fy = y(s);
    filterselector.attr("x", fx).attr("width", width-fx)
      .attr("height", fy);

  }
  var filter_visible = 1;
  function toggle() {
     svg.transition().duration(500).style('opacity', filter_visible ^= 1)
  }

  return Object.assign(svg.node(), {updatefilter, toggle});
};

var filterselector = selector();
filterselector.updatefilter(.9, 5);

const m = @M@; // number of values per series
const n = @N@; // number of series

const yz = @YZ_ARRAY@;
const xz = @XZ_ARRAY@; // list of X
const xp = @XP_ARRAY@; // window position to be used as X-axis label

function chart() {
  const margin = ({top: 5, right: 5, bottom: 20, left: 30});
  const width = 975;
  const height = 500;

  // for inspiration, go here: https://github.com/d3/d3-scale-chromatic#schemeAccent
  const z = {
    "blue": d3.scaleSequential(d3.interpolateBlues)
      .domain([-0.5 * n, 1.5 * n]),
    "ryb": d3.scaleSequential(d3.interpolateRdYlBu)
      .domain([0, n]),
    "spectral": d3.scaleSequential(d3.interpolateSpectral)
      .domain([0, n]),
    "rainbow": d3.scaleSequential(d3.interpolateRainbow)
      .domain([0, 12]),
    "set3": d3.scaleOrdinal(d3.schemeSet3)
      .domain([0, n]),
    "paired": d3.scaleOrdinal(d3.schemePaired)
      .domain([0, n])
  };

  const y01z = d3.stack()
      .keys(d3.range(n))
    (d3.transpose(yz)) // stacked yz
    .map((data, i) => data.map(([y0, y1]) => [y0, y1, i]));
  const y1Max = d3.max(y01z, y => d3.max(y, d => d[1]));
  const yMax = d3.max(yz, y => d3.max(y));
  const y = d3.scaleLinear()
    .domain([0, y1Max])
    .range([height - margin.bottom, margin.top]);

  const x = d3.scaleBand()
    .domain(xz)
    .rangeRound([margin.left, width - margin.right])
    .padding(0.08);

  const xAxis = svg => svg.append("g")
    .attr("transform", `translate(0,${height - margin.bottom})`)
    .style("font-size", `${Math.min((width/m).toFixed(2),10.00)}px`)
    .call(d3.axisBottom(x).tickSizeOuter(0).tickFormat((d, i) => xp[i]));

  const svg = d3.select('#stackedSVG')
    .style("width", "100%")
    .style("height", "auto");

  const gs = svg.selectAll("g")
    .data(y01z)
    .enter().append("g")
      .attr("fill", (d, i) => z["blue"](i))

  const rect = gs.selectAll("rect")
    .data(d => d)
    .join("rect")
      .attr("x", (d, i) => x(i))
      .attr("y", height - margin.bottom)
      .attr("width", x.bandwidth())
      .attr("height", 0);

  svg.append("g")
      .call(xAxis)
       .selectAll("text")
         .attr("y", 0)
         .attr("x", 7)
         .attr("dy", ".35em")
         .attr("transform", "rotate(90)")
         .style("text-anchor", "start");

  svg.append("g")
      .attr("class", "axis")
      .style("font-size", "8px")
      .attr("transform", `translate(${margin.left}, 0)`)
      .call(d3.axisLeft(y).ticks(null, "s"));

  function transitionGrouped() {
    y.domain([0, yMax]);

    rect.transition()
        .duration(500)
        .delay((d, i) => i * 20)
        .attr("x", (d, i) => x(i) + x.bandwidth() / n * d[2])
        .attr("width", x.bandwidth() / n)
      .transition()
        .attr("y", d => y(d[1] - d[0]))
        .attr("height", d => y(0) - y(d[1] - d[0]));
  }

  function transitionStacked() {
    y.domain([0, y1Max]);

    rect.transition()
        .duration(500)
        .delay((d, i) => i * 20)
        .attr("y", d => y(d[1]))
        .attr("height", d => y(d[0]) - y(d[1]))
      .transition()
        .attr("x", (d, i) => x(i))
        .attr("width", x.bandwidth());
  }

  function update(layout) {
    if (layout === "stacked") transitionStacked();
    else transitionGrouped();
  }

  function recolor(palette) {
    if (palette in z)
      gs.transition()
          .duration(500)
          .delay((d, i) => i * 20)
          .attr("fill", (d, i) => z[palette](i));
    else
      alert("Wrong color " + palette);
  }

  return Object.assign(svg.node(), {update, recolor});
}

var chrt = chart();
chrt.update('stacked');

</script>
</body>
END_MESSAGE


my @H;	# all haplotypes (over all windows of complete run)
my %H;

my %W;	# all windows
# my %d;
my @d;	# per-haplotype list of all "position->reads"
my %HN;	# per-window local number of local haplotypes

# for the filter's scatter plot
my @F;

my $file = 0;
opendir(my $dh, $path) or die "Can't open ${path}: $!";
while (readdir $dh) {
	# 	"support/w-HXB2-5849-5950.reads-support.fas.gz"
	next unless $_ =~ m{w-(?<chr>.*)-(?<w>[[:digit:]]+)-(?<e>[[:digit:]]+).reads-support.fas.gz};
	print STDERR $file++ . " - <$_> : ";

	my $w = $+{'w'};	# this windows' position
	my $hn = 0;	# counting haplotypes inside this windows
	my $htot = 0;

	open my $fh, "gunzip -kc $path/$_|" or die "Can't open ${path}: $!";
	while (<$fh>) {
		chomp;
		#	">hap_3|posterior=1 ave_reads=1224.37"
		next unless $_ =~ m{^\>(?<h>[^\|]+)\|posterior=(?<p>[[:digit:].]*) *ave_reads=(?<s>[[:digit:].]*)};
		my $h=$+{'h'};	# haplotype name ('hap_nnn')
		my $s=$+{'s'};	# support (as average number of reads per base)
		my $p=$+{'p'};	# posterior
		push @F, +[ $p, $s ];
		$h =~ m{_(?<n>[[:digit:]]+)$}; # just the number of the haplotype
		$H[$+{'n'}] = $h;
		$H{$h} = $+{'n'};
		$W{$w} = 1;
		$htot++;

		next unless ($s > 5.0 and $p > .8); # filter low quality
#		if (exists $d{$h} and ref $d{$h} eq ref {}) {
		if (exists $d[$hn] and ref $d[$hn] eq ref {}) {
			$d[$hn]->{$w} = $s;
# 			$d{$h}->{$w} = $s;
		} else {
 			$d[$hn] = +{ $w => $s };
# 			$d{$h} = +{ $w => $s };
		}
		$hn++;
	}
	close $fh;
	$HN{$w} = $hn;
	print STDERR "$htot haplotypes, $hn filtered\n";
}
close $dh;

print STDERR "creating report...";

# scatter plot for filter selector
my $PS_SCATTER = '[' . join(',', map { '[' . join(',', @{$_} ) . ']' } @F ) . ']';

# every single window
my @W = sort { $a <=> $b } keys %W;
my $m = @W;

# old style : every single haplotype...
my $n = @H;
die "\nIs there a missing haplotype ? Highest number is $n: $H[$#H] but only found " . (scalar keys %H) . "haplotypes"
	if ( $n != scalar keys %H );
# ...actually no only keep the filtered
$n = @d;

my $XZ = '[' . join(',', ( 0 .. $#W) ) . ']';
my $NZ = '[' . join(',', map { $HN{$_} } @W )  . ']';
my $XP = '[' . join(',', @W )  . ']';
my $YZ = '[' . join(",\n", map { my $hd = $_;
		'[' . join(',', map { (exists $hd->{$_} ) ? $hd->{$_} : 0 } @W) . ']'
	} @d) . ']';
# my $YZ = '[' . join(",\n", map { my $h = $_;
# 		'[' . join(',', map { (exists $d{$h} and exists $d{$h}->{$_} ) ? $d{$h}->{$_} : 0 } @W) . ']'
# 	} @H) . ']';

$report_html =~ s{\@M\@}{$m};
$report_html =~ s{\@N\@}{$n};
$report_html =~ s{\@NZ_ARRAY\@}{$NZ};
$report_html =~ s{\@XZ_ARRAY\@}{$XZ};
$report_html =~ s{\@XP_ARRAY\@}{$XP};
$report_html =~ s{\@YZ_ARRAY\@}{$YZ};
$report_html =~ s{\@PS_SCATTER\@}{$PS_SCATTER};
open my $o, '>', "report.html" or die "Cannot write report";
print $o $report_html;
close $o;
print STDERR "done\n";

exit 0;

## report_2VM.html
<!DOCTYPE html>
<meta charset="utf-8">
<title>Stacked-to-Grouped Bars</title>
<link rel="stylesheet" type="text/css" href="./inspector.css">
<body>
<script src="https://d3js.org/d3.v5.min.js"></script>
<form id=form name=form>
  <label style="margin-right:0.5em;"><input type=radio name=radio value="stacked" onchange="chrt.update(form.radio.value);" checked> Stacked</label>
  <label style="margin-right:0.5em;"><input type=radio name=radio value="grouped" onchange="chrt.update(form.radio.value);"> Grouped</label>
</form>
<svg id="stackedSVG" width=975 height=700 viewBox="0,0,975,700"></svg>
<script>

const margin = ({top: 0, right: 0, bottom: 10, left: 0});
const width = 975;
const height = 500;
const m = 21; // number of values per series
const n = 5; // number of series

const yz = [[37,53.9142,69.9611,88.7078,70.8582,82.9792,81.906,90.9153,82,87.9981,76,94.7667,104.696,76,81,68,72,68,72.7003,64.8661,16],
[39.2597,47,67,65,62.9975,76.9958,74,90,90.5048,87,88.802,85,89,90.7665,85.8044,86.8043,72.9517,75.6065,56,47,27.9167],
[0.168831,0,0,0.0281385,0,0,0,0.0184162,0.0558767,0,0.0222222,0.0111111,0.0463918,0.0379242,0.0139721,0.0150538,0,0.0393519,0.0335917,0.0238095,0.0151515],
[0.012987,0,0,0,0,0,0,0,0.0500963,0,0,0,0.0120275,0,0,0,0,0.037037,0.0129199,0,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0138889,0,0,0]];
const xz = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20];

const z = d3.scaleSequential(d3.interpolateBlues)
    .domain([-0.5 * n, 1.5 * n]);


const y01z = d3.stack()
    .keys(d3.range(n))
  (d3.transpose(yz)) // stacked yz
  .map((data, i) => data.map(([y0, y1]) => [y0, y1, i]));
const y1Max = d3.max(y01z, y => d3.max(y, d => d[1]));
const yMax = d3.max(yz, y => d3.max(y));
const y = d3.scaleLinear()
    .domain([0, y1Max])
    .range([height - margin.bottom, margin.top]);

const x = d3.scaleBand()
    .domain(xz)
    .rangeRound([margin.left, width - margin.right])
    .padding(0.08);

const xAxis = svg => svg.append("g")
    .attr("transform", `translate(0,${height - margin.bottom})`)
    .call(d3.axisBottom(x).tickSizeOuter(0).tickFormat(() => ""));

function chart() {
  const svg = d3.select('#stackedSVG')
    .style("width", "100%")
    .style("height", "auto");

  const rect = svg.selectAll("g")
    .data(y01z)
    .enter().append("g")
      .attr("fill", (d, i) => z(i))
    .selectAll("rect")
    .data(d => d)
    .join("rect")
      .attr("x", (d, i) => x(i))
      .attr("y", height - margin.bottom)
      .attr("width", x.bandwidth())
      .attr("height", 0);

  svg.append("g")
      .call(xAxis);

  function transitionGrouped() {
    y.domain([0, yMax]);

    rect.transition()
        .duration(500)
        .delay((d, i) => i * 20)
        .attr("x", (d, i) => x(i) + x.bandwidth() / n * d[2])
        .attr("width", x.bandwidth() / n)
      .transition()
        .attr("y", d => y(d[1] - d[0]))
        .attr("height", d => y(0) - y(d[1] - d[0]));
  }

  function transitionStacked() {
    y.domain([0, y1Max]);

    rect.transition()
        .duration(500)
        .delay((d, i) => i * 20)
        .attr("y", d => y(d[1]))
        .attr("height", d => y(d[0]) - y(d[1]))
      .transition()
        .attr("x", (d, i) => x(i))
        .attr("width", x.bandwidth());
  }

  function update(layout) {
    if (layout === "stacked") transitionStacked();
    else transitionGrouped();
  }

  return Object.assign(svg.node(), {update});
}

var chrt = chart();
chrt.update('stacked');

</script>
</body>

## report_5VM.html
<!DOCTYPE html>
<meta charset="utf-8">
<title>Stacked-to-Grouped Bars</title>
<link rel="stylesheet" type="text/css" href="./inspector.css">
<body>
<script src="https://d3js.org/d3.v5.min.js"></script>
<form id=form name=form>
  <label style="margin-right:0.5em;"><input type=radio name=radio value="stacked" onchange="chrt.update(form.radio.value);" checked> Stacked</label>
  <label style="margin-right:0.5em;"><input type=radio name=radio value="grouped" onchange="chrt.update(form.radio.value);"> Grouped</label>
  <label style="margin-right:0.5em;">Palette <select name=palette onChange="chrt.recolor(form.palette.value);"><option value="blue" selected>Blues</option><option value="ryb" selected>RdYlBu</option><option value="spectral" selected>Spectral</option><option value="rainbow">Less Angry Rainbow</option><option value="set3">Discrete Set3</option><option value="paired">Discrete Paired</option></select></label>
</form>
<svg id="stackedSVG" width=975 height=700 viewBox="0,0,975,700"></svg>
<script>

const margin = ({top: 0, right: 0, bottom: 10, left: 0});
const width = 975;
const height = 500;
const m = 282; // number of values per series
const n = 23; // number of series

const nz = [6,3,3,2,1,2,1,4,2,3,2,0,0,1,4,4,4,4,9,6,3,4,15,13,11,16,9,19,13,10,10,9,11,15,16,10,4,7,7,5,12,3,4,3,4,15,10,13,9,5,6,5,10,10,15,14,11,7,5,5,8,7,16,7,14,8,3,5,3,8,7,5,4,3,6,3,4,5,4,1,4,4,6,5,5,4,3,3,3,8,3,8,6,2,2,5,7,8,8,8,9,11,7,6,4,9,7,12,8,7,9,7,14,15,21,23,8,8,12,13,7,7,3,11,3,5,4,4,4,4,9,6,9,14,9,7,3,1,2,1,5,5,11,7,5,3,5,6,6,12,13,22,16,5,2,4,9,12,8,14,9,11,10,9,15,14,10,13,10,6,6,4,10,8,7,5,12,6,12,4,10,11,13,11,10,13,4,4,4,4,10,5,9,5,5,7,12,9,6,7,3,6,6,7,12,9,11,11,10,7,8,10,5,4,6,8,7,7,12,16,10,11,6,7,11,6,5,6,8,10,13,7,5,5,6,12,10,15,8,13,9,7,8,8,18,11,13,9,12,12,16,10,9,15,17,14,15,18,6,19,13,21,13,14,7,8,7,6,11,12,21,16,20,11,15,8,5,4,4,4,3,0]; // number of series in each value
const yz = [[180.246,413.23,512.774,742.719,764.229,736.495,701.913,520.011,297.842,168.259,57.1891,0,0,7.92424,558.003,933.084,1508.11,1410.78,2125.7,4240.41,2476.31,2184.64,112.771,2324.64,2222.29,1126.52,1325.8,1201.58,1317.06,2196.95,2835.48,3379.12,650.498,74.2504,3715.93,3258.79,3222.26,3461.45,506.959,2938.28,2549.88,3908.18,4021.52,6970.53,4366.12,384.987,1979.23,1275.2,1564.51,3008.11,2767.62,3891.68,3519.99,3143.28,473.614,238.158,435.383,2739.02,5922.31,4904.36,2236.37,3018.01,2140.7,1926.49,1774.67,3524.75,3083.27,3483.45,7443.28,300.161,4748.45,4197.43,4091.06,5497.91,4882.59,6590.27,5215.19,2304.07,7728.53,12367.1,5091.32,4411.27,5393.35,4940.1,5118.37,1669.42,6977.7,3938.52,5302.36,2443.7,7148.49,6562.14,9327.79,13065.3,12743.5,4370.57,2430.24,2407.73,2342.1,2157.79,6321.93,208.221,5471.21,9077.48,6270.02,2054.37,2022.39,5586.66,941.86,831.405,2125.64,4897.92,1748.25,112.622,318.255,5631.44,2793.31,1756.32,1942.05,66.3879,3154.89,118.221,7305.59,1294.49,7056.83,6830.18,4121.2,3248.21,3385.48,4271.26,2832.37,6363.85,5675.22,2646.65,4320.02,3632.2,4353.64,5696.11,4257.43,5494.76,2261.96,1980.84,2088.61,2415.72,2501.08,3326.03,1173.76,3294.49,2701.81,2565.7,2517.73,51.1784,2803.58,1990.68,8736.92,1852.44,668.693,48.0111,453.999,38.6368,2025.24,3310.27,3173.88,1965.61,1747.19,49.0103,31.2533,3068.61,36.5413,42.6531,811.552,3040.04,3654.35,3979.14,3705.68,4280.28,46.0116,1254.27,443,1235.52,9.92173,3835.14,1957.2,2046.58,8.0518,16.1614,3282.96,2717.17,2216.44,1645.13,22.9991,1455.67,4399.25,752.455,8.98976,1051.93,21.6816,6.86974,3026.08,147.976,3165.27,28.2236,759.957,660.39,4570.02,5380.89,4814.25,4358.39,1467.55,241,5.18105,16.5891,3075.3,2959.87,918.998,562.39,3391.19,18.8794,1160.14,11.0016,310.105,1857.84,1808.43,1796.87,152.954,2528.92,3063.5,3532.72,2075.57,1629.52,1640.73,447.043,1688.3,3149.72,1708.95,16.7233,21.4293,16.0058,4280.51,3225.46,5115.4,4386.57,3323.8,1908.61,2137.19,2143.8,129.228,13.682,2903.77,3102.68,3686.77,4048.75,3072.03,2982.69,44.4004,1927.49,54.1538,75.8446,42.4505,3033.61,92.9888,61.2858,313.295,45.5594,1983.11,2626.59,3939.4,99.9365,3367.25,2583.88,44.8929,59.0372,20.9016,36.0372,1289.75,958.426,233.393,835.083,965.933,415.351,196.18,0],
[9.58926,9.96212,19.7114,19.8379,0,5.03679,0,9.97644,8,5.06878,5.66169,0,0,0,29.9825,70.4076,831.743,942.772,1848.03,101.358,2516.02,2533.93,2155.14,1839.15,1885.44,13.0795,1857.99,1751.38,1838.59,1447.82,46.1346,629.895,3327.03,675.562,2933.95,3326.19,500.877,3434.63,2651.54,2601.47,2890.26,2953.78,3053.75,2278.19,3848.76,146.729,2234.92,1832.75,300.659,2638.55,3538.4,1854.99,87.8008,1541.58,1990.81,1852.97,49.4039,52.7771,3436.74,558.273,2852.44,2655.64,1641.58,1448.45,1504.8,1997.55,6132.02,3534.9,4038.4,282.776,3711.44,3089.83,4284.37,2462.65,78.3051,9267.89,2879.5,2416.32,1974.48,0,4789.2,4789,3878.57,4350.66,2069.31,2259.53,1768.84,1670.15,4575.52,1882.29,2042.14,2246.35,2255.84,2166.36,2153.29,5082.77,2830.84,5589.79,2502.32,905.235,2612.2,5973.22,1060.08,109.858,3029.13,1007.45,4739.98,2180.91,21.659,2663.14,2487.59,695.29,667.642,34.6245,53.9792,77.6558,1978.21,2523.73,34.5013,5427.88,6505.36,4081.56,4232.23,2712.44,3865.13,3437.7,7304.68,5120.5,4601.96,7331.18,4127.6,3466.22,17.789,2454.87,2551.98,1996.47,435.201,0,128.561,0,1783.05,402.821,350.77,2665.04,2806.81,1471.95,2686.84,2456.6,435.811,468.625,2701.97,19.3806,17.8751,3642.2,2088.83,3369.83,3464.69,554.021,794,764.608,9.73813,543.865,21.6725,3337.53,519.11,50.0107,6.01477,36.2197,92.7564,1661.11,2008,1099.85,9.78562,3817.91,70.1718,5156.29,4127.15,388.724,2580.79,2971.55,4367.71,2715.72,6.57331,615.142,3255.31,17.0588,5360.54,4717.14,1584.05,5056.94,1647.99,1353.91,1470.09,1473.72,3627.26,715,1315.5,2920.66,795.194,431.472,923.933,1241.95,1460.51,1324.49,25.7635,6.00811,10.9769,1319.97,261.684,969.762,1073.86,697.982,205.532,977,9.88972,942.442,13.9634,17,120.209,15.9145,3999.78,57.3612,5.26649,7,965.309,2694.58,53.8307,70.7929,3659.16,1101.68,28.5425,2243.99,3614.21,3711.03,3173.79,37.1834,1379.7,1305.28,25.0288,163.271,95.9407,16.8434,22.1672,3098.62,1836.85,67.0423,2425.1,2116.33,66.0038,2700.92,25.0473,2565.2,2647.06,71.7016,123.933,2044.92,32.3559,2502.07,571.182,6.95432,1756.45,9.89995,2432.79,83.9085,3344.18,2022.19,57.6042,3778.84,19.9312,19.8959,13.2799,1945.58,350.88,12.0001,144.739,13.0275,906.753,190.256,123.153,77.5114,35.9137,0],
[6.41074,10.9985,9.00725,0,0,0,0,24.7214,0,13,0,0,0,0,219.001,430.276,694,1108.78,16.5045,99.8947,3623.72,2555.81,93.622,2047.79,306.604,24.4521,2100.13,49.1065,1882.14,2478.22,53.0276,66.3427,27.2721,2981.57,152.578,2268.53,3293.2,523.208,2067.06,3330.72,1855.39,4736.21,3788.09,3193.66,78.2757,3406.76,17.689,56.6663,2762.02,3072.55,2515.4,2908.91,463.528,2330.74,3222.45,44.4817,2433.59,3565.84,2344.69,3074.57,2708.78,2335.13,334.971,86.9418,2735.04,139.546,3647,2309.49,4437.32,6369.46,198.594,1152.24,4814.6,12095,4994.8,4776.02,9152.61,8377.14,2131.99,0,5232.07,6011.14,4565.46,2475.83,3585.56,7247.27,1616.99,4013.2,1893.82,2058.69,2223.93,70.3503,1022.45,0,0,2082.92,936.237,117.204,2340.7,2324.31,2381.9,2903.83,2123.08,1319.81,1941.67,4790.49,2135.48,945.246,88.1725,2168.22,5335.65,2518.75,4487.32,729.458,30.0225,13.3065,5729.27,17.6652,2774.42,38.025,4202.89,7092.58,7828.5,3588.47,4377.54,72.0877,4112.72,4117.25,5038.12,3992,6859.43,2319.76,2956.91,25.5431,9.81079,2561.73,2673.26,0,0,0,66.3083,1911.43,1260.28,543.738,1493.49,2670.61,2783.32,599.648,2263.97,409.476,11.2454,40.0002,15.7531,945.792,0,3297.2,1002.46,3274.76,5.48776,23.1938,495.885,2024.15,28.6581,19.6803,47.0062,1646.83,16.4678,24.3739,2559.41,3493.37,2383.1,4106.59,6.47519,4784.83,5089.01,3625.98,11.0025,2360.92,9.05115,1876.04,1510.61,14.5616,24.8316,3497.67,5.66271,5215.26,2810.84,2424.22,4908.93,2022.18,4960,975.595,32.2126,12.2096,1006,1458.24,7.82769,5.00006,1403.92,1306.58,1895.2,3627.06,3993.9,35.7852,7.92815,607.942,40.667,13.6434,8.01133,467,8.00012,177.935,1003.39,815.999,2785.73,50.9075,1035.35,1312.62,872.935,35.3459,1873.27,943.609,3613.29,160.807,1500.4,91.3973,1790.41,2255.78,1094.2,57.6781,1209.6,5294.6,5455.8,5713.02,3693.54,3344.91,4319.89,30.5675,14.8836,1232.73,2739.36,24.1309,3113.52,943.656,45.3633,1866.33,68.5395,2876.14,15.5945,16.0236,778.59,2953.8,10.9439,8.62651,16.3288,93.4266,33.0293,3305.08,3691.54,418.7,223.551,2368.16,13.9651,130.944,54.5162,38.548,2847.05,34.1696,40.4567,784.232,91.6223,27.0379,7.60191,8.90166,19.0619,241,287.981,753.826,245.123,257.296,146.898,0],
[9,0,0,0,0,0,0,7.96702,0,0,0,0,0,0,179.073,458.999,122.47,1021.41,22.7708,186.895,0,302.008,1131.7,1188.57,47.7443,2119.03,21.3386,25.2606,21.7787,23.0576,2083.38,4106.68,2916.76,3147.7,2873.77,3127.93,4323.22,2808.34,3114.84,19.207,128.719,0,1668.37,0,2183.82,2628.26,2535.43,250.98,2667.96,2152.06,3119.43,2553.28,2274.42,20.6471,61.7797,126.23,3304.64,542.838,503.495,3336.04,1945.69,470.591,7.99534,2763.87,43.9483,3039.91,0,306.905,0,4366.21,3972.32,3102.72,3503.24,0,1958.52,0,5127.05,5433.7,4922.9,0,6698.95,4633.81,4257.28,5203.94,1276.51,919.436,0,0,0,5411.63,0,942.035,52.809,0,0,57.946,5559.47,2701.97,5436.68,5524.06,999.925,2302.72,1578.67,3100.18,3446.12,1735.8,2784.1,39.9099,2683.11,2063.86,759.671,1865.84,42.1909,86.3187,85.8209,184.27,2558.33,34.399,955.225,2208.68,2441.31,77.6022,0,7268.6,0,3608.99,3121.39,7911.41,7776.45,4407.12,3839.5,3677.65,953.159,48.2679,692.995,20.5119,0,0,0,0,916.384,933.8,525.266,1448.78,734.325,0,1646.39,51.1723,134.733,1478.73,29,2976.82,24.4813,3072.44,0,1919.94,84.5371,12.5716,1819.86,79.7626,799.968,9.08682,752.846,24.5743,61.7317,3024.8,2542.86,1647.06,1666.4,795.347,34.6835,2987.74,1224.37,1603.15,76.6492,1677.33,26.2061,3849.01,2215.55,3489.09,10.0147,13.0339,16.0081,14.5554,8.88434,3284.33,1821.1,1517.53,2173.87,1978.48,41.0071,8.91407,5.30723,4246.52,1391.41,3638,934.001,1455.43,452,779.348,0,16.6261,10.0428,1418.02,27.1191,36.1052,1684.08,1505.88,546.999,9,716.466,6.02703,463.085,621.998,561,179.663,971.023,984,3290.59,3602.61,17.2562,297.895,960,3192.27,1876.18,154.99,33.7491,53.0118,65.1962,27.018,54.8202,1544.87,3047.26,1724.01,5534,121.218,120.646,11,2456.22,11.0217,37.1558,2057.93,1163.39,2654.9,62.5787,11.9417,37.0737,52.15,37.3024,42.7466,2836.14,39.5478,22.0757,682.729,98.0549,226.743,1848.64,36.1241,41.6543,37.0034,16.2433,18.6229,47.897,1843.11,737.239,770.766,910.616,918.767,2915.45,61.1235,12.307,2138.4,9.05087,1270.71,17.7366,15.5984,951.206,305.155,58.2167,23.6193,0,0],
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const xz = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281];

// for inspiration, go here: https://github.com/d3/d3-scale-chromatic#schemeAccent
const z = {
  "blue": d3.scaleSequential(d3.interpolateBlues)
    .domain([-0.5 * n, 1.5 * n]),
  "ryb": d3.scaleSequential(d3.interpolateRdYlBu)
    .domain([0, n]),
  "spectral": d3.scaleSequential(d3.interpolateSpectral)
    .domain([0, n]),
  "rainbow": d3.scaleSequential(d3.interpolateRainbow)
    .domain([0, 12]),
  "set3": d3.scaleOrdinal(d3.schemeSet3)
    .domain([0, n]),
  "paired": d3.scaleOrdinal(d3.schemePaired)
    .domain([0, n])

};

const y01z = d3.stack()
    .keys(d3.range(n))
  (d3.transpose(yz)) // stacked yz
  .map((data, i) => data.map(([y0, y1]) => [y0, y1, i]));
const y1Max = d3.max(y01z, y => d3.max(y, d => d[1]));
const yMax = d3.max(yz, y => d3.max(y));
const y = d3.scaleLinear()
    .domain([0, y1Max])
    .range([height - margin.bottom, margin.top]);

const x = d3.scaleBand()
    .domain(xz)
    .rangeRound([margin.left, width - margin.right])
    .padding(0.08);

const xAxis = svg => svg.append("g")
    .attr("transform", `translate(0,${height - margin.bottom})`)
    .call(d3.axisBottom(x).tickSizeOuter(0).tickFormat(() => ""));

function chart() {
  const svg = d3.select('#stackedSVG')
    .style("width", "100%")
    .style("height", "auto");

  const gs = svg.selectAll("g")
    .data(y01z)
    .enter().append("g")
      .attr("fill", (d, i) => z["blue"](i))

  const rect = gs.selectAll("rect")
    .data(d => d)
    .join("rect")
      .attr("x", (d, i) => x(i))
      .attr("y", height - margin.bottom)
      .attr("width", x.bandwidth())
      .attr("height", 0);

  svg.append("g")
      .call(xAxis);

  function transitionGrouped() {
    y.domain([0, yMax]);

    rect.transition()
        .duration(500)
        .delay((d, i) => i * 20)
        .attr("x", (d, i) => x(i) + x.bandwidth() / n * d[2])
        .attr("width", x.bandwidth() / n)
      .transition()
        .attr("y", d => y(d[1] - d[0]))
        .attr("height", d => y(0) - y(d[1] - d[0]));
  }

  function transitionStacked() {
    y.domain([0, y1Max]);

    rect.transition()
        .duration(500)
        .delay((d, i) => i * 20)
        .attr("y", d => y(d[1]))
        .attr("height", d => y(d[0]) - y(d[1]))
      .transition()
        .attr("x", (d, i) => x(i))
        .attr("width", x.bandwidth());
  }

  function update(layout) {
    if (layout === "stacked") transitionStacked();
    else transitionGrouped();
  }

  function recolor(palette) {
    if (palette in z)
      gs.transition()
          .duration(500)
          .delay((d, i) => i * 20)
          .attr("fill", (d, i) => z[palette](i));
    else
      alert("Wrong color " + palette);
  }

  return Object.assign(svg.node(), {update, recolor});
}

var chrt = chart();
chrt.update('stacked');

</script>
</body>
	#!/usr/bin/env perl


	use strict;
	use Encode;

	my $path = 'support';

	my $report_html = <<'END_MESSAGE';
	<!DOCTYPE html>
	<meta charset="utf-8">
	<title>Stacked-to-Grouped Bars</title>
	<link rel="stylesheet" type="text/css" href="./inspector.css">
	<script src="https://d3js.org/d3.v5.min.js"></script>
	<body>
	<form id=form name=form>
	<label style="margin-right:0.5em;"><input type=radio name=radio value="stacked" onchange="chrt.update(form.radio.value);" checked> Stacked</label>
	<label style="margin-right:0.5em;"><input type=radio name=radio value="grouped" onchange="chrt.update(form.radio.value);"> Grouped</label>
	<label style="margin-right:0.5em;">Palette <select name=palette onChange="chrt.recolor(form.palette.value);"><option value="blue" selected>Blues</option><option value="ryb" selected>RdYlBu</option><option value="spectral" selected>Spectral</option><option value="rainbow">Less Angry Rainbow</option><option value="set3">Discrete Set3</option><option value="paired">Discrete Paired</option></select></label>
	</form>
	<div style="position: absolute;
	overflow: hidden;
	top: 0;
	right: 0;
	z-index: 9999;
	"><button onclick="filterselector.toggle()
	">Filter:</button> <br/><svg id="scatter_filter"></div>
	<svg id="stackedSVG" width=975 height=700 viewBox="0,0,975,700"></svg>
	<script>
	function selector() {
	// set the dimensions and margins of the graph
	const margin = {top: 10, right: 30, bottom: 30, left: 60},
	width = 460 - margin.left - margin.right,
	height = 400 - margin.top - margin.bottom;

	// append the svg object to the body of the page
	const svg = d3.select("#scatter_filter")
	.attr("cursor", "crosshair")
	.on("click", function() {
	var p = d3.mouse(this)
	;
	updatefilter(x.invert(p[0] - margin.left), y.invert(p[1], margin.top));
	})
	.attr("width", width + margin.left + margin.right)
	.attr("height", height + margin.top + margin.bottom)
	.attr("overflow", "hidden")
	.append("g")
	.attr("transform",
	`translate(${margin.left},${margin.top})`);

	//Read the data
	const data = @PS_SCATTER@;

	// Add X axis
	const x = d3.scaleLinear()
	.domain([0, 1.2])
	.range([ 0, width ]);
	svg.append("g")
	.attr("transform", `translate(0,${height})`)
	.call(d3.axisBottom(x));

	// Add Y axis
	const y = d3.scaleLog()
	.domain([0.01, 10000])
	.range([ height, 0 ])
	.base(10);
	svg.append("g")
	.call(d3.axisLeft(y));

	// Add dots
	svg.append('g')
	.selectAll("dot")
	.data(data)
	.enter()
	.append("circle")
	.attr("cx", d => x(d[0]) )
	.attr("cy", d => y(d[1]) )
	.attr("r", 1.5)
	.style("fill", "#69b3a2")
	;

	// Add selector
	const filterselector = svg
	.append('g')
	.style("fill", "#69b3a2")
	.style("opacity", ".2")
	.append("rect")
	.attr("y", 0);


	function updatefilter(p, s) {
	const fx = x(p);
	const fy = y(s);
	filterselector.attr("x", fx).attr("width", width-fx)
	.attr("height", fy);

	}
	var filter_visible = 1;
	function toggle() {
	svg.transition().duration(500).style('opacity', filter_visible ^= 1)
	}

	return Object.assign(svg.node(), {updatefilter, toggle});
	};

	var filterselector = selector();
	filterselector.updatefilter(.9, 5);

	const m = @M@; // number of values per series
	const n = @N@; // number of series

	const yz = @YZ_ARRAY@;
	const xz = @XZ_ARRAY@; // list of X
	const xp = @XP_ARRAY@; // window position to be used as X-axis label

	function chart() {
	const margin = ({top: 5, right: 5, bottom: 20, left: 30});
	const width = 975;
	const height = 500;

	// for inspiration, go here: https://github.com/d3/d3-scale-chromatic#schemeAccent
	const z = {
	"blue": d3.scaleSequential(d3.interpolateBlues)
	.domain([-0.5 * n, 1.5 * n]),
	"ryb": d3.scaleSequential(d3.interpolateRdYlBu)
	.domain([0, n]),
	"spectral": d3.scaleSequential(d3.interpolateSpectral)
	.domain([0, n]),
	"rainbow": d3.scaleSequential(d3.interpolateRainbow)
	.domain([0, 12]),
	"set3": d3.scaleOrdinal(d3.schemeSet3)
	.domain([0, n]),
	"paired": d3.scaleOrdinal(d3.schemePaired)
	.domain([0, n])
	};

	const y01z = d3.stack()
	.keys(d3.range(n))
	(d3.transpose(yz)) // stacked yz
	.map((data, i) => data.map(([y0, y1]) => [y0, y1, i]));
	const y1Max = d3.max(y01z, y => d3.max(y, d => d[1]));
	const yMax = d3.max(yz, y => d3.max(y));
	const y = d3.scaleLinear()
	.domain([0, y1Max])
	.range([height - margin.bottom, margin.top]);

	const x = d3.scaleBand()
	.domain(xz)
	.rangeRound([margin.left, width - margin.right])
	.padding(0.08);

	const xAxis = svg => svg.append("g")
	.attr("transform", `translate(0,${height - margin.bottom})`)
	.style("font-size", `${Math.min((width/m).toFixed(2),10.00)}px`)
	.call(d3.axisBottom(x).tickSizeOuter(0).tickFormat((d, i) => xp[i]));

	const svg = d3.select('#stackedSVG')
	.style("width", "100%")
	.style("height", "auto");

	const gs = svg.selectAll("g")
	.data(y01z)
	.enter().append("g")
	.attr("fill", (d, i) => z["blue"](i))

	const rect = gs.selectAll("rect")
	.data(d => d)
	.join("rect")
	.attr("x", (d, i) => x(i))
	.attr("y", height - margin.bottom)
	.attr("width", x.bandwidth())
	.attr("height", 0);

	svg.append("g")
	.call(xAxis)
	.selectAll("text")
	.attr("y", 0)
	.attr("x", 7)
	.attr("dy", ".35em")
	.attr("transform", "rotate(90)")
	.style("text-anchor", "start");

	svg.append("g")
	.attr("class", "axis")
	.style("font-size", "8px")
	.attr("transform", `translate(${margin.left}, 0)`)
	.call(d3.axisLeft(y).ticks(null, "s"));

	function transitionGrouped() {
	y.domain([0, yMax]);

	rect.transition()
	.duration(500)
	.delay((d, i) => i * 20)
	.attr("x", (d, i) => x(i) + x.bandwidth() / n * d[2])
	.attr("width", x.bandwidth() / n)
	.transition()
	.attr("y", d => y(d[1] - d[0]))
	.attr("height", d => y(0) - y(d[1] - d[0]));
	}

	function transitionStacked() {
	y.domain([0, y1Max]);

	rect.transition()
	.duration(500)
	.delay((d, i) => i * 20)
	.attr("y", d => y(d[1]))
	.attr("height", d => y(d[0]) - y(d[1]))
	.transition()
	.attr("x", (d, i) => x(i))
	.attr("width", x.bandwidth());
	}

	function update(layout) {
	if (layout === "stacked") transitionStacked();
	else transitionGrouped();
	}

	function recolor(palette) {
	if (palette in z)
	gs.transition()
	.duration(500)
	.delay((d, i) => i * 20)
	.attr("fill", (d, i) => z[palette](i));
	else
	alert("Wrong color " + palette);
	}

	return Object.assign(svg.node(), {update, recolor});
	}

	var chrt = chart();
	chrt.update('stacked');

	</script>
	</body>
	END_MESSAGE


	my @H; # all haplotypes (over all windows of complete run)
	my %H;

	my %W; # all windows
	# my %d;
	my @d; # per-haplotype list of all "position->reads"
	my %HN; # per-window local number of local haplotypes

	# for the filter's scatter plot
	my @F;

	my $file = 0;
	opendir(my $dh, $path) or die "Can't open ${path}: $!";
	while (readdir $dh) {
	# "support/w-HXB2-5849-5950.reads-support.fas.gz"
	next unless $_ =~ m{w-(?<chr>.*)-(?<w>[[:digit:]]+)-(?<e>[[:digit:]]+).reads-support.fas.gz};
	print STDERR $file++ . " - <$_> : ";

	my $w = $+{'w'}; # this windows' position
	my $hn = 0; # counting haplotypes inside this windows
	my $htot = 0;

	open my $fh, "gunzip -kc $path/$_\|" or die "Can't open ${path}: $!";
	while (<$fh>) {
	chomp;
	# ">hap_3\|posterior=1 ave_reads=1224.37"
	next unless $_ =~ m{^\>(?<h>[^\\|]+)\\|posterior=(?<p>[[:digit:].]) ave_reads=(?<s>[[:digit:].]*)};
	my $h=$+{'h'}; # haplotype name ('hap_nnn')
	my $s=$+{'s'}; # support (as average number of reads per base)
	my $p=$+{'p'}; # posterior
	push @F, +[ $p, $s ];
	$h =~ m{_(?<n>[[:digit:]]+)$}; # just the number of the haplotype
	$H[$+{'n'}] = $h;
	$H{$h} = $+{'n'};
	$W{$w} = 1;
	$htot++;

	next unless ($s > 5.0 and $p > .8); # filter low quality
	# if (exists $d{$h} and ref $d{$h} eq ref {}) {
	if (exists $d[$hn] and ref $d[$hn] eq ref {}) {
	$d[$hn]->{$w} = $s;
	# $d{$h}->{$w} = $s;
	} else {
	$d[$hn] = +{ $w => $s };
	# $d{$h} = +{ $w => $s };
	}
	$hn++;
	}
	close $fh;
	$HN{$w} = $hn;
	print STDERR "$htot haplotypes, $hn filtered\n";
	}
	close $dh;

	print STDERR "creating report...";

	# scatter plot for filter selector
	my $PS_SCATTER = '[' . join(',', map { '[' . join(',', @{$_} ) . ']' } @F ) . ']';

	# every single window
	my @W = sort { $a <=> $b } keys %W;
	my $m = @W;

	# old style : every single haplotype...
	my $n = @H;
	die "\nIs there a missing haplotype ? Highest number is $n: $H[$#H] but only found " . (scalar keys %H) . "haplotypes"
	if ( $n != scalar keys %H );
	# ...actually no only keep the filtered
	$n = @d;

	my $XZ = '[' . join(',', ( 0 .. $#W) ) . ']';
	my $NZ = '[' . join(',', map { $HN{$_} } @W ) . ']';
	my $XP = '[' . join(',', @W ) . ']';
	my $YZ = '[' . join(",\n", map { my $hd = $_;
	'[' . join(',', map { (exists $hd->{$_} ) ? $hd->{$_} : 0 } @W) . ']'
	} @d) . ']';
	# my $YZ = '[' . join(",\n", map { my $h = $_;
	# '[' . join(',', map { (exists $d{$h} and exists $d{$h}->{$_} ) ? $d{$h}->{$_} : 0 } @W) . ']'
	# } @H) . ']';

	$report_html =~ s{\@M\@}{$m};
	$report_html =~ s{\@N\@}{$n};
	$report_html =~ s{\@NZ_ARRAY\@}{$NZ};
	$report_html =~ s{\@XZ_ARRAY\@}{$XZ};
	$report_html =~ s{\@XP_ARRAY\@}{$XP};
	$report_html =~ s{\@YZ_ARRAY\@}{$YZ};
	$report_html =~ s{\@PS_SCATTER\@}{$PS_SCATTER};
	open my $o, '>', "report.html" or die "Cannot write report";
	print $o $report_html;
	close $o;
	print STDERR "done\n";

	exit 0;