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chromosome-browser.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Yulvil Chromosome Browser</title>
<script src="https://d3js.org/d3.v4.min.js"></script>
<style>
div.tooltip {
position: absolute;
text-align: left;
padding: 10px;
font: 12px sans-serif;
background: lightsteelblue;
border: 0px;
border-radius: 8px;
pointer-events: none;
z-index: 2000;
}
textarea {
width: 100%;
// height: 55px;
}
.drop_zone {
border: 2px dashed #000;
width: 250px;
height: 100px;
float: left;
text-align: center;
margin: 0px 20px 0px 0px;
}
input[type=number]{
width: 70px;
font-size: 16px;
text-align: center;
font-weight: bold;
}
#csvdiv0 {
display: none;
}
body {
margin: 0;
}
#topdiv {
position: static;
padding: 10px;
}
header {
margin: 0;
padding: 0;
overflow: hidden;
}
nav ul {
background-color: #333;
list-style-type: none;
margin: 0;
padding: 0;
overflow: hidden;
}
nav li {
float: left;
}
nav li a {
display: block;
color: white;
text-align: center;
padding: 14px 16px;
text-decoration: none;
}
/* Change the link color to #111 (black) on hover */
nav li a:hover {
background-color: #111;
}
nav .active {
background-color: #4CAF50;
}
nav {
margin: 0;
position: sticky;
top: 0;
right: 0;
left: 0;
z-index: 1000;
}
.inputs {
display: none;
padding: 10px;
}
.submenu {
background-color: #555;
color: white;
}
.chrbrowser {
padding: 5px;
}
#about a:link, #about a:visited {
color: white;
font-weight: bold;
}
</style>
</head>
<body>
<header>
</header>
<form id="myform" onsubmit="return false;">
<nav>
<ul>
<li><a href="#" onclick="showdiv('none');">Yulvil Chromosome Browser</a></li>
<li><a href="#Data" onclick="showdiv('data');">Data</a></li>
<li><a href="#Filters" onclick="showdiv('filters');">Filters</a></li>
<li><a href="#Display" onclick="showdiv('display');">Display</a></li>
<li style="float: right"><a href="#" onclick="showdiv('about');">About</a></li>
</ul>
<div class="submenu">
<div class="inputs" id="none">
</div>
<div class="inputs" id="data">
<div style="width: 100%; overflow: hidden;">
<div class="drop_zone" ondrop="dropHandler(event);" ondragover="dragOverHandler(event);">
<p>📁 Drag one or more files here</p>
</div>
<div class="drop_zone" ondrop="dropHandler(event);" ondragover="dragOverHandler(event);">
<p>
<label class="custom-file-upload">
<input type="file" multiple="multiple" accept=".csv, .txt" onchange="onFileSelect(this);" style="display: none;"/>
📁 Select files from your computer
</label>
</p>
</div>
<div style="float: left;">
<p>or
<input type="button" name="addCsv" id="addCsv" value="Add CSV data" onclick="addCsvInput();" />
</p>
</div>
</div>
<div id="csvdatadiv">
<div id="csvdiv0">
<br/><br/>
<label for="csvdata0">CSV Data</label>
<br/>
<textarea name="csvdata0" id="csvdata0" class="csvdata" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" onChange="loadData();updateAll();"></textarea>
</div>
</div>
</div>
<div class="inputs" id="filters">
<label for="minCm">Centimorgan size</label>
from <input id="minCm" type="number" value="10" onChange="updateCm();" onInput="updateCm();">
to <input id="maxCm" type="number" value="" onChange="updateCm();" onInput="updateCm();">
<br/><br/>
<label for="includekits">Only show these kits (one per line)</label>
<br/>
<textarea name="includekits" id="includekits" onChange="updateAll();"></textarea>
<br/><br/>
<label for="excludekits">Exclude these kits (one per line)</label>
<br/>
<textarea name="excludekits" id="excludekits" onChange="updateAll();"></textarea>
</div>
<div class="inputs" id="display">
<label for="chrview">Chromosome</label>
<select id="chrview" onChange="updateAll()">
<option value="0">All</option>
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
<option value="6">6</option>
<option value="7">7</option>
<option value="8">8</option>
<option value="9">9</option>
<option value="10">10</option>
<option value="11">11</option>
<option value="12">12</option>
<option value="13">13</option>
<option value="14">14</option>
<option value="15">15</option>
<option value="16">16</option>
<option value="17">17</option>
<option value="18">18</option>
<option value="19">19</option>
<option value="20">20</option>
<option value="21">21</option>
<option value="22">22</option>
<option value="23">X</option>
</select>
<br/><br/>
<label for="chrsize">Chromosome Size</label>
<select id="chrsize" onchange="updateDisplay();">
<option value="screenwidth" selected="selected">screen width</option>
<option value="proportional">proportional</option>
</select>
<br/><br/>
<label for="viewtype">View Type</label>
<select id="viewtype" onchange="updateDisplay();">
<option value="compact" selected="selected">Compact</option>
<option value="compactreverse">Compact (reverse)</option>
<option value="segment">By Segment</option>
<option value="segmentreverse">By Segment (reverse)</option>
<!--
<option value="kitsize">By Kit Size</option>
-->
</select>
<br/><br/>
<label for="segmentHeight">Segment Height</label>
<input id="segmentHeight" type="number" value="10" onChange="updateDisplay();" onInput="updateAll();">
<br/><br/>
<label for="fromkit">Active Kit</label>
<select id="fromkit" onchange="updateAll();">
</select>
</div>
<div class="inputs" id="about">
Copyright (c) 2018 yulvil <a href="https://github.com/yulvil/chromosome-browser">Help</a> and <a href="https://github.com/yulvil/chromosome-browser">Source Code</a>
</div>
</div>
</nav>
</form>
<div class="chrbrowser">
<svg id="topsvg" width="100%"/>
</div>
<script>
"use strict;";
var compareSegment = function (a, b) {
if (a.start < b.start) {
return -1;
} else if (a.start > b.start) {
return 1;
}
if (a.cm < b.cm) {
return 1;
} else if (a.cm > b.cm) {
return -1;
}
return -a.id.localeCompare(b.id);
};
var compareSegmentReverse = function (a, b) {
if (a.end > b.end) {
return -1;
} else if (a.end < b.end) {
return 1;
}
if (a.cm < b.cm) {
return 1;
} else if (a.cm > b.cm) {
return -1;
}
return -a.id.localeCompare(b.id);
};
function sortBySegment(data, fcmp) {
var d = data.sort(fcmp);
for (var i = 0; i < d.length; i++) {
d[i].row = i;
}
return {
"data": d,
"numRows": data.length
};
}
function sortByKitSize(data) {
var kits = {};
var numRows = 0;
for (var i = 0; i < data.length; i++) {
if (data[i].kit in kits) {
kits[data[i].kit].total += data[i].cm;
} else {
kits[data[i].kit] = {
"total": data[i].cm
};
}
}
var compareFunc = function (a, b) {
if (kits[a.kit].total < kits[b.kit].total) {
return 1;
} else if (kits[a.kit].total > kits[b.kit].total) {
return -1;
}
return -a.kit.localeCompare(b.kit);
}
var d = data.sort(compareFunc)
var currKit = d[0].kit;
var currRow = 0;
for (var i = 0; i < d.length; i++) {
if (currKit !== d[i].kit) {
currKit = d[i].kit;
currRow++;
}
d[i].row = currRow;
if (numRows < currRow + 1)
numRows = currRow + 1;
}
return {
"data": d,
"numRows": numRows
};
}
function compact(data, fcmp) {
var numRows = 1;
var d = data.sort(fcmp);
function overlap(s1, s2) {
if (s1.row == s2.row) {
if ((s1.start <= s2.start && s2.start <= s1.end) ||
(s1.start <= s2.end && s2.end <= s1.end)) {
return true;
}
}
return false;
}
function overlapPrevious(segments, until) {
for (var i = 0; i < until; i++) {
if (overlap(segments[i], segments[until])) {
return true;
}
}
return false;
}
for (var i = 0; i < d.length; i++) {
var j = 0;
d[i].row = j;
while (j < i && overlapPrevious(d, i)) {
j++;
d[i].row = j;
if (numRows < j + 1)
numRows = j + 1;
}
}
return {
"data": d,
"numRows": numRows
};
}
// Define the div for the tooltip
var div = d3.select("body").append("div")
.attr("class", "tooltip")
.style("opacity", 0);
// data = {
// "kit1": [segments],
// "kit2": [segments]
// }
var data = {};
var filteredData = [];
// kits = {
// "AZ123": {"name": "John Doe", "email": "a@b.c", "color": "..."},
// }
var kits = {};
var cat20 = d3.scaleOrdinal(d3.schemeCategory20);
function getSide(d) {
let v = d.side || d.Side || 0;
switch (v) {
case "Paternal":
case "paternal":
return 1;
case "Maternal":
case "maternal":
return 2;
default:
return +v % 3;
}
}
function csvParse(text) {
let currKit = Math.random().toString(36);
return d3.csvParse(text, function (d, i) {
var e = {};
e.kitFrom = d.kit1 || d.name || d.NAME || d.Name || currKit;
e.chr = (d.chr || d.Chr || d["CHROMOSOME"] || d["Chromosome"] || d["Chromosome Number"] || "0");
e.chr = e.chr.trim() === "X" || e.chr.trim() === "x" ? 23 : + ("" + e.chr.trim()).replace(/chr/, "");
if (e.chr < 1 || e.chr > 23) return;
e.start = + (d.start || d.Start || d["START LOCATION"] || d["Start Location"] || d["Chromosome Start Point"] || "0").replace(/,/g, "");
e.end = + (d.end || d.End || d["END LOCATION"] || d["End Location"] || d["Chromosome End Point"] || "0").replace(/,/g, "");
e.cm = + (d.cm || d.cM || d["CENTIMORGANS"] || d["Centimorgans"] || d["Genetic Distance"] || "0").replace(/,/g, "");
e.kitTo = d.kit2 || d.matchname || d.Match || d["MATCHNAME"] || d["Match name"] || d["Match Name"] || d["Display Name"] || "";
e.side = getSide(d);
if (!kits[e.kitFrom]) {
var nameFrom = (d.name1 || d.name || d.NAME || d.Name || "");
var emailFrom = (d.email1 || "");
kits[e.kitFrom] = {
"kit": e.kitFrom,
"name": nameFrom,
"email": emailFrom
};
}
if (!kits[e.kitTo]) {
var nameTo = d.name2 || d.Match || d["MATCHNAME"] || d["Match name"] || d["Display Name"] || "";
var emailTo = (d.email2 || "");
var color = d.color || d.Color || d.Colour || cat20(e.kitTo);
kits[e.kitTo] = {
"kit": e.kitTo,
"name": nameTo,
"email": emailTo,
"color": color
};
}
e.row = 0;
e.id = Math.random().toString(36);
d = null;
return e;
});
}
function rewriteData(id) {
var csvdata = document.getElementById(id).value;
var lines = csvdata.split("\n")
if (lines[0] == "Comparison\tChrom.\tStart Position\tEnd Position\tGenetic Distance (cM)\tNumber of SNPs\tIdentity") {
lines[0] = "NAME,MATCHNAME,chr,start,end,cm,snps,identity";
for (var i=1; i<lines.length; i++) {
lines[i] = lines[i].replace(" / ", "\t").split("\t").join(",");
}
document.getElementById(id).value = lines.join("\n")
}
}
function loadData() {
data = {};
kits = {};
filteredData = [];
var j = 1;
while (true) {
var csvdata = document.getElementById('csvdata' + j);
if (!csvdata) {
break;
}
rewriteData('csvdata' + j);
var raw = csvdata.value;
var d = csvParse(raw);
for (var i = 0; i < d.length; i++) {
if (d[i].kitFrom == null) {
continue;
}
data[d[i].kitFrom] = data[d[i].kitFrom] || [];
data[d[i].kitFrom].push(d[i]);
}
j++;
}
setOptions();
}
function setOptions() {
var sel = d3.select("#fromkit").selectAll("option").data(Object.keys(data).map(x => kits[x]), function(d) {return d.kit;});
sel.enter().append("option").attr("value", function (d) {
return d.kit
}).text(function (d) {
return d.kit + (d.name != d.kit ? " " + d.name : "")
});
sel.exit().remove();
}
// https://en.wikipedia.org/wiki/Chromosome#Human_chromosomes
const chrlen = [0, 247199719, 242751149, 199446827, 191263063, 180837866, 170896993, 158821424, 146274826, 140442298, 135374737, 134452384, 132289534, 114127980, 106360585, 100338915, 88822254, 78654742, 76117153, 63806651, 62435965, 46944323, 49528953, 154913754];
function filterData(segments, includekits, excludekits, minCm, maxCm) {
filteredData = [];
if (segments.length == 0) {
return;
}
var d = segments;
if (includekits.length > 0) {
d = d.filter(e => includekits.includes(e.kitTo));
}
d = d.filter(e => e.cm >= minCm);
d = d.filter(e => e.cm <= maxCm);
if (excludekits.length > 0) {
d = d.filter(e => !excludekits.includes(e.kitTo));
}
for (var i = 0; i <= 23; i++) {
for (var j = 0; j < 3; j++) {
var o = {
"chr": i,
"side": j,
"segments": []
};
filteredData.push(o);
}
}
for (var i = 0; i < d.length; i++) {
// filteredData[d[i].chr] = filteredData[d[i].chr] || {"segments": []};
filteredData[3*d[i].chr + d[i].side].segments.push(d[i]);
}
filteredData = filteredData.filter(e => e.segments.length > 0);
}
function sortData(data, viewType) {
var o = {};
for (var i = 0; i < data.length; i++) {
switch (viewType) {
case "compact":
o = compact(data[i].segments, compareSegment);
break;
case "compactreverse":
o = compact(data[i].segments, compareSegmentReverse);
break;
case "kitsize":
o = sortByKitSize(data[i].segments);
break;
case "segment":
o = sortBySegment(data[i].segments, compareSegment);
break;
case "segmentreverse":
o = sortBySegment(data[i].segments, compareSegmentReverse);
break;
}
data[i].segments = o.data;
data[i].numRows = o.numRows;
}
return data;
}
var width = window.innerWidth || document.width;
function updateChr(e, chrsize) {
var chrSvg = d3.select(`#chrg${e.chr}_${e.side}`);
var segmentHeight = +document.getElementById("segmentHeight").value;
var sc = d3.scaleLinear().domain([0, chrlen[e.chr]]).range([0, chrsize]);
var rectangles = chrSvg.selectAll(".segment").data(e.segments, function (d) {
return d.id
});
rectangles.exit().remove();
var rectangleAttributesEnter = rectangles.enter().append("rect")
.attr("class", "segment")
.attr("x", function (d) {
return sc(d.start);
})
.attr("y", function (d, i) {
return 1 + d.row * (segmentHeight + 1);
})
.attr("rx", 4)
.attr("ry", 4)
.attr("width", function (d) {
return sc(d.end) - sc(d.start);
})
.attr("height", segmentHeight)
.style("fill", function (d) {
return kits[d.kitTo].color;
})
.on("mouseover", function (d) {
name = "";
if (kits[d.kitTo].name !== d.kitTo) {
name = "<br>name " + kits[d.kitTo].name;
}
div.transition()
.duration(200)
.style("opacity", 1.0);
div.html(d.start.toLocaleString() + " to " + d.end.toLocaleString() + "<br>kit " + d.kitTo + name + "<br/>This segment " + d.cm.toFixed(1) + " cM")
.style("left", (d3.event.pageX) + "px")
.style("top", (d3.event.pageY - 28) + "px");
console.log(d.start + " to " + d.end + " kit [" + d.kitTo + "] name " + d.name);
})
.on("mouseout", function (d) {
div.transition()
.duration(500)
.style("opacity", 0);
});
rectangles
.transition()
.duration(400)
.attr("x", function (d) {
return sc(d.start);
})
.attr("y", function (d, i) {
return 1 + d.row * (segmentHeight + 1);
})
.attr("width", function (d) {
return sc(d.end) - sc(d.start);
})
.attr("height", segmentHeight)
d3.select(`#chrrect${e.chr}_${e.side}`).attr("height", 1 + e.numRows * (segmentHeight + 1))
}
function getChrBoxWidth(chr, chrsize) {
if (chrsize === 'proportional') {
return width * chrlen[chr] / chrlen[1];
}
return width;
}
function updateCm() {
let minCm = +document.getElementById("minCm").value || 10;
document.getElementById("minCm").value = minCm;
let maxCm = +document.getElementById("maxCm").value || "";
document.getElementById("maxCm").value = maxCm;
var params = new URLSearchParams(location.search);
if (params.has("minCm") || minCm != 10) {
params.set("minCm", minCm);
}
if (params.has("maxCm") || maxCm !== "") {
params.set("maxCm", maxCm);
}
window.history.replaceState({}, '', `${location.pathname}?${params}${window.location.hash}`);
updateAll();
}
function updateAll() {
updateData()
updateDisplay()
}
function updateDisplay() {
var viewType = document.getElementById("viewtype").value;
var chrview = +document.getElementById("chrview").value;
var segmentHeight = +document.getElementById("segmentHeight").value;
var chrsize = document.getElementById("chrsize").value;
var filteredByChr = filteredData;
if (chrview != 0 ) {
filteredByChr = filteredData.filter(e => e.chr == chrview);
}
var d = sortData(filteredByChr, viewType);
var topSvg = d3.select("#topsvg");
var chrUpdate = topSvg.selectAll("svg").data(d, function (d) {
return d.chr + "_" + d.side;
});
// Create chromosomes that were not previously displayed
var chrEnter = chrUpdate.enter();
var chrSvg = chrEnter.append("svg").attr("id", function (d) {
return `chrsvg${d.chr}_${d.side}`
}).attr("width", "100%");
chrSvg.append("text").attr("x", 20).attr("y", 10).attr("class", "chrlabel").attr("font-family", "Verdana").attr("font-size", 10).attr("font-weight", "700").attr("text-anchor", "end").attr("fill", "grey").text(function (d) {
return d.chr == 23 ? 'X' : `${d.chr}`
});
var g = chrSvg.append("g").attr("transform", "translate(30)").attr("id", function (d) {
return `chrg${d.chr}_${d.side}`
});
g.append("rect").attr("id", function (d) {
return `chrrect${d.chr}_${d.side}`
}).attr("class", "chrbox").attr("x", 0).attr("y", 0).attr("rx", 5).attr("ry", 5).attr("height", function (d, i) {
return 1 + d.numRows * (segmentHeight + 1)
}).style("fill", "white").style("stroke-width", "1").style("stroke", "grey");
var chrBoxUpdate = d3.selectAll(".chrbox");
chrBoxUpdate.attr("width", function (d) {
return getChrBoxWidth(d.chr, chrsize)
});
chrUpdate.attr("height", function (d) {
return 1 + d.numRows * (segmentHeight + 1)
});
for (var chr in d) {
updateChr(d[chr], getChrBoxWidth(d[chr].chr, chrsize))
}
// Remove chromosomes that should no longer be displayed
chrUpdate.exit().remove();
var y = 0;
for (var i = 0; i < d.length; i++) {
var node = d3.select(`#chrsvg${d[i].chr}_${d[i].side}`);
node.attr("y", y);
y += 1 + d[i].numRows * (segmentHeight + 1) + 15;
}
d3.select(`#topsvg`).attr("height", y).attr("viewBox", `0 0 ${width + 50} ${y}`).attr("preserveAspectRatio", "none");
}
function updateData() {
var fromkit = document.getElementById("fromkit").value;
var includekits = document.getElementById("includekits").value.split('\n').filter(e => e.length > 0);
var excludekits = document.getElementById("excludekits").value.split('\n').filter(e => e.length > 0);
var minCm = document.getElementById("minCm").value || 5;
var maxCm = document.getElementById("maxCm").value || 1000;
var segments = data[fromkit] || [];
filterData(segments, includekits, excludekits, minCm, maxCm);
}
function dragOverHandler(ev) {
// Prevent default behavior (Prevent file from being opened)
ev.preventDefault();
}
function loadFile(fileitem, resolve, reject) {
var file = fileitem;
var reader = new FileReader();
reader.onloadend = function () {
addCsvInput().value = reader.result;
resolve('');
}
reader.onerror = function () {
reject(arguments);
}
reader.readAsText(file);
}
function dropHandler(ev) {
// Prevent default behavior (Prevent file from being opened)
ev.preventDefault();
var tasks = [];
if (ev.dataTransfer.items) {
// Use DataTransferItemList interface to access the file(s)
for (var i = 0; i < ev.dataTransfer.items.length; i++) {
// If dropped items aren't files, reject them
if (ev.dataTransfer.items[i].kind === 'file') {
var t = new Promise((resolve, reject) => {
loadFile(ev.dataTransfer.items[i].getAsFile(), resolve, reject);
});
tasks.push(t);
}
}
} else {
// Use DataTransfer interface to access the file(s)
for (var i = 0; i < ev.dataTransfer.files.length; i++) {
// console .log('... file[' + i + '].name = ' + ev.dataTransfer.files[i].name);
}
}
// Pass event to removeDragData for cleanup
removeDragData(ev)
// Once all files are loaded
Promise.all(tasks).then((msg) => {
loadData();
updateAll();
});
}
function removeDragData(ev) {
if (ev.dataTransfer.items) {
// Use DataTransferItemList interface to remove the drag data
ev.dataTransfer.items.clear();
} else {
// Use DataTransfer interface to remove the drag data
ev.dataTransfer.clearData();
}
}
function addCsvInput() {
var div = document.getElementById("csvdatadiv");
var num = div.children.length;
var node = document.getElementById("csvdiv0").cloneNode(true);
node.id = "csvdiv" + num;
node.children[2].htmlFor = "csvdata" + num;
node.children[4].id = "csvdata" + num;
node.children[4].name = "csvdata" + num;
div.appendChild(node);
return node.children[4];
}
function showdiv(id) {
var currentStyle = d3.select("#" + id).attr("style");
if (currentStyle === 'display: block;') {
d3.select("#" + id).attr("style", "display: none;");
} else {
d3.select("#data").attr("style", "display: none;");
d3.select("#filters").attr("style", "display: none;");
d3.select("#display").attr("style", "display: none;");
d3.select("#about").attr("style", "display: none;");
if (id !== 'none') {
d3.select("#" + id).attr("style", "display: block;");
}
}
}
function onFileSelect(e) {
if (!e.files) {
return;
}
loadAll(e.files, loadFile);
}
function loadAll(arr, f) {
var tasks = [];
for (var i=0; i<arr.length; i++) {
console.log(arr[i]);
var t = new Promise((resolve, reject) => {
f(arr[i], resolve, reject);
});
tasks.push(t);
}
// Once all files are loaded
Promise.all(tasks).then((msg) => {
loadData();
updateAll();
});
}
function loadURL(url, resolve, reject) {
d3.text(url, function (error, data) {
if (error) {
reject(url + error);
}
addCsvInput().value = data;
resolve('');
});
}
function pageLoad() {
var urls = [];
if (typeof URLSearchParams === 'undefined') {
if (window.location.search.startsWith("?url=")) {
urls.push(window.location.search.substring(5));
}
} else {
var params = new URLSearchParams(location.search);
urls = params.getAll("url");
let minCm = +params.get("minCm");
if (minCm > 0 && minCm < 200) {
document.getElementById("minCm").value = minCm;
}
let maxCm = +params.get("maxCm");
if (maxCm > 0 && maxCm < 200) {
document.getElementById("maxCm").value = maxCm;
}
}
if (urls.length > 0) {
loadAll(urls, loadURL);
}
var h = window.location.hash;
if (h === '#Filters') {
showdiv('filters');
} else if (h === '#Display') {
showdiv('display');
} else if (h === '#none') {
showdiv('none');
} else {
showdiv('data');
}
}
pageLoad();
</script>
</body>
</html>