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index.html
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<!DOCTYPE html>
<meta charset="utf-8">
<title>Varroa samples</title>
<style>
.country:hover{
stroke: #fff;
stroke-width: 1.5px;
}
#container {
margin:10px 10%;
border:2px solid #000;
border-radius: 5px;
height:100%;
overflow:hidden;
background: #F0F8FF;
}
.hidden {
display: none;
}
div.tooltip {
color: #222;
font: 20px sans-serif;
background: #fff;
padding: .5em;
text-shadow: #f5f5f5 0 1px 0;
border-radius: 2px;
box-shadow: 0px 0px 2px 0px #a6a6a6;
opacity: 0.9;
position: absolute;
}
.graticule {
fill: none;
stroke: #bbb;
stroke-width: .5px;
stroke-opacity: .5;
}
.equator {
stroke: #ccc;
stroke-width: 1px;
}
body {
color: black;
font: 20px sans-serif;
}
button {
position: absolute;
right: 30px;
top: 30px;
}
.circle:before {
content: ' \25CF';
font-size: 20px;
ul {
list-style-type: none;
}
}
<button>Reset</button>
</style>
</head>
<body>
<h1><i>Varroa</i> mites world collection</h1>
<p>This world map shows the ongoing global sampling of honey bee ectoparasites Varroa mites. The collection aims to cover as many regions and host populations as possible in order to study the biogeography and demographic history of <i>V. destructor</i> and compare it to other mites species, using whole genome sequencing.</p>
<p><b>We are extremely grateful to all contributors to this project (name listed on sampling point). This ambitious work would not be possible without your precious help.</b></p>
<p><span class="circle" style="color: black" ></span> potential contact for samples <span class="circle" style="color: blue" ></span> sampling in progress <span class="circle" style="color: green" ></span> samples received at the lab</p>
<p>Sampling collection on honey bees (mainly <i>A. mellifera</i> but also <i>A. cerana</i>) with the following idea:</p>
<p><b>Per colony:</b> 2 to 30 mites (or more) are collected alive from adults or brood then freshly killed in one tube containing <90% ethanol.</p>
<p><b>Per site/apiary:</b> flexible but ideally 5 to 15 colonies. One tube per colony.</p>
<p><b>Per country/region:</b> also flexible, 3 to 5 distant sites or different beekeepers.</p>
<p> If you want to participe and later send us samples, please contact Sasha Mikheyev or Maeva Techer from <a href="http://homologo.us/">Ecology and Evolution lab, OIST</a></p>
<p><font color="red">Important: Japan importation rules are strict and only dead and preserved mites are seek for this project as <b>importation of honey bees is completely forbidden (whole or parts). </b> Please consult us and follow guidelines prior to any shipping.</font></p>
<p>Map raster shows the spread of <i>V. destructor</i> modified from Wilfert et al. 2016: recent (yellow) to old (red). Sampling points may be approximate in order to protect anonymous beekeepers participation.</p>
<div id="container"></div>
<script src="https://d3js.org/topojson.v1.min.js"></script>
<script src="https://d3js.org/d3.v3.min.js"></script>
<script>
d3.select(window).on("resize", throttle);
var zoom = d3.behavior.zoom()
.scaleExtent([1, 9])
.on("zoom", move);
var width = document.getElementById('container').offsetWidth;
var height = width / 2;
var topo,projection,path,svg,g;
var graticule = d3.geo.graticule();
var tooltip = d3.select("#container").append("div").attr("class", "tooltip hidden");
setup(width,height);
function setup(width,height){
projection = d3.geo.mercator()
.translate([(width/2), (height/2)])
.center([5,0])
.scale( width / 2 / Math.PI);
path = d3.geo.path().projection(projection);
svg = d3.select("#container").append("svg")
.attr("width", width)
.attr("height", height)
.call(zoom)
.on("click", click)
.append("g");
g = svg.append("g");
}
d3.json("json/world-topo-min.json", function(error, world) {
var countries = topojson.feature(world, world.objects.countries).features;
topo = countries;
draw(topo);
});
function draw(topo) {
svg.append("path")
.datum(graticule)
.attr("class", "graticule")
.attr("d", path);
g.append("path")
.datum({type: "LineString", coordinates: [[-180, 0], [-90, 0], [0, 0], [90, 0], [180, 0]]})
.attr("class", "equator")
.attr("d", path);
var country = g.selectAll(".country").data(topo);
country.enter().insert("path")
.attr("class", "country")
.attr("d", path)
.attr("id", function(d,i) { return d.id; })
.attr("title", function(d,i) { return d.properties.name; })
.style("fill", function(d, i) { return d.properties.color; });
//Add data on samples
d3.json("json/samples.json", function(err, samples) {
samples.forEach(function(i){
addpoint(i.longitude,i.latitude, i.name , i.status);
});
});
//offsets for tooltips
var offsetL = document.getElementById('container').offsetLeft+20;
var offsetT = document.getElementById('container').offsetTop+10;
country
.on("mousemove", function(d,i) {
var mouse = d3.mouse(svg.node()).map( function(d) { return parseInt(d); } );
tooltip.classed("hidden", false)
.attr("style", "left:"+(mouse[0]+offsetL)+"px;top:"+(mouse[1]+offsetT)+"px")
.html(d.properties.name);
})
.on("mouseout", function(d,i) {
tooltip.classed("hidden", true);
});
//function to add points and text to the map (used in plotting capitals)
function addpoint(lat,lon,text,status) {
var gpoint = g.append("g")
.attr("class", "gpoint")
.attr("title", text)
.style("fill", status);
var x = projection([lat,lon])[0];
var y = projection([lat,lon])[1];
gpoint.append("svg:circle")
.attr("cx", x)
.attr("cy", y)
.attr("class","point")
.attr("r", 5);
gpoint.on("mouseover", onMouseOver)
.on("mouseout", onMouseOut);
function onMouseOver () {
var mouse = d3.mouse(svg.node()).map( function(d) { return parseInt(d); } );
var display = "<center>" + this.getAttribute("title") ;
tooltip.classed("hidden", false)
.attr("style", "left:"+(mouse[0]+offsetL)+"px;top:"+(mouse[1]+offsetT)+"px")
.html(display);
d3.select(this).style("fill", "red");
};
function onMouseOut () {
tooltip.classed("hidden", true);
d3.select(this).style("fill", status);
}
}
}
function redraw() {
width = document.getElementById('container').offsetWidth;
height = width / 2;
d3.select('svg').remove();
setup(width,height);
draw(topo);
}
function move() {
var t = d3.event.translate;
var s = d3.event.scale;
zscale = s;
var h = height/4;
t[0] = Math.min(
(width/height) * (s - 1),
Math.max( width * (1 - s), t[0] )
);
t[1] = Math.min(
h * (s - 1) + h * s,
Math.max(height * (1 - s) - h * s, t[1])
);
zoom.translate(t);
g.attr("transform", "translate(" + t + ")scale(" + s + ")");
//adjust the country hover stroke width based on zoom level
d3.selectAll(".country").style("stroke-width", 1.5 / s);
d3.selectAll(".point").attr("r", 5 / s);
}
var throttleTimer;
function throttle() {
window.clearTimeout(throttleTimer);
throttleTimer = window.setTimeout(function() {
redraw();
}, 200);
}
//geo translation on mouse click in map
function click() {
var latlon = projection.invert(d3.mouse(this));
console.log(latlon);
}
</script>
</body>
</html>