barley network graph

<!DOCTYPE html>
<meta charset="utf-8">
<style>

body {
  font-family: Futura;
  font-size: 10px;
}

.nodes circle {
  fill: #ccc;
  stroke: #000;
}

.links {
  stroke: #999;
  stroke-width: 1.5px;
}

text {
  pointer-events: none;
  text-anchor: middle;
}

</style>
<svg width="960" height="600"></svg>
<script src="https://d3js.org/d3.v4.min.js"></script>
<script src="https://d3js.org/colorbrewer.v1.min.js"></script>
<script src="https://d3js.org/d3-color.v1.min.js"></script>
<script src="https://d3js.org/d3-interpolate.v1.min.js"></script>
<script src="https://d3js.org/d3-scale-chromatic.v1.min.js"></script>
<script>

var svg = d3.select("svg"),
    width = +svg.attr("width"),
    height = +svg.attr("height");

var simulation = d3.forceSimulation()
    .force("charge", d3.forceManyBody().strength(-50))
    .force("link", d3.forceLink().id(function(d) { return d.id; }))
    .force("x", d3.forceX(width / 2))
    .force("y", d3.forceY(height / 2));

var colorScale = d3.scaleOrdinal(d3.schemeCategory20b);

d3.tsv("barley.tsv", function(error, data) {

console.log(data);

var yieldLookup = {}

data.forEach(function(d) {
    d.site = d.site.replace(" ","").replace(". ", "")
    d.variety = d.variety.replace(" ","").replace(". ", "")
    yieldLookup[d.site + '-' + d.variety + "-" + d.year] = +d.yield;
  })

var nodes = [],
      links = [];

sites.forEach(function(site){
        nodes.push({"id" : site,
                    "shortName": site,
                    "radius": 10,
                    "colorScale": "#fff",
                    "classValue": "site" })
      })

siteVarieties.forEach(function(siteVariety) {
        nodes.push({"id" : siteVariety,
                    "shortName": siteVariety.split("-")[1],
                    "radius": 10,
                    "colorScale" : colorScale(siteVariety.split("-")[1]),
                    "classValue": siteVariety.split("-")[1].replace(".","") });

links.push({
          "source": siteVariety.split("-")[0],
          "target": siteVariety
        })

})

siteVarietiesYears.forEach(function(svy) {
        nodes.push({"id" : svy,
                    "shortName": svy.split("-")[2],
                    "radius": Math.sqrt(yieldLookup[svy])/Math.PI*10,
                    "colorScale": colorScale(svy.split("-")[1]),
                    "classValue": svy.split("-")[1].replace(".","") });

links.push({
          "source": svy.split("-")[0] + '-' + svy.split("-")[1],
          "target": svy
        })

})

var graph = {
   "nodes": nodes,
   "links": links
  }

console.log(sites);
  console.log(siteVarieties);
  console.log(siteVarietiesYears);

console.log(graph)
  var link = svg.append("g")
      .attr("class", "links")
      .selectAll("line")
      .data(graph.links)
    .enter().append("line");

var lookupClass = d.classValue;
      d3.selectAll("circle").style("fill-opacity", .1)
      d3.selectAll("." + lookupClass).style("fill-opacity", 1)

})
    .on("mouseleave", function(d) {

var lookupClass = d.classValue;
      d3.selectAll("circle").style("fill-opacity", 1)

})

var text = svg.append("g")
      .attr("class", "text")
      .selectAll("text")
      .data(graph.nodes)
    .enter().append("text")
      .text(function(d, i) { return d.shortName; })

simulation
      .nodes(graph.nodes)
      .on("tick", ticked);

simulation.force("link")
      .links(graph.links);

function ticked() {

link
        .attr("x1", function(d) { return d.source.x; })
        .attr("y1", function(d) { return d.source.y; })
        .attr("x2", function(d) { return d.target.x; })
        .attr("y2", function(d) { return d.target.y; });

node
        .attr("cx", function(d) { return d.x; })
        .attr("cy", function(d) { return d.y; });

text
        .attr("x", function(d) { return d.x; })
        .attr("y", function(d) { return d.y; });
  }

});

function dragstarted(d) {
  if (!d3.event.active) simulation.alphaTarget(0.3).restart();
  d.fx = d.x;
  d.fy = d.y;
}

function dragged(d) {
  d.fx = d3.event.x;
  d.fy = d3.event.y;
}

function dragended(d) {
  if (!d3.event.active) simulation.alphaTarget(0);
  d.fx = null;
  d.fy = null;
}

</script>

Modified http://d3js.org/colorbrewer.v1.min.js to a secure url

https://d3js.org/d3.v4.min.js

https://d3js.org/colorbrewer.v1.min.js

https://d3js.org/d3-color.v1.min.js

https://d3js.org/d3-interpolate.v1.min.js

https://d3js.org/d3-scale-chromatic.v1.min.js