score:1

Accepted answer

I rewrote your code. Check, please. Is it behavior what you need?

var jobject = `{"nodes":[
{"name":"ADH1A","degree":9},
{"name":"ADH1B","degree":10},
{"name":"ADH1C","degree":9},
{"name":"ADH4","degree":10},
{"name":"ADH5","degree":9},
{"name":"ADH7","degree":9},
{"name":"ALDH1A1","degree":11},
{"name":"ALDH2","degree":9},
{"name":"BDNF","degree":5},
{"name":"CHRNA5","degree":1},
{"name":"CHRNB4","degree":2},
{"name":"CNR1","degree":1},
{"name":"COMT","degree":13},
{"name":"CRHR1","degree":1},
{"name":"CYP2E1","degree":9},
{"name":"DRD1","degree":7},
{"name":"DRD2","degree":9},
{"name":"DRD3","degree":4},
{"name":"DRD4","degree":6},
{"name":"GABRA1","degree":9},
{"name":"GABRA2","degree":8},
{"name":"GABRA6","degree":7},
{"name":"GABRB1","degree":8},
{"name":"GABRB2","degree":8},
{"name":"GABRB3","degree":7},
{"name":"GABRG1","degree":5},
{"name":"GABRG2","degree":8},
{"name":"GAL","degree":5},
{"name":"GRIK3","degree":1},
{"name":"GRIN2B","degree":3},
{"name":"GRM8","degree":4},
{"name":"HTR1A","degree":2},
{"name":"HTR1B","degree":5},
{"name":"HTR2A","degree":5},
{"name":"MAOA","degree":17},
{"name":"NPY","degree":7},
{"name":"OPRD1","degree":4},
{"name":"OPRK1","degree":6},
{"name":"OPRM1","degree":3},
{"name":"PDYN","degree":6},
{"name":"POMC","degree":10},
{"name":"SLC6A3","degree":8},
{"name":"SLC6A4","degree":13},
{"name":"TPH1","degree":3}
],
"links":[
{"source":0,"target":1,"min_degree":9},
{"source":0,"target":2,"min_degree":9},
{"source":0,"target":3,"min_degree":9},
{"source":0,"target":4,"min_degree":9},
{"source":0,"target":5,"min_degree":9},
{"source":0,"target":6,"min_degree":9},
{"source":0,"target":7,"min_degree":9},
{"source":0,"target":8,"min_degree":9},
{"source":0,"target":11,"min_degree":9},
{"source":1,"target":2,"min_degree":9},
{"source":1,"target":3,"min_degree":10},
{"source":1,"target":4,"min_degree":9},
{"source":1,"target":5,"min_degree":9},
{"source":1,"target":6,"min_degree":10},
{"source":1,"target":7,"min_degree":10},
{"source":1,"target":8,"min_degree":9},
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{"source":1,"target":11,"min_degree":10},
{"source":2,"target":3,"min_degree":9},
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{"source":2,"target":5,"min_degree":9},
{"source":2,"target":6,"min_degree":9},
{"source":2,"target":8,"min_degree":9},
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{"source":2,"target":11,"min_degree":9},
{"source":3,"target":4,"min_degree":9},
{"source":3,"target":5,"min_degree":9},
{"source":3,"target":6,"min_degree":10},
{"source":3,"target":7,"min_degree":10},
{"source":3,"target":8,"min_degree":9},
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{"source":3,"target":11,"min_degree":10},
{"source":4,"target":5,"min_degree":9},
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{"source":4,"target":9,"min_degree":9},
{"source":4,"target":11,"min_degree":9},
{"source":5,"target":6,"min_degree":9},
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{"source":26,"target":34,"min_degree":9},
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{"source":29,"target":34,"min_degree":8},
{"source":30,"target":31,"min_degree":7},
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{"source":30,"target":34,"min_degree":8},
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{"source":32,"target":33,"min_degree":5},
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{"source":34,"target":36,"min_degree":3},
{"source":34,"target":37,"min_degree":5},
{"source":34,"target":43,"min_degree":3},
{"source":35,"target":36,"min_degree":1},
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{"source":38,"target":39,"min_degree":4},
{"source":38,"target":40,"min_degree":3},
{"source":38,"target":41,"min_degree":4},
{"source":39,"target":41,"min_degree":6},
{"source":40,"target":41,"min_degree":3}
]}`
var graph = JSON.parse(jobject);

var width = 960,
  height = 500;

var color = d3.scale.category20();

var force = d3.layout.force()
  .charge(-120)
  .linkDistance(30)
  .size([width, height]);

var x = d3.scale.linear()
  .domain([0, 20])
  .range([250, 80])
  .clamp(true);

var brush = d3.svg.brush()
  .y(x)
  .extent([0, 0]);

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

var links_g = svg.append("g");

var nodes_g = svg.append("g");

svg.append("g")
  .attr("class", "x axis")
  .attr("transform", "translate(" + (width - 20) + ",0)")
  .call(d3.svg.axis()
    .scale(x)
    .orient("left")
    .tickFormat(function(d) {
      return d;
    })
    .tickSize(0)
    .tickPadding(12))
  .select(".domain")
  .select(function() {
    return this.parentNode.appendChild(this.cloneNode(true));
  })
  .attr("class", "halo");

var slider = svg.append("g")
  .attr("class", "slider")
  .call(brush);

slider.selectAll(".extent,.resize")
  .remove();

var handle = slider.append("circle")
  .attr("class", "handle")
  .attr("transform", "translate(" + (width - 20) + ",0)")
  .attr("r", 5);

svg.append("text")
  .attr("x", width - 15)
  .attr("y", 60)
  .attr("text-anchor", "end")
  .attr("font-size", "12px")
  .style("opacity", 0.5)
  .text("degree threshold")


graph.links.forEach(function(d, i) {
  d.i = i;
});
graph.nodes.forEach(function(d, i) {
  d.i = i;
});

function brushed() {
  var value = brush.extent()[0];

  if (d3.event.sourceEvent) {
    value = x.invert(d3.mouse(this)[1]);
    brush.extent([value, value]);
  }
  handle.attr("cy", x(value));
  var threshold = value;

  var thresholded_nodes = graph.nodes.filter(function(d) {
    return (d.degree > threshold);
  });
  var thresholded_links = graph.links.filter(function(d) {
    return (d.min_degree > threshold);
  });


  force
    .links(thresholded_links);

  var link = links_g.selectAll(".link")
    .data(thresholded_links, function(d) {
      return d.i;
    });

  link.enter().append("line")
    .attr("class", "link")
    .style("stroke-width", function(d) {
      return Math.sqrt(d.value);
    });

  link.exit().remove();


  force.on("tick", function() {
    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("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
  });

  force.start();

}

force
  .nodes(graph.nodes);

var node = nodes_g.selectAll(".node")
  .data(graph.nodes)
  .enter()
  .append('g')
  .attr("class", "node")
  .call(force.drag);
  
  node.append("circle")
  .attr("r", 5)
  // .style("fill", function(d) { return color(1); })
  .style("fill", function(d) {
    return color(1);
  })
  
 node.append("text")
      .attr("dx", 4)
      .attr("dy", ".35em")
      .text(function(d) { return d.name });
      
node.append("title")
  .text(function(d) {
    return d.name;
  });

brush.on("brush", brushed);

slider
  .call(brush.extent([5, 5]))
  .call(brush.event);
.node {
  stroke: #fff;
  stroke-width: 1.5px;
}

.link {
  stroke: #999;
  stroke-opacity: .6;
}

.axis {
  opacity: 0.5;
  font: 10px sans-serif;
  -webkit-user-select: none;
  -moz-user-select: none;
  user-select: none;
}

.axis .domain {
  fill: none;
  stroke: #000;
  stroke-opacity: .3;
  stroke-width: 4px;
  stroke-linecap: round;
}

.axis .halo {
  fill: none;
  stroke: #ddd;
  stroke-width: 3px;
  stroke-linecap: round;
}


text {
  pointer-events: none;
  font: 8px sans-serif;
  stroke: none;
  fill: red;
}

.slider .handle {
  fill: #fff;
  stroke: #000;
  stroke-opacity: .5;
  stroke-width: 1.25px;
  cursor: grab;
}
<script src="https://d3js.org/d3.v3.min.js"></script>


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