graph.js

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

var color = d3.scaleOrdinal(d3.schemeCategory20);

var simulation = d3.forceSimulation()
                .force("link", d3.forceLink().id(function(d) { return d.path; }))
                .force("charge", d3.forceManyBody())
                .force("center", d3.forceCenter(width / 2, height / 2));

/*
 * Input file generated with
 * zk graph --format json > data/notes2.json
 */

d3.json("data/notes.json", function(error, json) {
                if (error) throw error;

                // Create list of existing paths/IDs
                var validPaths = json.notes.map(n => n.path);

                // Filter broken links and format notes so that d3 can untderstand them
                var edges = json.links
                                .filter( edge => ( validPaths.includes(edge.targetPath) && (validPaths.includes(edge.sourcePath) )))
                                .map(function(e){
                                                ne = {};
                                                ne.source = e.sourcePath;
                                                ne.target = e.targetPath;
                                                return ne;
                                });

                var link = svg.append("g")
                                .attr("class", "links")
                                .selectAll("line")
                                .data(edges)
                                .enter().append("line")
                                .attr("stroke-width", function(d) { return Math.sqrt(d.value); });

                var node = svg.append("g")
                                .attr("class", "nodes")
                                .selectAll("g")
                                .data(json.notes)
                                .enter().append("g")

                var circles = node.append("circle")
                                .attr("r", 5)
                                .attr("fill", function(d) { return color(d.group); })
                // We could use wordCount here, to denote the length of a note with it's color
                // .attr("fill", function(d) { return color(d.wordCount); })
                                .call(d3.drag()
                                                .on("start", dragstarted)
                                                .on("drag", dragged)
                                                .on("end", dragended));

                var lables = node.append("text")
                                .text(function(d) {
                                                return d.title;
                                })
                                .attr('x', 6)
                                .attr('y', 3);

                // Add title to nodes
                node.append("title")
                                .text(function(d) { return d.title; });

                simulation
                                .nodes(json.notes)
                                .on("tick", ticked);

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

                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("transform", function(d) {
                                                                return "translate(" + d.x + "," + 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;
}

index.html

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

.links line {
  stroke: #999;
  stroke-opacity: 0.6;
}

.nodes circle {
  stroke: #fff;
  stroke-width: 1.5px;
}

text {
  font-family: sans-serif;
  font-size: 10px;
}

</style>
<svg width="960" height="600"></svg>
<script src="https://d3js.org/d3.v4.min.js"></script>
                <script src="graph.js"></script>
<script>
</script>