d3js force directed graph arrows not showing up - d3.js

Question

I have a force directed graph using version 5 of d3.js and would like to include arrow heads for each link. I've included the code below and posted a jsfiddle. I'm seeking guidance on why the arrow heads (id=end-arrow) are not showing up in the graph. I'm referencing the end-arrow as an attribute in the declaration of link: .attr("marker-end","url(#end-arrow)"), and I don't know how to troubleshoot this.
HTML:
<svg id="viz"></svg>
Javascript with d3.js version 5:
// based on https://bl.ocks.org/mapio/53fed7d84cd1812d6a6639ed7aa83868
var width = 600;
var height = 400;
var border = 1;
var bordercolor="black";
var color = d3.scaleOrdinal(d3.schemeCategory10); // coloring of nodes
var graph = {
"nodes": [
{"id": "4718871", "group": 2, "img": "https://derivationmap.net/static/multiplybothsidesby.png", "width": 298, "height": 30, "linear index": 2},
{"id": "2131616531", "group": 0, "img": "https://derivationmap.net/static/2131616531.png", "width": 103, "height": 30, "linear index": 0},
{"id": "9565166889", "group": 0, "img": "https://derivationmap.net/static/9565166889.png", "width": 24, "height": 23, "linear index": 0},
{"id": "9040079362", "group": 0, "img": "https://derivationmap.net/static/9040079362.png", "width": 18, "height": 30, "linear index": 0},
{"id": "9278347", "group": 1, "img": "https://derivationmap.net/static/declareinitialexpr.png", "width": 270, "height": 30, "linear index": 1},
{"id": "6286448", "group": 4, "img": "https://derivationmap.net/static/declarefinalexpr.png", "width": 255, "height": 30, "linear index": 4},
{"id": "2113211456", "group": 0, "img": "https://derivationmap.net/static/2113211456.png", "width": 121, "height": 34, "linear index": 0},
{"id": "2169431", "group": 3, "img": "https://derivationmap.net/static/dividebothsidesby.png", "width": 260, "height": 30, "linear index": 3},
{"id": "3131111133", "group": 0, "img": "https://derivationmap.net/static/3131111133.png", "width": 121, "height": 34, "linear index": 0}
],
"links": [
{"source": "2169431", "target": "2113211456", "value": 1},
{"source": "2113211456", "target": "6286448", "value": 1},
{"source": "9278347", "target": "3131111133", "value": 1},
{"source": "4718871", "target": "2131616531", "value": 1},
{"source": "9040079362", "target": "4718871", "value": 1},
{"source": "2131616531", "target": "2169431", "value": 1},
{"source": "3131111133", "target": "4718871", "value": 1},
{"source": "9565166889", "target": "2169431", "value": 1}
]
};
var label = {
"nodes": [],
"links": []
};
graph.nodes.forEach(function(d, i) {
label.nodes.push({node: d});
label.nodes.push({node: d});
label.links.push({
source: i * 2,
target: i * 2 + 1
});
});
var labelLayout = d3.forceSimulation(label.nodes)
.force("charge", d3.forceManyBody().strength(-50))
.force("link", d3.forceLink(label.links).distance(0).strength(2));
var graphLayout = d3.forceSimulation(graph.nodes)
.force("charge", d3.forceManyBody().strength(-3000))
.force("center", d3.forceCenter(width / 2, height / 2))
.force("x", d3.forceX(width / 2).strength(1))
.force("y", d3.forceY(height / 2).strength(1))
.force("link", d3.forceLink(graph.links).id(function(d) {return d.id; }).distance(50).strength(1))
.on("tick", ticked);
var adjlist = [];
graph.links.forEach(function(d) {
adjlist[d.source.index + "-" + d.target.index] = true;
adjlist[d.target.index + "-" + d.source.index] = true;
});
function neigh(a, b) {
return a == b || adjlist[a + "-" + b];
}
var svg = d3.select("#viz").attr("width", width).attr("height", height);
// define arrow markers for graph links
svg.append("svg:defs").append("svg:marker")
.attr("id", "end-arrow")
.attr("viewBox", "0 -5 10 10")
.attr("refX", 6)
.attr("markerWidth", 3)
.attr("markerHeight", 3)
.attr("orient", "auto")
.append("svg:line")
.attr("d", "M0,-5L10,0L0,5")
.attr("fill", "black");
// http://bl.ocks.org/AndrewStaroscik/5222370
var borderPath = svg.append("rect")
.attr("x", 0)
.attr("y", 0)
.attr("height", height)
.attr("width", width)
.style("stroke", bordercolor)
.style("fill", "none")
.style("stroke-width", border);
var container = svg.append("g");
svg.call(
d3.zoom()
.scaleExtent([.1, 4])
.on("zoom", function() { container.attr("transform", d3.event.transform); })
);
var link = container.append("g").attr("class", "links")
.selectAll("line")
.data(graph.links)
.enter()
.append("line")
.attr("stroke", "#aaa")
.attr("stroke-width", "1px")
.attr("marker-end","url(#end-arrow)");
var node = container.append("g").attr("class", "nodes")
.selectAll("g")
.data(graph.nodes)
.enter()
.append("circle")
.attr("r", 5)
.attr("fill", function(d) { return color(d.group); })
node.on("mouseover", focus).on("mouseout", unfocus);
node.call(
d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
.on("end", dragended)
);
var labelNode = container.append("g").attr("class", "labelNodes")
.selectAll("text")
.data(label.nodes)
.enter()
.append("image")
// alternative option, unverified: https://stackoverflow.com/questions/39908583/d3-js-labeling-nodes-with-image-in-force-layout
// I have no idea why the i%2 is needed; without it I get two images per node
// switching between i%2==1 and i%2==0 produces different image locations (?)
.attr("xlink:href", function(d, i) { return i % 2 == 1 ? "" : d.node.img; } )
.attr("x", 0)
.attr("y", 0)
// the following alter the image size
.attr("width", function(d, i) { return d.node.width/2; })
.attr("height", function(d, i) { return d.node.height/2; })
// .append("text")
// .text(function(d, i) { return i % 2 == 0 ? "" : d.node.id; })
// .style("fill", "#555")
// .style("font-family", "Arial")
// .style("font-size", 12)
.style("pointer-events", "none"); // to prevent mouseover/drag capture
node.on("mouseover", focus).on("mouseout", unfocus);
function ticked() {
node.call(updateNode);
link.call(updateLink);
labelLayout.alphaTarget(0.3).restart();
labelNode.each(function(d, i) {
if(i % 2 == 0) {
d.x = d.node.x;
d.y = d.node.y;
} else {
var b = this.getBBox();
var diffX = d.x - d.node.x;
var diffY = d.y - d.node.y;
var dist = Math.sqrt(diffX * diffX + diffY * diffY);
var shiftX = b.width * (diffX - dist) / (dist * 2);
shiftX = Math.max(-b.width, Math.min(0, shiftX));
var shiftY = 16;
this.setAttribute("transform", "translate(" + shiftX + "," + shiftY + ")");
}
});
labelNode.call(updateNode);
}
function fixna(x) {
if (isFinite(x)) return x;
return 0;
}
function focus(d) {
var index = d3.select(d3.event.target).datum().index;
node.style("opacity", function(o) {
return neigh(index, o.index) ? 1 : 0.1;
});
labelNode.attr("display", function(o) {
return neigh(index, o.node.index) ? "block": "none";
});
link.style("opacity", function(o) {
return o.source.index == index || o.target.index == index ? 1 : 0.1;
});
}
function unfocus() {
labelNode.attr("display", "block");
node.style("opacity", 1);
link.style("opacity", 1);
}
function updateLink(link) {
link.attr("x1", function(d) { return fixna(d.source.x); })
.attr("y1", function(d) { return fixna(d.source.y); })
.attr("x2", function(d) { return fixna(d.target.x); })
.attr("y2", function(d) { return fixna(d.target.y); });
}
function updateNode(node) {
node.attr("transform", function(d) {
return "translate(" + fixna(d.x) + "," + fixna(d.y) + ")";
});
}
function dragstarted(d) {
d3.event.sourceEvent.stopPropagation();
if (!d3.event.active) graphLayout.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) graphLayout.alphaTarget(0);
d.fx = null;
d.fy = null;
}

Answer 1

Based on feedback in the d3js Slack channel, there were two issues:
In the definition of the arrow, needed .append("svg:path")
With that fixed, the arrows were too small and were hidden behind the node circles. By making the arrows larger, they were visible.
I've updated http://bl.ocks.org/bhpayne/0a8ef2ae6d79aa185dcf2c3a385daf25 and the revised code is below:
HTML
<svg id="viz"></svg>
Javascript + d3js
// based on https://bl.ocks.org/mapio/53fed7d84cd1812d6a6639ed7aa83868
var width = 600;
var height = 400;
var border = 3;
var bordercolor = "black";
var color = d3.scaleOrdinal(d3.schemeCategory10); // coloring of nodes
var graph = {
"nodes": [{
"id": "4718871",
"group": 2,
"img": "https://derivationmap.net/static/multiplybothsidesby.png",
"width": 298,
"height": 30,
"linear index": 2
},
{
"id": "2131616531",
"group": 0,
"img": "https://derivationmap.net/static/2131616531.png",
"width": 103,
"height": 30,
"linear index": 0
},
{
"id": "9565166889",
"group": 0,
"img": "https://derivationmap.net/static/9565166889.png",
"width": 24,
"height": 23,
"linear index": 0
},
{
"id": "9040079362",
"group": 0,
"img": "https://derivationmap.net/static/9040079362.png",
"width": 18,
"height": 30,
"linear index": 0
},
{
"id": "9278347",
"group": 1,
"img": "https://derivationmap.net/static/declareinitialexpr.png",
"width": 270,
"height": 30,
"linear index": 1
},
{
"id": "6286448",
"group": 4,
"img": "https://derivationmap.net/static/declarefinalexpr.png",
"width": 255,
"height": 30,
"linear index": 4
},
{
"id": "2113211456",
"group": 0,
"img": "https://derivationmap.net/static/2113211456.png",
"width": 121,
"height": 34,
"linear index": 0
},
{
"id": "2169431",
"group": 3,
"img": "https://derivationmap.net/static/dividebothsidesby.png",
"width": 260,
"height": 30,
"linear index": 3
},
{
"id": "3131111133",
"group": 0,
"img": "https://derivationmap.net/static/3131111133.png",
"width": 121,
"height": 34,
"linear index": 0
}
],
"links": [{
"source": "2169431",
"target": "2113211456",
"value": 1
},
{
"source": "2113211456",
"target": "6286448",
"value": 1
},
{
"source": "9278347",
"target": "3131111133",
"value": 1
},
{
"source": "4718871",
"target": "2131616531",
"value": 1
},
{
"source": "9040079362",
"target": "4718871",
"value": 1
},
{
"source": "2131616531",
"target": "2169431",
"value": 1
},
{
"source": "3131111133",
"target": "4718871",
"value": 1
},
{
"source": "9565166889",
"target": "2169431",
"value": 1
}
]
};
var label = {
"nodes": [],
"links": []
};
graph.nodes.forEach(function(d, i) {
label.nodes.push({
node: d
});
label.nodes.push({
node: d
});
label.links.push({
source: i * 2,
target: i * 2 + 1
});
});
var labelLayout = d3.forceSimulation(label.nodes)
.force("charge", d3.forceManyBody().strength(-50))
.force("link", d3.forceLink(label.links).distance(0).strength(2));
var graphLayout = d3.forceSimulation(graph.nodes)
.force("charge", d3.forceManyBody().strength(-3000))
.force("center", d3.forceCenter(width / 2, height / 2))
.force("x", d3.forceX(width / 2).strength(1))
.force("y", d3.forceY(height / 2).strength(1))
.force("link", d3.forceLink(graph.links).id(function(d) {
return d.id;
}).distance(50).strength(1))
.on("tick", ticked);
var adjlist = [];
graph.links.forEach(function(d) {
adjlist[d.source.index + "-" + d.target.index] = true;
adjlist[d.target.index + "-" + d.source.index] = true;
});
function neigh(a, b) {
return a == b || adjlist[a + "-" + b];
}
var svg = d3.select("#viz").attr("width", width).attr("height", height);
// define arrow markers for graph links
svg.append("svg:defs").append("svg:marker")
.attr("id", "end-arrow")
.attr("viewBox", "0 -5 10 10")
.attr("refX", 10)
.attr("markerWidth", 20)
.attr("markerHeight", 20)
.attr("orient", "auto")
.append("svg:path")
.attr("d", "M0,-5L20,0L0,5")
.attr("fill", "#000");
// http://bl.ocks.org/AndrewStaroscik/5222370
var borderPath = svg.append("rect")
.attr("x", 0)
.attr("y", 0)
.attr("height", height)
.attr("width", width)
.style("stroke", bordercolor)
.style("fill", "none")
.style("stroke-width", border);
var container = svg.append("g");
svg.call(
d3.zoom()
.scaleExtent([.1, 4])
.on("zoom", function() {
container.attr("transform", d3.event.transform);
})
);
var link = container.append("g").attr("class", "links")
.selectAll("line")
.data(graph.links)
.enter()
.append("line")
.attr("stroke", "#aaa")
.attr("marker-end", "url(#end-arrow)")
.attr("stroke-width", "1px");
var node = container.append("g").attr("class", "nodes")
.selectAll("g")
.data(graph.nodes)
.enter()
.append("circle")
.attr("r", 10)
.attr("fill", function(d) {
return color(d.group);
})
node.on("mouseover", focus).on("mouseout", unfocus);
node.call(
d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
.on("end", dragended)
);
var labelNode = container.append("g").attr("class", "labelNodes")
.selectAll("text")
.data(label.nodes)
.enter()
.append("image")
// alternative option, unverified: https://stackoverflow.com/questions/39908583/d3-js-labeling-nodes-with-image-in-force-layout
// I have no idea why the i%2 is needed; without it I get two images per node
// switching between i%2==1 and i%2==0 produces different image locations (?)
.attr("xlink:href", function(d, i) {
return i % 2 == 1 ? "" : d.node.img;
})
.attr("x", 0)
.attr("y", 0)
// the following alter the image size
.attr("width", function(d, i) {
return d.node.width / 2;
})
.attr("height", function(d, i) {
return d.node.height / 2;
})
// .append("text")
// .text(function(d, i) { return i % 2 == 0 ? "" : d.node.id; })
// .style("fill", "#555")
// .style("font-family", "Arial")
// .style("font-size", 12)
.style("pointer-events", "none"); // to prevent mouseover/drag capture
node.on("mouseover", focus).on("mouseout", unfocus);
function ticked() {
node.call(updateNode);
link.call(updateLink);
labelLayout.alphaTarget(0.3).restart();
labelNode.each(function(d, i) {
if (i % 2 == 0) {
d.x = d.node.x;
d.y = d.node.y;
} else {
var b = this.getBBox();
var diffX = d.x - d.node.x;
var diffY = d.y - d.node.y;
var dist = Math.sqrt(diffX * diffX + diffY * diffY);
var shiftX = b.width * (diffX - dist) / (dist * 2);
shiftX = Math.max(-b.width, Math.min(0, shiftX));
var shiftY = 16;
this.setAttribute("transform", "translate(" + shiftX + "," + shiftY + ")");
}
});
labelNode.call(updateNode);
}
function fixna(x) {
if (isFinite(x)) return x;
return 0;
}
function focus(d) {
var index = d3.select(d3.event.target).datum().index;
node.style("opacity", function(o) {
return neigh(index, o.index) ? 1 : 0.1;
});
labelNode.attr("display", function(o) {
return neigh(index, o.node.index) ? "block" : "none";
});
link.style("opacity", function(o) {
return o.source.index == index || o.target.index == index ? 1 : 0.1;
});
}
function unfocus() {
labelNode.attr("display", "block");
node.style("opacity", 1);
link.style("opacity", 1);
}
function updateLink(link) {
link.attr("x1", function(d) {
return fixna(d.source.x);
})
.attr("y1", function(d) {
return fixna(d.source.y);
})
.attr("x2", function(d) {
return fixna(d.target.x);
})
.attr("y2", function(d) {
return fixna(d.target.y);
});
}
function updateNode(node) {
node.attr("transform", function(d) {
return "translate(" + fixna(d.x) + "," + fixna(d.y) + ")";
});
}
function dragstarted(d) {
d3.event.sourceEvent.stopPropagation();
if (!d3.event.active) graphLayout.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) graphLayout.alphaTarget(0);
d.fx = null;
d.fy = null;
}