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Sankey diagram with D3 v7 - mouseover node highlights links

I am making a Sankey diagram with D3 v7 where I hope that on mouseover of the node all connected paths will be highlighted and the other nodes will lower in opacity.
I’ve tried to follow this example: D3.js Sankey Chart - How can I highlight the set of links coming from a node? but I am new to JS so am not sure what this part is doing
function (l) {return l.source === d || l.target === d ? 0.5 : 0.2;});
I am finding that there are many examples of this for v4 of d3 but I can’t find one that works on v7.
In addition, I would like fade out all nodes that are not connected to the selected node. Is this possible?
Any advice would be very much appreciated!
Screen shot of current layout:
Would like it to be like this on mouseover of node:
// set the dimensions and margins of the graph
var margin = { top: 10, right: 50, bottom: 10, left: 50 },
width = 1920 - margin.left - margin.right,
height = 800 - margin.top - margin.bottom;
// format variables
var formatNumber = d3.format(",.0f"), // zero decimal places
format = function (d) { return formatNumber(d); },
color = d3.scaleOrdinal().range(["#002060ff", "#164490ff", "#4d75bcff", "#98b3e6ff", "#d5e2feff", "#008cb0ff"]);
// append the svg object to the body of the page
var svg = d3.select("body").append("svg")
.attr("width", width + margin.left + margin.right)
.attr("height", height + margin.top + margin.bottom)
.append("g")
.attr("transform",
"translate(" + margin.left + "," + margin.top + ")");
// Set the sankey diagram properties
var sankey = d3.sankey()
.nodeWidth(100)
.nodePadding(40)
.size([width, height]);
var path = sankey.links();
// load the data
d3.json("sankey.json").then(function (sankeydata) {
graph = sankey(sankeydata);
// add in the links
var link = svg.append("g").selectAll(".link")
.data(graph.links)
.enter().append("path")
.attr("class", "link")
.attr("d", d3.sankeyLinkHorizontal())
.attr("stroke-width", function (d) { return d.width; });
// add the link titles
link.append("title")
.text(function (d) {
return d.source.name + " → " +
d.target.name;
});
// add in the nodes
var node = svg.append("g").selectAll(".node")
.data(graph.nodes)
.enter().append("g")
.attr("class", "node")
// add the rectangles for the nodes
node.append("rect")
.attr("x", function (d) { return d.x0; })
.attr("y", function (d) { return d.y0; })
.attr("height", function (d) { return d.y1 - d.y0; })
.attr("width", sankey.nodeWidth())
.style("fill", function (d) {
return d.color = color(d.name.replace(/ .*/, ""));
})
// Attempt at getting whole length of link to highlight
.on("mouseover", function (d) {
link
.transition()
.duration(300)
.style("stroke-opacity", function (l) {
return l.source === d || l.target === d ? 0.5 : 0.2;
});
})
.on("mouseleave", function (d) {
link
.transition()
.duration(300)
.style("stroke-opacity", 0.2);
})
// Node hover titles
.append("title")
.text(function (d) {
return d.name + "\n" + format(d.value);
});
// add in the title for the nodes
node.append("text")
.style("fill", "#3f3f3f")
.attr("x", function (d) { return d.x0 - 6; })
.attr("y", function (d) { return (d.y1 + d.y0) / 2; })
.attr("dy", "0.35em")
.attr("text-anchor", "end")
.text(function (d) { return d.name; })
.filter(function (d) { return d.x0 < width / 2; })
.attr("x", function (d) { return d.x1 + 6; })
.attr("text-anchor", "start")
;
});

how to change stack order of text label in JavaScript?

I am trying to plot a network graph using networkD3 in R. I wanted to make some changes to the display so that the text labels (which appears when mouseover) can be easily read.
Please refer to the link here for an example. Note: Jump to the d3ForceNetwork plot.
As seen in the example, the labels are hard to read due to its colour and it often gets obstructed by the surrounding nodes. I have been messing around with the JS file and managed to change the text label color to black. However, having no knowledge of JS or CSS (I can't even tell the difference between the 2 actually), I have no idea how I can change the stack order such that the text labels will always be displayed above any other objects.
Can anyone advise me on how I can achieve the desired outcome?
Below is the full JS file:
HTMLWidgets.widget({
name: "forceNetwork",
type: "output",
initialize: function(el, width, height) {
d3.select(el).append("svg")
.attr("width", width)
.attr("height", height);
return d3.layout.force();
},
resize: function(el, width, height, force) {
d3.select(el).select("svg")
.attr("width", width)
.attr("height", height);
force.size([width, height]).resume();
},
renderValue: function(el, x, force) {
// Compute the node radius using the javascript math expression specified
function nodeSize(d) {
if(options.nodesize){
return eval(options.radiusCalculation);
}else{
return 6}
}
// alias options
var options = x.options;
// convert links and nodes data frames to d3 friendly format
var links = HTMLWidgets.dataframeToD3(x.links);
var nodes = HTMLWidgets.dataframeToD3(x.nodes);
// get the width and height
var width = el.offsetWidth;
var height = el.offsetHeight;
var color = eval(options.colourScale);
// set this up even if zoom = F
var zoom = d3.behavior.zoom();
// create d3 force layout
force
.nodes(d3.values(nodes))
.links(links)
.size([width, height])
.linkDistance(options.linkDistance)
.charge(options.charge)
.on("tick", tick)
.start();
// thanks http://plnkr.co/edit/cxLlvIlmo1Y6vJyPs6N9?p=preview
// http://stackoverflow.com/questions/22924253/adding-pan-zoom-to-d3js-force-directed
var drag = force.drag()
.on("dragstart", dragstart)
// allow force drag to work with pan/zoom drag
function dragstart(d) {
d3.event.sourceEvent.preventDefault();
d3.event.sourceEvent.stopPropagation();
}
// select the svg element and remove existing children
var svg = d3.select(el).select("svg");
svg.selectAll("*").remove();
// add two g layers; the first will be zoom target if zoom = T
// fine to have two g layers even if zoom = F
svg = svg
.append("g").attr("class","zoom-layer")
.append("g")
// add zooming if requested
if (options.zoom) {
function redraw() {
d3.select(el).select(".zoom-layer").attr("transform",
"translate(" + d3.event.translate + ")"+
" scale(" + d3.event.scale + ")");
}
zoom.on("zoom", redraw)
d3.select(el).select("svg")
.attr("pointer-events", "all")
.call(zoom);
} else {
zoom.on("zoom", null);
}
// draw links
var link = svg.selectAll(".link")
.data(force.links())
.enter().append("line")
.attr("class", "link")
.style("stroke", function(d) { return d.colour ; })
//.style("stroke", options.linkColour)
.style("opacity", options.opacity)
.style("stroke-width", eval("(" + options.linkWidth + ")"))
.on("mouseover", function(d) {
d3.select(this)
.style("opacity", 1);
})
.on("mouseout", function(d) {
d3.select(this)
.style("opacity", options.opacity);
});
// draw nodes
var node = svg.selectAll(".node")
.data(force.nodes())
.enter().append("g")
.attr("class", "node")
.style("fill", function(d) { return color(d.group); })
.style("opacity", options.opacity)
.on("mouseover", mouseover)
.on("mouseout", mouseout)
.on("click", click)
.call(force.drag);
node.append("circle")
.attr("r", function(d){return nodeSize(d);})
.style("stroke", "#fff")
.style("opacity", options.opacity)
.style("stroke-width", "1.5px");
node.append("svg:text")
.attr("class", "nodetext")
.attr("dx", 12)
.attr("dy", ".35em")
.text(function(d) { return d.name })
.style("font", options.fontSize + "px " + options.fontFamily)
.style("opacity", options.opacityNoHover)
.style("pointer-events", "none");
function tick() {
node.attr("transform", function(d) {
if(options.bounded){ // adds bounding box
d.x = Math.max(nodeSize(d), Math.min(width - nodeSize(d), d.x));
d.y = Math.max(nodeSize(d), Math.min(height - nodeSize(d), d.y));
}
return "translate(" + d.x + "," + d.y + ")"});
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; });
}
function mouseover() {
d3.select(this).select("circle").transition()
.duration(750)
.attr("r", function(d){return nodeSize(d)+5;});
d3.select(this).select("text").transition()
.duration(750)
.attr("x", 13)
.style("stroke-width", ".5px")
.style("font", options.clickTextSize + "px ")
.style('fill', 'black')
.style('position','relative')
.style("opacity", 1);
}
function mouseout() {
d3.select(this).select("circle").transition()
.duration(750)
.attr("r", function(d){return nodeSize(d);});
d3.select(this).select("text").transition()
.duration(1250)
.attr("x", 0)
.style("font", options.fontSize + "px ")
.style("opacity", options.opacityNoHover);
}
function click(d) {
return eval(options.clickAction)
}
// add legend option
if(options.legend){
var legendRectSize = 18;
var legendSpacing = 4;
var legend = svg.selectAll('.legend')
.data(color.domain())
.enter()
.append('g')
.attr('class', 'legend')
.attr('transform', function(d, i) {
var height = legendRectSize + legendSpacing;
var offset = height * color.domain().length / 2;
var horz = legendRectSize;
var vert = i * height+4;
return 'translate(' + horz + ',' + vert + ')';
});
legend.append('rect')
.attr('width', legendRectSize)
.attr('height', legendRectSize)
.style('fill', color)
.style('stroke', color);
legend.append('text')
.attr('x', legendRectSize + legendSpacing)
.attr('y', legendRectSize - legendSpacing)
.style('fill', 'darkOrange')
.text(function(d) { return d; });
}
// make font-family consistent across all elements
d3.select(el).selectAll('text').style('font-family', options.fontFamily);
},
});
I suspect I need to make some changes to the code over here:
function mouseover() {
d3.select(this).select("circle").transition()
.duration(750)
.attr("r", function(d){return nodeSize(d)+5;});
d3.select(this).select("text").transition()
.duration(750)
.attr("x", 13)
.style("stroke-width", ".5px")
.style("font", options.clickTextSize + "px ")
.style('fill', 'black')
.style("opacity", 1);
}

You need to resort the node groups holding the circles and text so the currently mouseover'ed one is the last in that group, and thus the last one drawn so it appears on top of the others. See the first answer here -->
Updating SVG Element Z-Index With D3
In your case, if your data doesn't have an id field you may have to use 'name' instead as below (adapted to use the mouseover function you've got):
function mouseover(d) {
d3.selectAll("g.node").sort(function (a, b) {
if (a.name != d.name) return -1; // a is not the hovered element, send "a" to the back
else return 1; // a is the hovered element, bring "a" to the front (by making it last)
});
// your code continues
The pain might be that you have to do this edit for every d3 graph generated by this R script, unless you can edit the R code/package itself. (or you could suggest it to the package author as an enhancement.)

Overlapping legend d3.js

I am creating the legends with triangle shapes. One is "Yes", the other one is "No". By running the code below, it generate two triangles but they are overlapping. I am trying to seperate them by using this line of code .attr("y", function(d,i) {return 50+i*40;}) but seems like it doesn't work.
Can anyone tell me how to fix it? Thanks!
Click here! This is an html sreenshot for this part of script
var legendname = ["Yes","No"];
var legend = svg.selectAll(".legend")
.data(legendname)
.enter().append("g")
.attr("class", "legend")
.attr("transform", function(d, i) {
return "translate(" + (w + 150) + "," + (m.t - 30) + ")";
});
legend.append("path")
.attr("d", d3.svg.symbol().type("triangle-up").size(128))
*** .attr("y", function(d,i) {return 50+i*40;})
.style('fill', function(d) {return color(d);});
legend.append("text")
.attr("y", function(d,i) {return 50+i*20;})
.attr("x", 30)
.text(function(d) { return d; })

You will have to update the translate y attribute of groups instead of the paths. And also there is no need for extra calculations for y attributes of texts and paths then.
.attr("transform", function(d, i) {
return "translate(" + (w + 150) + "," + (30+i*40) + ")";
});
Working Code Snippet:
var w=40; //Sample chart width
var color = d3.scale.category20c();
var svg = d3.select("body").append("svg").attr({ height: 500, width: 400 });
var legendname = ["Yes", "No"];
var legend = svg.selectAll(".legend")
.data(legendname)
.enter().append("g")
.attr("class", "legend")
.attr("transform", function(d, i) {
return "translate(" + (w + 150) + "," + (30+i*40) + ")";
});
legend.append("path")
.attr("d", d3.svg.symbol().type("triangle-up").size(128))
.style('fill', function(d,i) {
return color(i);
});
legend.append("text")
.attr("dx",10)
.attr("dy",".4em")
.text(function(d) {
return d;
})
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.4.11/d3.min.js"></script>

Undefined function when loading D3 circle pack

I'm building a bubble chart from d3js but keep receiving a TypeError: undefined is not a function with the enter() method. I've tried just about everything and I can't determine why this error is being produced besides the fact that the filter method is returning null. Currently the bubble chart itself is not displayed.
var diameter = 310,
format = d3.format(",d"),
color = d3.scale.category20c();
var bubble = d3.layout.pack()
.sort(null)
.size([diameter, diameter])
.padding(1.5);
var svg = d3.select("bubble")
.append("svg")
.attr("width", diameter)
.attr("height", diameter)
.attr("class", "bubble");
var node = svg.selectAll(".node")
.data(bubble.nodes({children: [{packageName: "food", className: "food", value: 100}]}))
.filter(function(d) { return !d.children; })
// ================================
// This is causing the error below
// ================================
.enter()
.append("g")
.attr("class", "node")
.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
node.append("title")
.text(function(d) { return d.className + ": " + format(d.value); });
node.append("circle")
.attr("r", function(d) { return d.r; })
.style("fill", function(d) { return color(d.packageName); });
node.append("text")
.attr("dy", ".3em")
.style("text-anchor", "middle")
.text(function(d) { return d.className.substring(0, d.r / 3); });
d3.select(self.frameElement).style("height", diameter + "px");
JsFiddle: http://jsfiddle.net/26Tra/

In your data binding, you are using keys such as packageName and className that are generated by the classes function, which is missing from your code. I added it and now your data binding is correct:
var node = svg.selectAll(".node")
.data(bubble.nodes(classes(root)).filter(function (d) {return !d.children;}))
.enter()
...
NOTE: because I mocked some very simple data, with only one packageName, fruits, I used className instead of packageName for the coloring. I also changed the color category to category10() to give it more contrast.
Complete FIDDLE.

Updating the coordinates in d3js for a tree layout

I am currently using the d3.layout.tree() to compute the positions of my data.
var tree = d3.layout.tree()
.sort(null)
.size([size.height, size.width - maxLabelLength * options.fontSize])
.children(function(d)
{
return (!d.contents || d.contents.length === 0) ? null : d.contents;
});
Initially I compute and add my nodes like this:
var nodes = tree.nodes(treeData);
var nodeGroup = layoutRoot.selectAll("g.node")
.data(nodes, function (d) { return d.name })
.enter()
.append("svg:g")
.attr("class", "node")
.attr("transform", function(d)
{
return "translate(" + d.y + "," + d.x + ")";
});
nodeGroup.append("svg:circle")
.attr("class", "node-dot")
.attr("r", options.nodeRadius);
Now I add a new node to the treeData and also to the layoutRoot:
var grp = layoutRoot.selectAll("g.node")
.data(nodes, function (d) { return d.name })
.enter()
.append('svg:g')
.attr("transform", function (d)
{
return "translate(" + d.y + "," + d.x + ")";
})
grp.append("svg:circle")
.attr("class", "node-dot")
.attr("r", options.nodeRadius)
The problem is now, that the newly computed nodes that are already present in the rootLayout have different x,y coordinates after having added a new node. But they are not within the enter() or exit() selection and are thus not redrawn at their correct position. How is this supposed to be handled, ie. how should the position of the nodes that have not changed anything but their coordinates be updated/refreshed?
I a noob to d3js. So don't be too harsh :D

I would separate the enter() selection from the update of nodes like this :
var nodeGroup = layoutRoot.selectAll("g.node")
.data(nodes, function (d) { return d.name });
// Enter selection
nodeGroup.enter()
.append("svg:g")
.attr("class", "node")
// Update
nodeGroup.attr("transform", function(d) {
return "translate(" + d.y + "," + d.x + ")";
});
var nodeDots = layoutRoot.selectAll("g.node-dot")
.data(nodes, function (d) { return d.name });
// Enter
nodeDots.enter()
.append("circle")
.attr("class", "node-dot")
// Update
nodeDots.attr("r", options.nodeRadius);
Hope this helps, but in a general way of speaking, it is perhaps easier to code this way, with separation of enter and updates (see here for more info)