hiv-hiveplot.html

<!DOCTYPE html><html lang="en"><head> <meta charset="utf-8">
<title>Network of individuals at risk of HIV</title>

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<style type="text/css">
     	
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  		width: 1200px;
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    	h1{font-family: 'Lato', sans-serif;
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        p {
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        table {
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            opacity:0.75;
            font-size:18px;
            font-family: 'Lato', sans-serif;
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        svg {
        	display: block;
        	color: white
        }
        
.axis {
  stroke: white;
  stroke-width: 1.5px;
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.node circle {
  stroke: #000;
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.link {
  fill: none;
  //stroke: #999;
  stroke-width: 1.5px;
  stroke-opacity: .2;
}

.link.active {
  stroke: #DC143C;
  stroke-width: 4px;
  stroke-opacity: 0.8;
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.mainlegendtext {
   fill:"white";
   font-family: 'Lato', sans-serif;
}

</style>

</head>

<script src="http://d3js.org/d3.v2.js?2.8.1"></script>
<body>

<h1> Hive Plot of Network of Individuals at Risk of HIV</h1>
<p id="info">Loading… </p>

<p id="explanation"> This is a d3-based visualization of the HIV network data for
  Harvard's Stat 221 class (see original visualization <a href="http://theory.info/harvardstat221#?v=network-of-individuals-at-risk-of-hiv">here</a>). This plot is 
  based off of the <a href="http://bost.ocks.org/mike/hive/">hive plot method for visualizing networks</a>. 
  There are 2 axes, defined by HIV status. Along each axis, individuals are
  first grouped and color-coded by gender. Then, within gender
  categories, they are sorted by degree (number of friends). Nodes
  with higher degree attributes are located closer to the origin of
  the hive plot. The links connecting the two axes denote links between serodiscordant 
  individuals, while links connecting individuals on the same axis denote links between 
  individuals of the same HIV status. One can mouse over both links and nodes to display
  information in the legend. </p>


<script type="text/javascript">

var width = 750,
    height = 850,
    innerRadius = 40,
    outerRadius = 540,
    majorAngle = 2 * Math.PI / 3,
    minorAngle = 1 * Math.PI / 12;


var angle = d3.scale.ordinal()
    .domain(["neg", "pos"])
    .range([0, majorAngle - minorAngle]);

var radius = d3.scale.linear()
    .range([innerRadius, outerRadius]);


var svgLegend = d3.select("body").append("div")
    .attr("id", "legend")
    .attr("style", "float:left")
    .attr("height", height)
    .attr("width", "350")
    .append("svg").attr("width", 350).attr("height", height)

var svg = d3.select("body").append("div")
    .attr("id", "visualization")
    .attr("height", height)
    .attr("margin-left", "350px")
    .append("svg")
    .attr("width", width)
    .attr("height", height)
    .append("g")
    .attr("transform", "translate(" + outerRadius * .20 + "," + outerRadius * .57 + ")");


var formatNumber = d3.format(",d"),
    defaultInfo;


// start loading data and visualization here

d3.csv("/data/refnetwork-nodes.csv", function (csv) {

    nodesByIndex = csv.map(function (el) {
        el.binaryAttribute = +el.binaryAttribute;
        el.index = +el.index; // change to ID b/c want to use that lates
        el.degree = +el.degree; // number of friends (links)
        if (el.binaryAttribute == 1) {
            el.type = "HIV-Positive";
        } else {
            el.type = "HIV-Negative";
        }
        return el;
    });

    // array of degrees (to calculate min and max later)
    degs = nodesByIndex.map(function (d) {
        return d.degree;
    });


    // group nodes by HIV+ / 
    var nodesByType = d3.nest().key(function (d) {
        return d.binaryAttribute;
    }).sortKeys(d3.ascending).entries(nodesByIndex);

    // sort (apply function defined above)
    nodesByType.forEach(function (type) {
        type.values = type.values.sort(compare) // return array in order of  
    });

    // now assign plotIndex values

    nodesByType.forEach(function (type) {
        var lastgender = type.values[0].gender,
            count = 0;
        type.values.forEach(function (d, i) {
            if (d.gender != lastgender) lastgender = d.gender, count += 2;
            d.plotIndex = count++;
            nodesByIndex[d.index].plotIndex = d.plotIndex;
        });
        type.count = count - 1;
    });

    nodesByType[0].key = "neg"
    nodesByType[1].key = "pos"


    // load edges within here
    d3.csv('/data/refnetwork-edges.csv', function (csv) {
        edges = [];

        // first convert the data to numeric: this returns array of 413 elements (corresponding to 
        // rows of the spreadsheet (as csv)
        csv = csv.map(function (el) {
            el.source = +el.source;
            el.target = +el.target;
            el.distance = +el.distance;
            el.wdistance = +el.wdistance;
            return el;
        });

        // process the edges data to form the necessary object

        // create new object
        var el, sourceType, targetType, linkType;
        // loop over all links (over 413 elements in csv array of link objects)
        for (var ii = 0; ii < csv.length; ii++) {
            el = csv[ii];

            if (nodesByIndex[el.source].binaryAttribute == 0) {
                sourceType = "neg";
            } else {
                sourceType = "pos";
            }
            if (nodesByIndex[el.target].binaryAttribute == 0) {
                targetType = "neg";
            } else {
                targetType = "pos";
            }

            // type of link by gender
            if (nodesByIndex[el.source].gender == nodesByIndex[el.target].gender) {
                if (nodesByIndex[el.source].gender == "male") {
                    linkType = "m-m";
                } else {
                    linkType = "f-f";
                }
            } else {
                linkType = "m-f";
            }

            edges.push({
                source: {
                    type: sourceType,
                    node: nodesByIndex[el.source]
                }, // push node object instead of just node index
                target: {
                    type: targetType,
                    node: nodesByIndex[el.target]
                }, // push  node object instead of just node index
                distance: el.distance, // push 
                wdistance: el.wdistance, //push distance
                typeByGender: linkType
            });
        }

        var info = d3.select("#info").text(defaultInfo = "Showing " + formatNumber(edges.length) + " friendships among " + formatNumber(nodesByIndex.length) + " individuals.");

        var nodename = d3.select("#nodename").text(defaultText = "");
        var nodehiv = d3.select("#nodehiv").text(defaultText = "Mouse over links or nodes to view attributes...");
        var nodegender = d3.select("#nodegender").text(defaultText = "");
        var nodefriends = d3.select("#nodefriends").text(defaultText = "");
        var nodephiv = d3.select("#phiv").text(defaultText = "");
        var nodepfemale = d3.select("#pfemale").text(defaultText = "");

        var name1 = d3.select("#name1").text(defaultText = "");
        var name2 = d3.select("#name2").text(defaultText = "");
        var gender1 = d3.select("#gender1").text(defaultText = "");
        var gender2 = d3.select("#gender2").text(defaultText = "");
        var hiv1 = d3.select("#hiv1").text(defaultText = "");
        var hiv2 = d3.select("#hiv2").text(defaultText = "");

        // Set the radius domain.
        radius.domain([0, d3.max([nodesByType[0].count, nodesByType[1].count])]);
        // gives back extent of axis (largest index)

        // Draw the axes.
        svg.selectAll(".axis")
            .data(nodesByType)
            .enter().append("line")
            .attr("class", "axis")
            .attr("transform", function (d) {
                return "rotate(" + degrees(angle(d.key)) + ")";
            })
            .attr("x1", radius(-2))
            .attr("x2", function (d) {
                return radius(d.count + 2);
            });

        svg.append("text")
            .attr("id", "hivposlabel")
            .attr("transform", "rotate(" + degrees(majorAngle) + ")")
            .attr("x", radius(82))
            .attr("y", 0)
            .text("HIV-Positive")
            .attr("text-anchor", "middle")
            .attr("style", "fill: white")
            .attr("transform", "" + degrees(majorAngle))
            .attr("dy", 150);

        svg.append("text")
            .attr("id", "hivneglabel")
            .attr("x", 0)
            .attr("y", 0)
            .text("HIV-Negative")
            .attr("text-anchor", "middle")
            .attr("style", "fill: white")
            .attr("dy", -230)
            .attr("dx", 0);


        // Draw the links.
        svg.append("g")
            .attr("class", "links")
            .selectAll(".link")
            .data(edges)
            .enter().append("path")
            .attr("class", "link")
            .attr("d", link()
                .angle(function (d) {
                    return angle(d.type);
                })
                .radius(function (d) {
                    return radius(d.node.plotIndex);
                }))
            .attr("stroke", function (d) {
                return linkColor(d.typeByGender);
            })
            .on("mouseover", linkMouseover)
            .on("mouseout", mouseout);

        // Draw nodes

        svg.append("g")
            .attr("class", "nodes")
            .selectAll(".type")
            .data(nodesByType)
            .enter().append("g")
            .attr("class", function (d) {
                return d.key + "nodes";
            })
            .attr("transform", function (d) {
                return "rotate(" + degrees(angle(d.key)) + ")";
            })
            .selectAll("circle")
            .data(function (d) {
                return d.values;
            })
            .enter().append("circle")
            .attr("cx", function (d) {
                return radius(d.plotIndex);
            })
            .attr("r", 4)
            .attr("fill", function (d) {
                return color(d.gender);
            })
            .on("mouseover", nodeMouseover)
            .on("mouseout", mouseout);


        // Highlight the link and connected nodes on mouseover.
        function linkMouseover(d) {
            svg.selectAll(".link").classed("active", function (p) {
                return p === d;
            });
            svg.selectAll("circle").classed("active", function (p) {
                return p === d.source.node || p === d.target.node;
            });
            name1.text(d.source.node.name).style("fill", linkColor(d.typeByGender)).style("opacity", "0.75");
            name2.text(d.target.node.name).style("fill", linkColor(d.typeByGender)).style("opacity", "0.75");
            gender1.text(capitalizeFirstLetter(d.source.node.gender)).style("fill", linkColor(d.typeByGender)).style("opacity", "0.75");
            gender2.text(capitalizeFirstLetter(d.target.node.gender)).style("fill", linkColor(d.typeByGender)).style("opacity", "0.75");
            hiv1.text(d.source.node.type).style("fill", linkColor(d.typeByGender)).style("opacity", "0.75");
            hiv2.text(d.target.node.type).style("fill", linkColor(d.typeByGender)).style("opacity", "0.75");
            nodehiv.text("↔").style("fill", linkColor(d.typeByGender)).style("opacity", "0.75").style("font-size", "34");
        }

        // Highlight the node and connected links on mouseover.
        function nodeMouseover(d) {
            var neiNodeList = [];
            svg.selectAll(".link").classed("active", function (p) {
                if (p.source.node == d) {
                    neiNodeList.push(p.target.node);
                }
                if (p.target.node == d) {
                    neiNodeList.push(p.source.node);
                }
                return p.source.node === d || p.target.node === d;
            });
            d3.select(this).classed("active", true);
            nodename.text(d.name);
            nodehiv.text(d.type);
            nodegender.text(capitalizeFirstLetter(d.gender));
            nodefriends.text(d.degree + " friends");

            var percentfemale = d3.sum(neiNodeList.map(
                function (d) {
                    return d.gender == 'female';
                })) / neiNodeList.length;
            var percenthiv = d3.sum(neiNodeList.map(
                function (d) {
                    return d.binaryAttribute;
                })) / neiNodeList.length;
            var pfemale = d3.round(100 * percentfemale, 2) + "%";
            var phiv = d3.round(100 * percenthiv, 2) + "%";

            nodephiv.text(phiv + " of friends are HIV-Positive");
            nodepfemale.text(pfemale + " of friends are female");
        }

        // Clear any highlighted nodes or links.
        function mouseout() {
            svg.selectAll(".active").classed("active", false);
            name1.text(defaultText);
            name2.text(defaultText);
            gender1.text(defaultText);
            gender2.text(defaultText);
            hiv1.text(defaultText);
            hiv2.text(defaultText);
            nodename.text(defaultText);
            nodehiv.text(defaultText).style("font-size", "16").style("fill", "white").style("opacity", "1");
            nodegender.text(defaultText);
            nodefriends.text(defaultText);
            nodephiv.text(defaultText);
            nodepfemale.text(defaultText);
        }

    }); // close of edges csv   

}); // close of node csv


// create sort function that will place females first, then males
// within those two categories, it will sort in descending order by degree (more connected nodes first) 
function compare(a, b) {
    if (a.gender < b.gender)
        return -1;
    if (a.gender > b.gender)
        return 1;
    if (a.gender == b.gender) {
        if (a.degree > b.degree)
            return -1;
        if (a.degree < b.degree)
            return 1;
        return 0;
    }
}

// colors for male / female nodes 
function color(g) {
    if (g == "male") {
        return "steelblue";
    } else {
        return "#FF66CC";
    }
}

// link colors
function linkColor(g) {
    if (g == "f-f") {
        return "#FF66FF";
    } else if (g == "m-m") {
        return "steelblue";
    } else {
        return "#FFCC66";
    }
}

// function to convert radians into degrees
function degrees(radians) {
    return radians / Math.PI * 180 - 90;
}


function capitalizeFirstLetter(string) {
    return string.charAt(0).toUpperCase() + string.slice(1);
}


// A shape generator for Hive links, based on a source and a target.
// Adapted from http://bost.ocks.org/mike/hive/
// The source and target are defined in polar coordinates (angle and radius).
// Ratio links can also be drawn by using a startRadius and endRadius.
// This class is modeled after d3.svg.chord
function link() {
    var source = function (d) {
        return d.source;
    },
        target = function (d) {
            return d.target;
        },
        angle = function (d) {
            return d.angle;
        },
        startRadius = function (d) {
            return d.radius;
        },
        endRadius = startRadius,
        arcOffset = -Math.PI / 2;

    function link(d, i) {
        var s = node(source, this, d, i),
            t = node(target, this, d, i),
            x;
        if (t.a < s.a) x = t, t = s, s = x;
        if (t.a - s.a > Math.PI) s.a += 2 * Math.PI;
        var a1 = s.a + (t.a - s.a) / 3,
            a2 = t.a - (t.a - s.a) / 3;

        // draw cubic bezier curves for nodes on different axes
        if (s.a != t.a) {
            return s.r0 - s.r1 || t.r0 - t.r1 ? "M" + Math.cos(s.a) * s.r0 + "," + Math.sin(s.a) * s.r0 + "L" + Math.cos(s.a) * s.r1 + "," + Math.sin(s.a) * s.r1 + "C" + Math.cos(a1) * s.r1 + "," + Math.sin(a1) * s.r1 + " " + Math.cos(a2) * t.r1 + "," + Math.sin(a2) * t.r1 + " " + Math.cos(t.a) * t.r1 + "," + Math.sin(t.a) * t.r1 + "L" + Math.cos(t.a) * t.r0 + "," + Math.sin(t.a) * t.r0 + "C" + Math.cos(a2) * t.r0 + "," + Math.sin(a2) * t.r0 + " " + Math.cos(a1) * s.r0 + "," + Math.sin(a1) * s.r0 + " " + Math.cos(s.a) * s.r0 + "," + Math.sin(s.a) * s.r0 : "M" + Math.cos(s.a) * s.r0 + "," + Math.sin(s.a) * s.r0 + "C" + Math.cos(a1) * s.r1 + "," + Math.sin(a1) * s.r1 + " " + Math.cos(a2) * t.r1 + "," + Math.sin(a2) * t.r1 + " " + Math.cos(t.a) * t.r1 + "," + Math.sin(t.a) * t.r1;
        }
        // draw quadratic bezier curves for nodes on same axis
        else {
            a = s.a
            var aCtrl = d.source.type === "pos" ? aCtrl = a + minorAngle * 2 : aCtrl = a - minorAngle * 2
            m = Math.abs(s.r1 - t.r1)
            rCtrl = s.r1 + m
            return "M" + Math.cos(s.a) * s.r0 + "," + Math.sin(s.a) * s.r0 + "Q" + Math.cos(aCtrl) * rCtrl + "," + Math.sin(aCtrl) * rCtrl + " " + Math.cos(t.a) * t.r1 + "," + Math.sin(t.a) * t.r1;
        }
    }

    function node(method, thiz, d, i) {
        var node = method.call(thiz, d, i),
            a = +(typeof angle === "function" ? angle.call(thiz, node, i) : angle) + arcOffset,
            r0 = +(typeof startRadius === "function" ? startRadius.call(thiz, node, i) : startRadius),
            r1 = (startRadius === endRadius ? r0 : +(typeof endRadius === "function" ? endRadius.call(thiz, node, i) : endRadius));
        return {
            r0: r0,
            r1: r1,
            a: a
        };
    }

    link.source = function (_) {
        if (!arguments.length) return source;
        source = _;
        return link;
    };

    link.target = function (_) {
        if (!arguments.length) return target;
        target = _;
        return link;
    };

    link.angle = function (_) {
        if (!arguments.length) return angle;
        angle = _;
        return link;
    };

    link.radius = function (_) {
        if (!arguments.length) return startRadius;
        startRadius = endRadius = _;
        return link;
    };

    link.startRadius = function (_) {
        if (!arguments.length) return startRadius;
        startRadius = _;
        return link;
    };

    link.endRadius = function (_) {
        if (!arguments.length) return endRadius;
        endRadius = _;
        return link;
    };

    return link;
};


//* Legend goes here *//
var lw = 300;
var lh = 350;

svgLegend.append("rect")
    .attr("class", "legendcont")
    .attr("x", (350 - lw) / 2)
    .attr("y", 150)
    .attr("width", lw)
    .attr("height", lh)
    .attr("fill", "#181818")
    .attr("opacity", 0.5)
    .attr("stroke", "white")
    .attr("stroke-width", "3px")
    .attr("rx", 15)
    .attr("ry", 15);

var legendContainer = svgLegend.append("g").attr("transform", "translate(" + (350 - lw) / 2 + ",150)");
var legendContainerMargin = 50;


legendContainer.append("text")
    .attr("x", lw / 2)
    .attr("y", 20)
    .text("Gender")
    .attr("text-anchor", "middle")
    .attr("style", "fill: white; font-size:18");

legendContainer.append("circle")
    .attr("cx", legendContainerMargin)
    .attr("cy", legendContainerMargin)
    .attr("r", 7)
    .attr("fill", "#FF66CC");

legendContainer.append("circle")
    .attr("cx", (lw + legendContainerMargin) / 2)
    .attr("cy", legendContainerMargin)
    .attr("r", 7)
    .attr("fill", "steelblue");

legendContainer.append("text")
    .attr("class", "mainlegendtext")
    .attr("x", legendContainerMargin + 15)
    .attr("y", legendContainerMargin)
    .text("Female")
    .attr("text-anchor", "start")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("text")
    .attr("class", "mainlegendtext")
    .attr("x", (lw + legendContainerMargin) / 2 + 15)
    .attr("y", legendContainerMargin)
    .text("Male")
    .attr("text-anchor", "start")
    .attr("dy", "4")
    .attr("style", "fill: white");


legendContainer.append("text")
    .attr("x", lw / 2)
    .attr("y", 20 + 75)
    .text("Link Type")
    .attr("text-anchor", "middle")
    .attr("style", "fill: white; font-size:18");

var legendLinkTypespacing = (lw - 2 * (legendContainerMargin - 10)) / 3;


legendContainer.append("rect")
    .attr("x", legendContainerMargin - 10)
    .attr("y", legendContainerMargin + 75)
    .attr("width", 20)
    .attr("height", 2)
    .attr("fill", "#FF66FF")
    .attr("opacity", "0.6");

legendContainer.append("text")
    .attr("class", "mainlegendtext")
    .attr("x", legendContainerMargin + 15)
    .attr("y", legendContainerMargin + 75)
    .text("F-F")
    .attr("text-anchor", "start")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("rect")
    .attr("x", legendContainerMargin - 10 + legendLinkTypespacing + 20)
    .attr("y", legendContainerMargin + 75)
    .attr("width", 20)
    .attr("height", 2)
    .attr("fill", "#FFCC66")
    .attr("opacity", "0.6");

legendContainer.append("text")
    .attr("class", "mainlegendtext")
    .attr("x", legendContainerMargin - 10 + legendLinkTypespacing + 45)
    .attr("y", legendContainerMargin + 75)
    .text("F-M")
    .attr("text-anchor", "start")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("rect")
    .attr("x", legendContainerMargin - 10 + 2 * legendLinkTypespacing + 20)
    .attr("y", legendContainerMargin + 75)
    .attr("width", 20)
    .attr("height", 2)
    .attr("fill", "steelblue")
    .attr("opacity", "0.6");

legendContainer.append("text")
    .attr("class", "mainlegendtext")
    .attr("x", legendContainerMargin - 10 + 2 * legendLinkTypespacing + 45)
    .attr("y", legendContainerMargin + 75)
    .text("M-M")
    .attr("text-anchor", "start")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("line")
    .attr("x1", 0)
    .attr("y1", legendContainerMargin + 100)
    .attr("x2", lw)
    .attr("y2", legendContainerMargin + 100)
    .attr("stroke", "white");

/// Changing here:   

// if select node:
legendContainer.append("text")
    .attr("id", "nodename")
    .attr("x", lw / 2)
    .attr("y", legendContainerMargin + 150)
    .text("Name")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white; font-size:18");

legendContainer.append("text")
    .attr("id", "nodehiv")
    .attr("x", lw / 2)
    .attr("y", legendContainerMargin + 175)
    .text("HIV")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");


legendContainer.append("text")
    .attr("id", "nodegender")
    .attr("x", lw / 2)
    .attr("y", legendContainerMargin + 200)
    .text("Gender")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");
legendContainer.append("text")
    .attr("id", "nodefriends")
    .attr("x", lw / 2)
    .attr("y", legendContainerMargin + 225)
    .text("Gender")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("text")
    .attr("id", "phiv")
    .attr("x", lw / 2)
    .attr("y", legendContainerMargin + 250)
    .text("")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("text")
    .attr("id", "pfemale")
    .attr("x", lw / 2)
    .attr("y", legendContainerMargin + 275)
    .text("")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");


// if select link:

legendContainer.append("text")
    .attr("id", "name1")
    .attr("x", lw / 4)
    .attr("y", legendContainerMargin + 150)
    .text("Name1")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white; font-size:18");

legendContainer.append("text")
    .attr("id", "name2")
    .attr("x", 3 * lw / 4)
    .attr("y", legendContainerMargin + 150)
    .text("Name2")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white; font-size:18");


legendContainer.append("text")
    .attr("id", "hiv1")
    .attr("x", lw / 4)
    .attr("y", legendContainerMargin + 175)
    .text("HIV1")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("text")
    .attr("id", "hiv2")
    .attr("x", 3 * lw / 4)
    .attr("y", legendContainerMargin + 175)
    .text("HIV2")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("text")
    .attr("id", "gender1")
    .attr("x", lw / 4)
    .attr("y", legendContainerMargin + 200)
    .text("Gender1")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");

legendContainer.append("text")
    .attr("id", "gender2")
    .attr("x", 3 * lw / 4)
    .attr("y", legendContainerMargin + 200)
    .text("Gender2")
    .attr("text-anchor", "middle")
    .attr("dy", "4")
    .attr("style", "fill: white");
    
</script>
</body>
</html>