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@@ -41,7 +41,7 @@
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selector: selector of an element that will contain the SVG
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nodes: JS object of nodes
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Options:
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- width
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+ width
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Width of the vis, will attempt to set a default based on the width of
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the container.
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height
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@@ -63,219 +63,256 @@
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Skip the tick rule.
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skipBranchLengthScaling
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Make a dendrogram instead of a phylogram.
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-
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+
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d3.phylogram.buildRadial(selector, nodes, options)
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Creates a radial dendrogram.
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- Options: same as build, but without diagonal, skipTicks, and
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+ Options: same as build, but without diagonal, skipTicks, and
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skipBranchLengthScaling
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-
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+
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d3.phylogram.rightAngleDiagonal()
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Similar to d3.diagonal except it create an orthogonal crook instead of a
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smooth Bezier curve.
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-
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+
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d3.phylogram.radialRightAngleDiagonal()
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d3.phylogram.rightAngleDiagonal for radial layouts.
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*/
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-if (!d3) { throw "d3 wasn't included!"};
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-(function() {
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+if (!d3) {
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+ throw "d3 wasn't included!"
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+}
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+;
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+(function () {
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d3.phylogram = {}
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- d3.phylogram.rightAngleDiagonal = function() {
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- var projection = function(d) { return [d.y, d.x]; }
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-
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- var path = function(pathData) {
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- return "M" + pathData[0] + ' ' + pathData[1] + " " + pathData[2];
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+ d3.phylogram.rightAngleDiagonal = function () {
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+ var projection = function (d) {
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+ return [d.y, d.x];
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+ }
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+
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+ var path = function (pathData) {
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+ return "M" + pathData[0] + " " + pathData[1] + " " + pathData[2];
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}
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-
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+
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function diagonal(diagonalPath, i) {
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var source = diagonalPath.source,
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- target = diagonalPath.target,
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- midpointX = (source.x + target.x) / 2,
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- midpointY = (source.y + target.y) / 2,
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- pathData = [source, {x: target.x, y: source.y}, target];
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+ target = diagonalPath.target,
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+ midpointX = (source.x + target.x) / 2,
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+ midpointY = (source.y + target.y) / 2,
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+ pathData = [source, {x: target.x, y: source.y}, target];
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pathData = pathData.map(projection);
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- return path(pathData)
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+ return path(pathData);
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}
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-
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- diagonal.projection = function(x) {
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- if (!arguments.length) return projection;
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+
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+ diagonal.projection = function (x) {
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+ if (!arguments.length) {
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+ return projection;
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+ }
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projection = x;
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return diagonal;
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};
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-
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- diagonal.path = function(x) {
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- if (!arguments.length) return path;
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+
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+ diagonal.path = function (x) {
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+ if (!arguments.length) {
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+ return path;
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+ }
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path = x;
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return diagonal;
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};
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-
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+
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return diagonal;
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}
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-
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- d3.phylogram.radialRightAngleDiagonal = function() {
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+
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+ d3.phylogram.radialRightAngleDiagonal = function () {
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return d3.phylogram.rightAngleDiagonal()
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- .path(function(pathData) {
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+ .path(function (pathData) {
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var src = pathData[0],
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- mid = pathData[1],
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- dst = pathData[2],
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- radius = Math.sqrt(src[0]*src[0] + src[1]*src[1]),
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- srcAngle = d3.phylogram.coordinateToAngle(src, radius),
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- midAngle = d3.phylogram.coordinateToAngle(mid, radius),
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- clockwise = Math.abs(midAngle - srcAngle) > Math.PI ? midAngle <= srcAngle : midAngle > srcAngle,
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- rotation = 0,
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- largeArc = 0,
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- sweep = clockwise ? 0 : 1;
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+ mid = pathData[1],
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+ dst = pathData[2],
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+ radius = Math.sqrt(src[0] * src[0] + src[1] * src[1]),
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+ srcAngle = d3.phylogram.coordinateToAngle(src, radius),
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+ midAngle = d3.phylogram.coordinateToAngle(mid, radius),
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+ clockwise = Math.abs(midAngle - srcAngle) > Math.PI ? midAngle <= srcAngle : midAngle > srcAngle,
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+ rotation = 0,
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+ largeArc = 0,
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+ sweep = clockwise ? 0 : 1;
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return 'M' + src + ' ' +
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- "A" + [radius,radius] + ' ' + rotation + ' ' + largeArc+','+sweep + ' ' + mid +
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+ "A" + [radius, radius] + ' ' + rotation + ' ' + largeArc + ',' + sweep + ' ' + mid +
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'L' + dst;
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})
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- .projection(function(d) {
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+ .projection(function (d) {
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var r = d.y, a = (d.x - 90) / 180 * Math.PI;
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return [r * Math.cos(a), r * Math.sin(a)];
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- })
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+ });
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}
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-
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+
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// Convert XY and radius to angle of a circle centered at 0,0
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- d3.phylogram.coordinateToAngle = function(coord, radius) {
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+ d3.phylogram.coordinateToAngle = function (coord, radius) {
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var wholeAngle = 2 * Math.PI,
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- quarterAngle = wholeAngle / 4
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-
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+ quarterAngle = wholeAngle / 4
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+
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var coordQuad = coord[0] >= 0 ? (coord[1] >= 0 ? 1 : 2) : (coord[1] >= 0 ? 4 : 3),
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- coordBaseAngle = Math.abs(Math.asin(coord[1] / radius))
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-
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+ coordBaseAngle = Math.abs(Math.asin(coord[1] / radius))
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+
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// Since this is just based on the angle of the right triangle formed
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- // by the coordinate and the origin, each quad will have different
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+ // by the coordinate and the origin, each quad will have different
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// offsets
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switch (coordQuad) {
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case 1:
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coordAngle = quarterAngle - coordBaseAngle
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- break
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+ break;
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case 2:
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coordAngle = quarterAngle + coordBaseAngle
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- break
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+ break;
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case 3:
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- coordAngle = 2*quarterAngle + quarterAngle - coordBaseAngle
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- break
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+ coordAngle = 2 * quarterAngle + quarterAngle - coordBaseAngle
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+ break;
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case 4:
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- coordAngle = 3*quarterAngle + coordBaseAngle
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+ coordAngle = 3 * quarterAngle + coordBaseAngle
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}
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- return coordAngle
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+ return coordAngle;
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}
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- function scaleBranchLengths(nodes, w) {
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+ function scaleBranchLengths(nodes, w, options) {
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// Visit all nodes and adjust y pos width distance metric
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- var visitPreOrder = function(root, callback) {
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+ var visitPreOrder = function (root, callback) {
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callback(root)
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if (root.children) {
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- for (var i = root.children.length - 1; i >= 0; i--){
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+ for (var i = root.children.length - 1; i >= 0; i--) {
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visitPreOrder(root.children[i], callback);
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- };
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+ }
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}
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}
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- visitPreOrder(nodes[0], function(node) {
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- node.rootDist = (node.parent ? node.parent.rootDist : 0) + (node.length || 0)
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+ visitPreOrder(nodes[0], function (node) {
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+ node.rootDist = (node.parent ? node.parent.rootDist : 0) + (node.length || 0);
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})
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- var rootDists = nodes.map(function(n) { return n.rootDist; });
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- var yscale = d3.scale.linear()
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- .domain([0, d3.max(rootDists)])
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- .range([0, w]);
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- visitPreOrder(nodes[0], function(node) {
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- node.y = yscale(node.rootDist)
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+ var rootDists = nodes.map(function (n) {
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+ return n.rootDist;
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+ });
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+ var yscale;
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+ switch (parseInt(options.phylogram_scale)) {
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+ case 1:
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+ yscale = d3.scale.linear()
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+ .domain([0, d3.max(rootDists)])
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+ .range([0, w]);
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+ break;
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+ case 2:
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+ yscale = d3.scale.log()
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+ .domain([0.01, d3.max(rootDists)])
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+ .range([0, w]);
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+ break;
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+ default: // shouldn't happen
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+ break;
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+ }
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+ visitPreOrder(nodes[0], function (node) {
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+ node.y = yscale(node.rootDist);
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})
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- return yscale
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+ return yscale;
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}
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-
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- d3.phylogram.build = function(selector, nodes, options) {
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+
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+ d3.phylogram.build = function (selector, nodes, options) {
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options = options || {}
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var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'),
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- h = options.height || d3.select(selector).style('height') || d3.select(selector).attr('height'),
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- w = parseInt(w),
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- h = parseInt(h);
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- var fill = options.fill || function(d) {
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+ h = options.height || d3.select(selector).style('height') || d3.select(selector).attr('height'),
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+ w = parseInt(w),
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+ h = parseInt(h);
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+ var fill = options.fill || function (d) {
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return 'cyan';
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};
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- var size = options.size || function(d) {
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+ var size = options.size || function (d) {
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return 6;
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}
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- var nodeMouseOver = options.nodeMouseOver || function(d) {};
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- var nodeMouseOut = options.nodeMouseOut || function(d) {};
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- var nodeMouseDown = options.nodeMouseDown || function(d) {};
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-
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+ var nodeMouseOver = options.nodeMouseOver || function (d) {
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+ };
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+ var nodeMouseOut = options.nodeMouseOut || function (d) {
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+ };
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+ var nodeMouseDown = options.nodeMouseDown || function (d) {
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+ };
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+
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var tree = options.tree || d3.layout.cluster()
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.size([h, w])
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- .sort(function(node) { return node.children ? node.children.length : -1; })
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- .children(options.children || function(node) {
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+ .sort(function (node) {
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+ return node.children ? node.children.length : -1;
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+ })
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+ .children(options.children || function (node) {
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return node.children;
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});
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var diagonal = options.diagonal || d3.phylogram.rightAngleDiagonal();
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var vis = options.vis || d3.select(selector).append("svg:svg")
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- .attr("width", w + 300)
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- .attr("height", h + 30)
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- .append("svg:g")
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- .attr("transform", "translate(20, 20)");
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- var nodes = tree(nodes);
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-
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+ .attr("width", w + 300)
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+ .attr("height", h + 30)
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+ .append("svg:g")
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+ .attr("transform", "translate(20, 20)");
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+ nodes = tree(nodes);
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+
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if (options.skipBranchLengthScaling) {
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- var yscale = d3.scale.linear()
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- .domain([0, w])
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- .range([0, w]);
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- }
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- else {
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- var yscale = scaleBranchLengths(nodes, w)
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+ switch (options.phylogram_scale) {
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+ case 1:
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+ var yscale = d3.scale.linear()
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+ .domain([0, d3.max(rootDists)])
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+ .range([0, w]);
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+ case 2:
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+ var yscale = d3.scale.log()
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+ .domain([0.01, d3.max(rootDists)])
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+ .range([0, w]);
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+ }
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+
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+ } else {
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+ yscale = scaleBranchLengths(nodes, w, options);
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}
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-
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+
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if (!options.skipTicks) {
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vis.selectAll('line')
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- .data(yscale.ticks(10))
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- .enter().append('svg:line')
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- .attr('y1', 0)
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- .attr('y2', h)
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- .attr('x1', yscale)
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- .attr('x2', yscale)
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- .attr("stroke", "#ddd");
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+ .data(yscale.ticks(10))
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+ .enter().append('svg:line')
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+ .attr('y1', 0)
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+ .attr('y2', h)
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+ .attr('x1', yscale)
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+ .attr('x2', yscale)
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+ .attr("stroke", "#ddd");
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vis.selectAll("text.rule")
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- .data(yscale.ticks(10))
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- .enter().append("svg:text")
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- .attr("class", "rule")
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- .attr("x", yscale)
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- .attr("y", 0)
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- .attr("dy", -3)
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- .attr("text-anchor", "middle")
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- .attr('font-size', '9px')
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- .attr('fill', 'grey')
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- .text(function(d) { return Math.round(d*100) / 100; });
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+ .data(yscale.ticks(10))
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+ .enter().append("svg:text")
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+ .attr("class", "rule")
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+ .attr("x", yscale)
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+ .attr("y", 0)
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+ .attr("dy", -3)
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+ .attr("text-anchor", "middle")
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+ .attr('font-size', '9px')
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+ .attr('fill', 'grey')
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+ .text(function (d) {
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+ return Math.round(d * 100) / 100;
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+ });
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}
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-
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+
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var link = vis.selectAll("path.link")
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- .data(tree.links(nodes))
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- .enter().append("svg:path")
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- .attr("class", "link")
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- .attr("d", diagonal)
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- .attr("fill", "none")
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- .attr("stroke", "#aaa")
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- .attr("stroke-width", "4px");
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-
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+ .data(tree.links(nodes))
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+ .enter().append("svg:path")
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+ .attr("class", "link")
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+ .attr("d", diagonal)
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+ .attr("fill", "none")
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+ .attr("stroke", "#aaa")
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+ .attr("stroke-width", "4px");
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+
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var node = vis.selectAll("g.node")
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- .data(nodes)
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- .enter().append("svg:g")
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- .attr("class", function(n) {
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- if (n.children) {
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- if (n.depth == 0) {
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- return "root node"
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- }
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- else {
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- return "inner node"
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- }
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- }
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- else {
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- return "leaf node"
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+ .data(nodes)
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+ .enter().append("svg:g")
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+ .attr("class", function (n) {
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+ if (n.children) {
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+ if (n.depth == 0) {
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+ return "root node"
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+ } else {
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+ return "inner node"
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}
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- })
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- .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; })
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+ } else {
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+ return "leaf node"
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+ }
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+ })
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+ .attr("transform", function (d) {
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+ return "translate(" + d.y + "," + d.x + ")";
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+ })
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- // style the root node
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- vis.selectAll('g.root.node')
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+ // style the root node
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+ vis.selectAll('g.root.node')
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.append('svg:circle')
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.on('click', nodeMouseDown)
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.on('mouseover', nodeMouseOver)
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|
@@ -305,16 +342,16 @@ if (!d3) { throw "d3 wasn't included!"};
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.attr('stroke', 'dimgrey')
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.attr('stroke-width', '2px')
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.attr('fill', 'white');
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-
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+
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if (!options.skipLabels) {
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vis.selectAll('g.inner.node')
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.append("svg:text")
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- .attr("dx", -6)
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- .attr("dy", -6)
|
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|
- .attr("text-anchor", 'end')
|
|
|
- .attr('font-size', '9px')
|
|
|
- .attr('fill', 'black')
|
|
|
- //.text(function(d) { return d.length.toFixed(4); }); // hide length
|
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+ .attr("dx", -6)
|
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|
+ .attr("dy", -6)
|
|
|
+ .attr("text-anchor", 'end')
|
|
|
+ .attr('font-size', '9px')
|
|
|
+ .attr('fill', 'black')
|
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|
+ //.text(function(d) { return d.length.toFixed(4); }); // hide length
|
|
|
|
|
|
vis.selectAll('g.leaf.node').append("svg:text")
|
|
|
.attr("dx", 8)
|
|
|
@@ -323,80 +360,101 @@ if (!d3) { throw "d3 wasn't included!"};
|
|
|
.attr('font-family', 'Helvetica Neue, Helvetica, sans-serif')
|
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|
.attr('font-size', '10px')
|
|
|
.attr('fill', 'black')
|
|
|
- .text(function(d) {
|
|
|
+ .text(function (d) {
|
|
|
// return d.name + ' (' + d.length.toFixed(4) + ')'; // hide length
|
|
|
return d.name;
|
|
|
- });
|
|
|
+ });
|
|
|
}
|
|
|
return {tree: tree, vis: vis}
|
|
|
}
|
|
|
-
|
|
|
- d3.phylogram.buildRadial = function(selector, nodes, options) {
|
|
|
+
|
|
|
+ d3.phylogram.buildRadial = function (selector, nodes, options) {
|
|
|
options = options || {};
|
|
|
-
|
|
|
- var fill = options.fill || function(d) {
|
|
|
+
|
|
|
+ var fill = options.fill || function (d) {
|
|
|
return 'cyan';
|
|
|
};
|
|
|
- var size = options.size || function(d) {
|
|
|
+ var size = options.size || function (d) {
|
|
|
return 6;
|
|
|
}
|
|
|
- var nodeMouseOver = options.nodeMouseOver || function(d) {};
|
|
|
- var nodeMouseOut = options.nodeMouseOut || function(d) {};
|
|
|
- var nodeMouseDown = options.nodeMouseDown || function(d) {};
|
|
|
-
|
|
|
+ var nodeMouseOver = options.nodeMouseOver || function (d) {
|
|
|
+ };
|
|
|
+ var nodeMouseOut = options.nodeMouseOut || function (d) {
|
|
|
+ };
|
|
|
+ var nodeMouseDown = options.nodeMouseDown || function (d) {
|
|
|
+ };
|
|
|
+
|
|
|
var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'),
|
|
|
- r = w / 2,
|
|
|
- labelWidth = options.skipLabels ? 10 : options.labelWidth || 120;
|
|
|
-
|
|
|
+ r = w / 2,
|
|
|
+ labelWidth = options.skipLabels ? 10 : options.labelWidth || 120;
|
|
|
+
|
|
|
var vis = d3.select(selector).append("svg:svg")
|
|
|
- .attr("width", r * 2)
|
|
|
- .attr("height", r * 2)
|
|
|
- .append("svg:g")
|
|
|
- .attr("transform", "translate(" + r + "," + r + ")");
|
|
|
-
|
|
|
+ .attr("width", r * 2)
|
|
|
+ .attr("height", r * 2)
|
|
|
+ .append("svg:g")
|
|
|
+ .attr("transform", "translate(" + r + "," + r + ")");
|
|
|
+
|
|
|
var tree = d3.layout.tree()
|
|
|
.size([360, r - labelWidth])
|
|
|
- .sort(function(node) { return node.children ? node.children.length : -1; })
|
|
|
- .children(options.children || function(node) {
|
|
|
+ .sort(function (node) {
|
|
|
+ return node.children ? node.children.length : -1;
|
|
|
+ })
|
|
|
+ .children(options.children || function (node) {
|
|
|
return node.children;
|
|
|
})
|
|
|
- .separation(function(a, b) { return (a.parent == b.parent ? 1 : 2) / a.depth; });
|
|
|
+ .separation(function (a, b) {
|
|
|
+ return (a.parent == b.parent ? 1 : 2) / a.depth;
|
|
|
+ });
|
|
|
|
|
|
var phylogram = d3.phylogram.build(selector, nodes, {
|
|
|
vis: vis,
|
|
|
tree: tree,
|
|
|
- fill : fill,
|
|
|
+ fill: fill,
|
|
|
size: size,
|
|
|
- nodeMouseOver : nodeMouseOver,
|
|
|
- nodeMouseOut : nodeMouseOut,
|
|
|
- nodeMouseDown : nodeMouseDown,
|
|
|
+ nodeMouseOver: nodeMouseOver,
|
|
|
+ nodeMouseOut: nodeMouseOut,
|
|
|
+ nodeMouseDown: nodeMouseDown,
|
|
|
skipBranchLengthScaling: true,
|
|
|
skipTicks: true,
|
|
|
skipLabels: options.skipLabels,
|
|
|
diagonal: d3.phylogram.radialRightAngleDiagonal()
|
|
|
})
|
|
|
vis.selectAll('g.node')
|
|
|
- .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")"; })
|
|
|
-
|
|
|
+ .attr("transform", function (d) {
|
|
|
+ return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")";
|
|
|
+ })
|
|
|
+
|
|
|
if (!options.skipLabels) {
|
|
|
vis.selectAll('g.leaf.node text')
|
|
|
- .attr("dx", function(d) { return d.x < 180 ? 8 : -8; })
|
|
|
+ .attr("dx", function (d) {
|
|
|
+ return d.x < 180 ? 8 : -8;
|
|
|
+ })
|
|
|
.attr("dy", ".31em")
|
|
|
- .attr("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
|
|
|
- .attr("transform", function(d) { return d.x < 180 ? null : "rotate(180)"; })
|
|
|
+ .attr("text-anchor", function (d) {
|
|
|
+ return d.x < 180 ? "start" : "end";
|
|
|
+ })
|
|
|
+ .attr("transform", function (d) {
|
|
|
+ return d.x < 180 ? null : "rotate(180)";
|
|
|
+ })
|
|
|
.attr('font-family', 'Helvetica Neue, Helvetica, sans-serif')
|
|
|
.attr('font-size', '10px')
|
|
|
.attr('fill', 'black')
|
|
|
- .text(function(d) {
|
|
|
+ .text(function (d) {
|
|
|
return d.name;
|
|
|
});
|
|
|
|
|
|
vis.selectAll('g.inner.node text')
|
|
|
- .attr("dx", function(d) { return d.x < 180 ? -6 : 6; })
|
|
|
- .attr("text-anchor", function(d) { return d.x < 180 ? "end" : "start"; })
|
|
|
- .attr("transform", function(d) { return d.x < 180 ? null : "rotate(180)"; });
|
|
|
+ .attr("dx", function (d) {
|
|
|
+ return d.x < 180 ? -6 : 6;
|
|
|
+ })
|
|
|
+ .attr("text-anchor", function (d) {
|
|
|
+ return d.x < 180 ? "end" : "start";
|
|
|
+ })
|
|
|
+ .attr("transform", function (d) {
|
|
|
+ return d.x < 180 ? null : "rotate(180)";
|
|
|
+ });
|
|
|
}
|
|
|
-
|
|
|
+
|
|
|
return {tree: tree, vis: vis}
|
|
|
}
|
|
|
}());
|
Bradford Condon