29:null 2a:["$","title",null,{"children":"Phylogeny | Mazumder Lab | Observable"}] 2f:T439c,function WeightedTree() { // Variable Declaration // var width, height, margin = {top: 20, right: 10, bottom: 20, left: 120}, levelWidth = [1], // Data related i = 0, dataset, dataRoot, _rootNode, aRootHistory = [], aOpenNodesUid = [], valueFormatter = d3.format(".2s"), duration = 750, // Vertical Gap between adjacent nodes iNodeSize = 50, iLevelGap = 250, iDefaultLevel = 2, colorScale = d3.scale.category10().range(aColors), nodeSizeScale = d3.scale.sqrt().range([2, 22]).clamp(true), fnValueField = function(d){ return d.value; }, fnChildren = function(d){ return d.values; }, isResized = false, // Layout related tree, diagonal, // DOM related svg, gOuter, gLinks, gNodes; function graph() { // re-initialise variables // init(); } function init() { nodeSizeScale .domain([0, fnValueField(dataset)]); tree = d3.layout.tree() //.size([height, width]) .nodeSize([iNodeSize, iNodeSize]) .children(fnChildren); diagonal = d3.svg.diagonal() .projection(function(d) { return [d.y, d.x]; }); gOuter = d3.select(svg) .attr("width", width + margin.right + margin.left) .attr("height", height + margin.top*0 + margin.bottom*0) .classed("weighted-tree", true) /* // Reset to root node when clicked on the SVG .on("click", function(d){ _rootNode = dataRoot; update(dataRoot); })*/ .append("g") .attr("transform", "translate(" + margin.left + "," + ( iNodeSize/2 + height/2) + ")"); gLinks = gOuter.append("g") .classed("links", true); gNodes = gOuter.append("g") .classed("nodes", true); dataRoot = _rootNode = dataset; dataRoot.x0 = height / 2; dataRoot.y0 = 0; // Collapse upto default level function visitNode(d) { if (d.depth < iDefaultLevel){ fnChildren(d).forEach(visitNode); }else if(d.depth >= iDefaultLevel){ collapseNode(d); } } // Collapse a Node; Recursively function collapseNode(d) { if (d.values && !isExpanded(d)) { d._children = d.values; d._children.forEach(collapseNode); d.children = null; d.values = null; }else if (d.values){ // expanded node // only close the non expanded nodes d.values.forEach(collapseNode); } } // is this node expanded function isExpanded(d) { return aOpenNodesUid.indexOf(d.uid) > -1; } visitNode(dataRoot); update(dataRoot); // reset default open nodes aOpenNodesUid = []; //centerNode(dataRoot); } /** * Returns an array of nodes that are open in the graph * @return {array} */ function getExpandedNodes() { var aNodeIds = []; function visitNode(d) { if (d.children){ aNodeIds.push(d.uid); d.children.forEach(visitNode); } } visitNode(dataRoot); return aNodeIds; } function getRootNode() { return _rootNode; } function _getGradientId(d) { return 'lgd-' + d.source.uid + '-' + d.target.uid; } function _getLinkUrl(d) { return 'url(#'+ _getGradientId(d) +')'; } function _getLinkColor(d, bIsSource) { var sName = bIsSource ? 'source' : 'target', vf = getValueField() + '-net', bIsNegative = d.target[vf] < 0; if (bIsNegative) { // reverse color if link's net Value is negative sName = bIsSource ? 'target' : 'source'; } return d[sName].color; } function update(source) { // Compute the new tree layout. var nodes = tree.nodes(getRootNode()).reverse(), links = tree.links(nodes); // Normalize for fixed-depth. nodes.forEach(function(d) { d.y = d.depth * iLevelGap; }); // Update the nodes… var node = gNodes.selectAll("g.node") .data(nodes, function(d) { return d.id || (d.id = ++i); }); // Enter any new nodes at the parent's previous position. var nodeEnter = node.enter().append("g") .attr("class", "node") .attr("transform", function(d) { return "translate(" + source.y0 + "," + source.x0 + ")"; }) .on("click", click); nodeEnter.append("circle") .attr("r", 1e-6) .style("opacity", function(d) { return d._children ? 1 : 0.5; }) .style("fill", function(d) { return (d.color = colorScale(d.key)); }); nodeEnter.append("text") .attr("x", function(d) { return fnChildren(d) || d._children ? -15 : 15; }) .attr("dy", ".35em") .attr("text-anchor", function(d) { return fnChildren(d) || d._children ? "end" : "start"; }) .text(function(d) { return d.key; }) .style("fill-opacity", 1e-6); node.on("click", click) .on("mousemove", onEdgeMouseover) .on("mouseout", onMouseout); // Transition nodes to their new position. var nodeUpdate = node.transition() .duration(duration) .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }); nodeUpdate.select("circle") .attr("r", function(d){ return nodeSizeScale(fnValueField(d)); }) .style("opacity", function(d) { return d._children ? 1 : 0.5; }) .style("fill", function(d) { return d.color || (d.color = colorScale(d.key)); }); nodeUpdate.select("text") .style("fill-opacity", 1); // Transition exiting nodes to the parent's new position. var nodeExit = node.exit().transition() .duration(duration) .attr("transform", function(d) { return "translate(" + source.y + "," + source.x + ")"; }) .remove(); nodeExit.select("circle") .attr("r", 1e-6); nodeExit.select("text") .style("fill-opacity", 1e-6); // Update the links… var link = gLinks.selectAll("g.link") .data(links, function(d) { return d.target.id; }); // Enter any new links at the parent's previous position. var newLink = link .enter() .append("g") .style("mix-blend-mode", "multiply") .classed("link", true); var gradient = newLink.append("linearGradient") .attr("gradientUnits", "userSpaceOnUse") .attr("id", function(d){ return _getGradientId(d); }) .attr("x1", function(d){ return d.source.y; }) .attr("x2", function(d){ return d.target.y; }); gradient.append("stop") .attr("offset", "10%") .attr("stop-color", function(d){ return _getLinkColor(d, true); }); gradient.append("stop") .attr("offset", "90%") .attr("stop-color", function(d){ return _getLinkColor(d); }); newLink.append("path") .attr("d", function(d) { var o = {x: source.x0, y: source.y0}; return diagonal({source: o, target: o}); }) .attr("stroke", function(d) { //return d.source.color; return _getLinkUrl(d); }) .attr("stroke-width", function(d){ return 2 * nodeSizeScale((fnChildren(d.target) || d.target._children || []).length); }) .on("click", function(d){ highlightNode(d.source); }); // Update // var uGradient = link.select("linearGradient") .attr("id", function(d){ return _getGradientId(d); }) .attr("x1", function(d){ return d.source.y; }) .attr("x2", function(d){ return d.target.y; }); // reset uGradient.selectAll("stop") .remove(); uGradient.append("stop") .attr("offset", "10%") .attr("stop-color", function(d){ return _getLinkColor(d, true); }); uGradient.append("stop") .attr("offset", "90%") .attr("stop-color", function(d){ return _getLinkColor(d); }); link.on("click", function(d){ highlightNode(d.source); }) .on("mousemove", onFlowMouseover) .on("mouseout", onMouseout); // Transition links to their new position. link.select("path") .transition() .duration(duration) .attr("d", diagonal) .attr("stroke", function(d) { //return d.source.color; return _getLinkUrl(d); }) .attr("stroke-width", function(d){ return 2 * nodeSizeScale(fnValueField(d.target)); }); // Transition exiting nodes to the parent's new position. link.exit() .transition() .duration(duration) .remove(); link.exit() .select("path") .transition() .duration(duration) .attr("d", function(d) { var o = {x: source.x, y: source.y}; return diagonal({source: o, target: o}); }); //.remove(); // Stash the old positions for transition. nodes.forEach(function(d) { d.x0 = d.x; d.y0 = d.y; }); // pan the source node panSourceNode(nodes, source); } function childCount(level, n) { if (n.children && n.children.length > 0) { if (levelWidth.length <= level + 1) levelWidth.push(0); levelWidth[level + 1] += n.children.length; n.children.forEach(function(d) { childCount(level + 1, d); }); } }; function getTopmostNode(d){ while (d.depth > 1 || (d.depth==0 && d.parent)){ d = d.parent; } return d; } function onEdgeMouseover(d, i) { d3.event.stopPropagation(); var oPayload = { iDepthOffset: -1, datapoint: d, tree: [d] }; } function onFlowMouseover(d, i) { d3.event.stopPropagation(); var oPayload = { iDepthOffset: -1, datapoint: d.target, tree: [d.source, d.target] }; } function onMouseout(d,i) { } // Toggle children on click. function click(d) { d3.event.preventDefault(); d3.event.stopPropagation(); if (d.children) { d._children = d.children; d.children = null; d.values = null; } else { d.values = d._children; d.children = d._children; d._children = null; } update(d); } /** * Highlight a node. * This node will replace the root node. * @param {[type]} source [description] */ function highlightNode(sourceNode) { d3.event.preventDefault(); d3.event.stopPropagation(); // if already highlighted, return to normal state if (sourceNode.bHighlighted) { delete sourceNode.bHighlighted; // get last root node from history // _rootNode = aRootHistory.length ? aRootHistory.pop() : dataRoot; }else{ // push current node in history // aRootHistory.push(_rootNode); // mark current node as highlighted sourceNode.bHighlighted = true; // replace as root node _rootNode = sourceNode; } update(_rootNode); // Update breadcrumb // do not update for root node if (_rootNode.iDepth > 0) { } } // Center currently opened/clicked node // Only to be used when tree.size() is in use /* function centerNode(source) { var scale = 1, x = -source.y0, y = -source.x0, marginRight = 100; // put root node at center of the screen. // other nodes to a little on the right to // maximise screen space usage x = source.depth == 0 ? (x * scale + width / 2) : (x * scale + width - marginRight), y = y * scale + height / 2; gOuter.transition() .duration(duration) .attr("transform", "translate(" + x + "," + y + ")scale(" + scale + ")"); } */ /** * Update the svg dimensions and position the * souce node such that it is in focus * @param {array} nodes current nodes * @param {object} source clicked node */ function panSourceNode(nodes, source) { var depth = d3.max(nodes, function(d){ return d.depth; }), xExtent = d3.extent(nodes, function(a) { return a.x }), yMax = d3.max(nodes, function(a) { return a.y }), minY = xExtent[0], maxY = xExtent[1], bbox = gOuter.node().getBBox(), bIsSourceCollpasing = !!source._children, marginRight = 100, iPossibleNextWidth = bbox.width + (bIsSourceCollpasing ? -iLevelGap : iLevelGap), wCalc = depth * iLevelGap, hCalc = maxY - minY, w = (wCalc < width ? width : wCalc) + margin.left + marginRight, //Math.min(width, depth * iLevelGap) h = (hCalc < height ? height : hCalc ) + margin.top, //Math.max(height, maxY - minY) translateY = h / 2 + iNodeSize/2, scrollTop, scrollLeft, midY = height /2, elSvg = d3.select(svg), elSvgParent = elSvg.node().parentNode, elSvgParentWidth = elSvgParent.getBoundingClientRect().width, midYSourceDiff = (midY + minY); elSvg //.transition() //.duration(duration) .style("height", (h + 100) + "px") .style("width", w + "px"); /** * Determine gOuter translateY position */ if(midYSourceDiff < 0){ translateY = minY * -1 + iNodeSize; }else if(midYSourceDiff > 0 && midYSourceDiff < midY){ translateY = midY; } /** * Determine svg container's scrollTop * when the content size gets bigger than pre-defined height */ if (h > height) { if (translateY < height) { var currentScrollTop = elSvgParent.scrollTop; if(source.x0 < 0){ //var newScrollTop = (height - translateY); var newScrollTop = Math.min(0, translateY - Math.abs(source.x0) - elSvgParent.scrollTop); if ( (Math.abs(minY) + maxY) < height && newScrollTop <= midY && currentScrollTop < midY ) { }else{ scrollTop = newScrollTop; } } else { scrollTop = currentScrollTop || 0; } }else{ scrollTop = source.x0 + translateY - midY; } elSvgParent.scrollTop = scrollTop; } /** * Determine svg container's scrollLeft * when the content size gets bigger than pre-defined width */ //if (w > yMax && source.depth > 0) { if (w > yMax && yMax > elSvgParentWidth && source.depth > 0) { scrollLeft = w - yMax + marginRight + margin.left + iNodeSize*2; }else if (!bIsSourceCollpasing) { scrollLeft = 0; } if (bIsSourceCollpasing && yMax < (elSvgParentWidth-margin.left)) { scrollLeft = 0; } if (scrollLeft !== undefined) { elSvgParent.scrollLeft = scrollLeft; } // For root node if (source.depth == 0) { gOuter.transition() .duration(duration) .attr("transform", "translate(" + margin.left + "," + translateY + ")"); //(iNodeSize + height/2) }else{ // For non-root nodes gOuter.transition() .duration(duration) .attr("transform", "translate(" + (margin.left - marginRight*0) + "," + translateY + ")"); } } /** * Re-renders the graph using dataset and parameters * @return {[type]} [description] */ graph.update = function(){ // re-initialise variables nodeSizeScale .domain([0, fnValueField(dataset)]); d3.select(svg) .attr("width", width + margin.right + margin.left) .attr("height", height + margin.top*0 + margin.bottom*0); gOuter .attr("transform", "translate(" + margin.left + "," + ( iNodeSize/2 + height/2) + ")"); _rootNode.x0 = height / 2; _rootNode.y0 = 0; // Update graph // update(getRootNode()); } // Public Methods / APIs // --------------------- /** * Handle Resizing after the graph has been rendered once */ graph.resize = function(){ isResized = true; graph.update(); } graph.width = function(_){ if (!arguments.length) { return width; } width = _; return graph; } graph.height = function(_){ if (!arguments.length) { return height; } height = _; return graph; } graph.valueFormatter = function(_){ if (!arguments.length) { return valueFormatter; } valueFormatter = _; return graph; } graph.colorScale = function(_){ if (!arguments.length) { return colorScale; } colorScale = _; return graph; } graph.fnValueField = function(_){ if (!arguments.length) { return fnValueField; } fnValueField = _; return graph; } graph.fnChildren = function(_){ if (!arguments.length) { return fnChildren; } fnChildren = _; return graph; } graph.svg = function(_){ if (!arguments.length) { return svg; } svg = _; return graph; } graph.dataset = function(_){ if (!arguments.length) { return dataset; } dataset = _; return graph; } graph.defaultDepth = function(_){ if (!arguments.length) { return iDefaultLevel; } iDefaultLevel = Math.max(1, _); return graph; } graph.openNodes = function(_){ if (!arguments.length) { return aOpenNodesUid; } aOpenNodesUid = _; return graph; } graph.getExpandedNodes = getExpandedNodes; return graph; }30:[{"id":"f01792e36d38e1a310eebfdf8edd4cbbb24dda26e97ccdce3ae7ce870a23d09c6759c6856e5def2963e869001daf1d5b4972a849e4601db47f9527e123ca9174","href":"https://static.observableusercontent.com/files/f01792e36d38e1a310eebfdf8edd4cbbb24dda26e97ccdce3ae7ce870a23d09c6759c6856e5def2963e869001daf1d5b4972a849e4601db47f9527e123ca9174","name":"treeFinal.json","type":"application/json","lastModified":1669929748774.006,"size":3703}] 2d:{"id":"b8228191851c1e4b","slug":null,"title":"Phylogeny","thumbnail":"f326f51b7fc206b4010ddf977a10481f72bcc7773e58403033530a1465378556","access_level":"public","create_time":"$D2022-12-01T21:22:28.774Z","update_time":"$D2022-12-02T16:12:25.000Z","view_time":null,"first_public_time":"$D2022-12-01T21:22:28.774Z","fork":{"id":"41104a9b940ea57d","slug":null,"title":"Phylogeny","owner":{"id":"adea462ffc6621bd","login":"jgergely","name":"Joe Gergely"}},"stars":0,"starred":false,"owner":{"type":"team","id":"aa1425a69e325a3f","login":"mazumderlab","name":"Mazumder Lab ","avatar_url":"https://avatars-next.observableusercontent.com/612c9561c00393c62d3d7f6a55bd4c293d74f9fd29500b5b4f919b0feaae2287","tier":"starter_2024"},"version":185,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"9d5322b35a731b90","login":"neurogenomics","name":"Jonathon Keeney","avatar_url":"https://avatars-next.observableusercontent.com/0b97a1e0fdca2e9eb5d751c94674364f41b99edb7e767c78c0e366f8c4e754e4","tier":null}],"members":[{"type":"team","id":"aa1425a69e325a3f","login":"mazumderlab","name":"Mazumder Lab ","avatar_url":"https://avatars-next.observableusercontent.com/612c9561c00393c62d3d7f6a55bd4c293d74f9fd29500b5b4f919b0feaae2287","tier":"starter_2024","role":"editor"},{"type":"individual","id":"9d5322b35a731b90","login":"neurogenomics","name":"Jonathon Keeney","avatar_url":"https://avatars-next.observableusercontent.com/0b97a1e0fdca2e9eb5d751c94674364f41b99edb7e767c78c0e366f8c4e754e4","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Phylogeny","cells":[{"id":0,"value":"# Phylogeny","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":4,"value":"chart = {\n\n return d3.select(DOM.svg(width, height)).node();\n \n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":6,"value":"draw = {\n // clear\n d3.select(chart).html('');\n \n var tree = WeightedTree()\n .svg(chart)\n .width(width)\n .height(height)\n .dataset(dataset)\n .fnValueField(function(d){\n return d[valueField];\n });\n\n tree();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":8,"value":"width = 720","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":36,"value":"height = 1800","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":12,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":14,"value":"function getValueField(){\n return valueField;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":16,"value":"valueField = \"weight\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":18,"value":"aColors = [\"#66c2a5\", \"#66c2a5\", \"#3288bd\"]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":20,"value":"//dataset = d3fetch.json('https://raw.githubusercontent.com/Jgergely11/test2/main/.github/workflows/phylogeny.json')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":22,"value":"d3fetch = import('d3-fetch')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":26,"value":"d3 = require(\"d3@3\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":24,"value":"css = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":106,"value":"dataset = FileAttachment(\"treeFinal.json\").json()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2e:"$2d:body"