2b:null 2c:["$","title",null,{"children":"Sub-Network Graph | lazyTsunday's Workspace | Observable"}] 31:T2746,chart = { let links = data.links.map(d => Object.create(d)); let nodes = data.nodes.map(d => Object.create(d)); let linkedByIndex = {}; data.links.forEach(d => { linkedByIndex[`${d.source},${d.target}`] = true; }); // nodes map let nodesById = {}; data.nodes.forEach(d => { nodesById[d.id] = {...d}; }) const [width, height] = [1000, 1000]; const svg = d3.select(DOM.svg(width, height)); //const groups = data.groups.map(d => Object.create(d)); // const layout = cola.d3adaptor(d3) // .size([width, height]); /* layout .nodes(nodes) .links(links) .groups(groups) .constraints(constraints) .jaccardLinkLengths(150, 0.1) .avoidOverlaps(true) .start(50); */ // props passed down: const centerLevel = 4; const totalLevels = 4; const aiScoreMinDiff = 0.2; const isConnectedAsSource = (a, b) => linkedByIndex[`${a},${b}`]; const isConnectedAsTarget = (a, b) => linkedByIndex[`${b},${a}`]; const isConnected = (a, b) => isConnectedAsTarget(a, b) || isConnectedAsSource(a, b) || a === b; const isEqual = (a, b) => a === b; const nodeRadius = (d) => Math.pow(40.0 * d.size, 1 / 3); const baseGroup = svg.append("g"); function zoomed() { baseGroup.attr("transform", d3.event.transform); } const zoom = d3.zoom() .scaleExtent([0.2, 8]) //.translateExtent([[-1000, -1000], [width + 1000, height + 1000]]) .on("zoom", zoomed); svg.call(zoom); let ifClicked = false; const nodeRadius2 = d => 15 * d.support; let simulation = d3.forceSimulation() .force("link", d3.forceLink().id(function(d) { return d.id; }).strength(0.4)) .force("charge", d3.forceManyBody()) .force("y", d3.forceY(height/2).strength(0.1)) .force("center", d3.forceCenter(width / 2 + 100, height / 2)) // TODO: modify + 100 for center force .force("x", d3.forceX(d => { if (d.level === centerLevel) { return width/2; // width/5 - 50 - 400; } return width/2 + width/7 * (d.level - centerLevel); // width/5 * d.group - 400; }).strength(0.9)) .force("collide", d3.forceCollide().radius(d => nodeRadius2(d) + 0.5).iterations(2)); let link = baseGroup.append("g") .selectAll(".link") .data(links) .enter().append('line') .attr('class', 'link') .attr('id', d => d.id) .style("stroke-width", 0.3) .style('stroke', d => { const aiScoreDiff = nodesById[d.target].aiScore - nodesById[d.source].aiScore; if (Math.abs(aiScoreDiff) < aiScoreMinDiff) { return '#999'; } else { if (aiScoreDiff > 0) { return "#84c942"; // inactive -> active } else { return "#e85335"; // active -> inactive } } }); // .style("stroke-opacity", d => { // const aiScoreDiff = nodesById[d.target].aiScore - nodesById[d.source].aiScore; // if (Math.abs(aiScoreDiff) < aiScoreMinDiff) { // return 0.4; // } // return 1; // }); link.exit().remove(); let node = baseGroup.append("g") .selectAll(".node") .data(nodes) .enter().append('circle') .attr('class', 'node') .attr("r", d => nodeRadius2(d)) .style("fill", nodeColor); node.exit().remove(); // edit context menu const rightClickItems = ['Expand sub-network of the pattern', 'Mark the pattern', 'Mark compound population']; const menuItems = baseGroup.selectAll(".menuitems") .data(rightClickItems) .join('g') .classed('menuitems', true) .attr('visibility', "hidden") .attr('transform', `translate(${0}, ${0})`) //.on('click', rightClickActions); menuItems.append('rect') .attr('x', 0) .attr('y', (d,i) => i * 20) .attr('width', 180) .attr('height', 20); menuItems.append('text') .text(d => d) .attr('x', 3) .attr('y', (d,i) => 13 + i * 20) .style('fill', 'black') .style('font-size', '11px'); function ticked() { link .attr("x1", function(d) { return d.source.x; }) .attr("y1", function(d) { return d.source.y; }) .attr("x2", function(d) { return d.target.x; }) .attr("y2", function(d) { return d.target.y; }); node .attr("cx", function(d) { return d.x; }) .attr("cy", function(d) { return d.y; }); } simulation .nodes(nodes) .on("tick", ticked); simulation.force("link") .links(links); const mouseOverFunction = d => { console.log(d) tooltip.style("visibility", "visible") .html(() => { const content = `Pattern: {${d.id.replace(/-/g, ',')}}`+'
' +`aiScore: ${d3.format('.2f')(d.aiScore)}`; return content; }); if (ifClicked) return; node .transition(500) .style('opacity', o => { const isConnectedValue = isConnected(o.id, d.id); if (isConnectedValue) { return 1.0; } return 0.1; }); link .transition(500) .style('stroke-opacity', o => (o.source === d || o.target === d ? 1 : 0.1)) // .transition(500) // .attr('marker-end', o => (o.source === d || o.target === d ? 'url(#arrowhead)' : 'url()')); }; const mouseOutFunction = d => { tooltip.style("visibility", "hidden"); if (ifClicked) return; node .transition(500) .style('opacity', 1); link .transition(500) //.style('opacity', 0.4); .style("stroke-opacity", o => 0.4); }; const rightClickActions = (d, menuItem, i) => { // d is the clicked node, i is the menuItem index console.log(d.id, menuItem, i) // Expand sub-network of the patter if (i === 0) { // sending d.id (pattern) to backend to get sub-network }; menuItems.attr('visibility', "hidden"); }; const rightClickFunction = d => { console.log(d) d3.event.preventDefault(); // add clicked effect: highlight right-clicked item ifClicked = true; node .transition(500) .style('opacity', 1) link .transition(500); node .transition(500) .style('opacity', o => { const isConnectedValue = isConnected(o.id, d.id); if (isConnectedValue) { return 1.0; } return 0.1 }) link .transition(500) .style('stroke-opacity', o => (o.source === d || o.target === d ? 1 : 0.1)) .transition(500) .attr('marker-end', o => (o.source === d || o.target === d ? 'url(#arrowhead)' : 'url()')); tooltip.style("visibility", "hidden"); const position = {x: d.x, y: d.y}; menuItems.attr('visibility', "visible") .attr('transform', `translate(${position.x}, ${position.y})`) .on('click', (menuItem, i) => rightClickActions(d, menuItem, i)); }; const mouseClickFunction = d => { // we don't want the click event bubble up to svg d3.event.stopPropagation(); menuItems.attr('visibility', "hidden"); ifClicked = true; node .transition(500) .style('opacity', 1) link .transition(500); node .transition(500) .style('opacity', o => { const isConnectedValue = isConnected(o.id, d.id); if (isConnectedValue) { return 1.0; } return 0.1 }) link .transition(500) .style('stroke-opacity', o => (o.source === d || o.target === d ? 1 : 0.1)) .transition(500) .attr('marker-end', o => (o.source === d || o.target === d ? 'url(#arrowhead)' : 'url()')); if (true) { const newLinks = data1.links.map(d => Object.create(d)) const newNodes = data1.nodes.map(d => Object.create(d)) console.log(newLinks, newNodes) data1.links.forEach(d => { linkedByIndex[`${d.source},${d.target}`] = true; }); data1.nodes.forEach(d => { nodesById[d.id] = {...d}; }) link = link.data(newLinks) .join("line") .classed('link', true) .attr("stroke-width", 0.3) .style('stroke', d => { const aiScoreDiff = nodesById[d.target].aiScore - nodesById[d.source].aiScore; if (Math.abs(aiScoreDiff) < aiScoreMinDiff) { return '#999'; } else { if (aiScoreDiff > 0) { return "#84c942"; // inactive -> active } else { return "#e85335"; // active -> inactive } } }); node = node.data(newNodes) .join('circle') .classed('node', true) .attr("r", d => nodeRadius2(d)) .attr("fill", nodeColor) .on('mouseover', mouseOverFunction) .on('mouseout', mouseOutFunction) .on('click', mouseClickFunction) .on('contextmenu', rightClickFunction) .on('mousemove', () => tooltip.style("top", (d3.event.pageY-10)+"px").style("left",(d3.event.pageX+10)+"px")); simulation .nodes(newNodes) .on("tick", ticked); simulation.force("link") .links(newLinks); simulation.alpha(1).restart(); console.log(baseGroup.selectAll('line')) } }; node.on('mouseover', mouseOverFunction) .on('mouseout', mouseOutFunction) .on('click', mouseClickFunction) .on('contextmenu', rightClickFunction) .on('mousemove', () => tooltip.style("top", (d3.event.pageY-10)+"px").style("left",(d3.event.pageX+10)+"px")); svg.on('click', () => { ifClicked = false; node .transition(500) .style('opacity', 1); link .transition(500) .style("stroke-opacity", 0.4) menuItems.attr('visibility', "hidden"); }); //invalidation.then(() => layout.stop()); return svg.node(); }32:T5bf,html ``33:[] 2f:{"id":"5073f6bc4c462adb","slug":null,"title":"Sub-Network Graph","thumbnail":"8440b32f4779ca53639816c1605626bc25515413d48752638f460b0df9dce2ac","access_level":"public","create_time":"$D2023-09-27T08:19:58.723Z","update_time":"$D2023-09-27T08:19:58.723Z","view_time":null,"first_public_time":"$D2023-09-27T08:19:58.723Z","has_unpublished_edits":null,"fork":{"id":"850f3c82e55f34e8","slug":"sub-network-graph","title":"Sub-Network Graph","owner":{"id":"550720cff471c380","login":"ravengao","name":"Raven Gao"}},"stars":0,"starred":false,"owner":{"type":"team","id":"35064f1f895f02be","login":"lazytsunday-ws","name":"lazyTsunday's Workspace","avatar_url":"https://avatars-next.observableusercontent.com/fbe879bc229f98e89bb08f328c24ede7467e5305900c8211b70d85097af0bc59","tier":"starter_2024"},"version":767,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"31750da39446aea6","login":"lazytsunday","name":"lazyTsunday","avatar_url":"https://avatars-next.observableusercontent.com/17550ca905941dc09cb9786af45c346b43376504e403d96244ed70f80c73d733","tier":null}],"members":[{"type":"individual","id":"31750da39446aea6","login":"lazytsunday","name":"lazyTsunday","avatar_url":"https://avatars-next.observableusercontent.com/17550ca905941dc09cb9786af45c346b43376504e403d96244ed70f80c73d733","tier":null,"role":"editor"},{"type":"team","id":"35064f1f895f02be","login":"lazytsunday-ws","name":"lazyTsunday's 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interested`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"$31","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":473,"value":"tooltip = d3.select(\"body\").append(\"div\")\n .attr(\"class\", \"svg-tooltip\")\n .style(\"position\", \"absolute\")\n .style(\"visibility\", \"hidden\")\n .text(\"I'm a circle!\");","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":3,"value":"// filter by: support > 0.4\ndata1 = d3.json(\"https://gist.githubusercontent.com/ravengao/259fc321a3aabde12374e7bb1844f65f/raw/ce69744076645917854a9b39164adfd3d231a4ea/subnetwork_supp%253E0.4.json\")\n// data = d3.json(\"https://gist.githubusercontent.com/ravengao/a548cc4a7dd38f1afe0fe4b31ba8901b/raw/fd86a4e94e31ca2497ee78e1006dbed798f62e67/sample_data_supp%253E0.4_new.json\")\n\n// data = d3.json(\"https://gist.githubusercontent.com/ravengao/5b65551b7a0199e01380ddc1b13248a0/raw/d31bd24ef9286cb5a6eb4520f99f6a3c6b68c330/sample_v2.json\")\n\n// filter by: support > 0.3\n//data = d3.json(\"https://gist.githubusercontent.com/ravengao/3a6deb4f4add94eb485b570d04128c81/raw/02b60190a410f2143ccdc13c24b614073bb592a7/sample_v2%253E0.3.json\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":658,"value":"data = d3.json(\"https://gist.githubusercontent.com/ravengao/374bef2aeaa921c29009b7b88a0e253c/raw/b5e5fcd773cc87d04a359bc2c232b14d7635d9fa/subnetwork_init.json\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"height = 600","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":266,"value":"// calculate node color with aiScore, in a range of (0.3, 0.6)\nnodeColor = {\n const scale = d3.scaleLinear().domain([0.3, 0.6]).range([0, 1]);\n return d => d3.interpolateRdYlGn(scale(d.aiScore || 0));\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":76,"value":"drag = simulation => {\n \n function dragstarted(d) {\n if (!d3.event.active) simulation.alphaTarget(0.3).restart();\n d.fx = d.x;\n d.fy = d.y;\n }\n \n function dragged(d) {\n d.fx = d3.event.x;\n d.fy = d3.event.y;\n }\n \n function dragended(d) {\n if (!d3.event.active) simulation.alphaTarget(0);\n d.fx = null;\n d.fy = null;\n }\n \n return d3.drag()\n .on(\"start\", dragstarted)\n .on(\"drag\", dragged)\n .on(\"end\", dragended);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"d3 = require(\"d3@5\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":134,"value":"cola = require(\"webcola@3/WebCola/cola.min.js\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"$32","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1"}} 30:"$2f:body"