2b:null 2c:["$","title",null,{"children":"Active compound intersection -> Pattern Network | Raven Gao | Observable"}] 31:T208e,chart = { const data = data1; const links = data.links.map(d => Object.create(d)); const nodes = data.nodes.map(d => Object.create(d)); const [width, height] = [1000, 1000]; const svg = d3.select(DOM.svg(width, height)); const aiScoreMinDiff = 0.2; // create link reference let linkedByIndex = {}; data.links.forEach(d => { linkedByIndex[`${d.source},${d.target}`] = true; }); // nodes map let nodesById = {}; data.nodes.forEach(d => { nodesById[d.id] = {...d }; }) const isConnectedAsSource = (a, b) => linkedByIndex[`${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.sqrt(d.support) + 3; // TODO const baseGroup = svg.append("g"); function zoomed() { baseGroup.attr("transform", d3.event.transform); } const zoom = d3.zoom() .scaleExtent([0.2, 8]) //.translateExtent([[-100, -100], [width + 1000, height + 1000]]) .on("zoom", zoomed); svg.call(zoom); let ifClicked = false; const simulation = d3.forceSimulation() .force("link", d3.forceLink().id(function (d) { return d.id; }).strength(0.3)) .force("charge", d3.forceManyBody()) .force("y", d3.forceY(height / 2).strength(0.1)) //.force("center", d3.forceCenter(width / 2, height / 2)) .force("x", d3.forceX(d => { if (d.level === 1) { return width / 6 - 50; // width/5 - 50 - 400; } return width / 6 * d.level; // width/5 * d.group - 400; }).strength(0.95)) .force("collide", d3.forceCollide().radius(d => nodeRadius(d) + 1).iterations(2)); const link = baseGroup.append("g") .selectAll("line") .data(links) .join("line") .classed('link', true) .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 0.5; } else { return 1; } }) .style('stroke-width', d => { const aiScoreDiff = nodesById[d.target].aiScore - nodesById[d.source].aiScore; if (Math.abs(aiScoreDiff) < aiScoreMinDiff) { return 0.5; } else { return 1.5; } }); const node = baseGroup.append("g") .selectAll("circle") .data(nodes) .join("circle") .classed('node', true) .attr("r", d => nodeRadius(d)) .attr("fill", nodeColor); // 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}, ${0})`) //.on('click', rightClickActions); menuItems.append('rect') .attr('x', 0) .attr('y', (d, i) => i * 20) .attr('width', 180) .attr('height', 20); menuItems.append('text') .text(d => d) .attr('x', 3) .attr('y', (d, i) => 13 + i * 20) .style('fill', 'black') .style('font-size', '11px'); function ticked() { link .attr("x1", function (d) { return d.source.x; }) .attr("y1", function (d) { return d.source.y; }) .attr("x2", function (d) { return d.target.x; }) .attr("y2", function (d) { return d.target.y; }); node .attr("cx", function (d) { return d.x; }) .attr("cy", function (d) { return d.y; }); } simulation .nodes(nodes) .on("tick", ticked); simulation.force("link") .links(links); const mouseOverFunction = d => { tooltip.style("visibility", "visible") .html(() => { const content = `Pattern: {${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 => { return (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("stroke-opacity", d => { const aiScoreDiff = nodesById[d.target.id].aiScore - nodesById[d.source.id].aiScore; if (Math.abs(aiScoreDiff) < aiScoreMinDiff) { return 0.5; } else { return 1; } }) .style('stroke-width', d => { const aiScoreDiff = nodesById[d.target.id].aiScore - nodesById[d.source.id].aiScore; if (Math.abs(aiScoreDiff) < aiScoreMinDiff) { return 0.5; } else { return 1.5; } }); }; 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()')); }; 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 => { 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}, ${position.y})`) .on('click', (menuItem, i) => rightClickActions(d, menuItem, i)); }; node.on('mouseover', mouseOverFunction) .on('mouseout', mouseOutFunction) .on('click', mouseClickFunction) .on('contextmenu', rightClickFunction) .on('mousemove', () => tooltip.style("top", (d3.event.pageY - 10) + "px").style("left", (d3.event.pageX + 10) + "px")); svg.on('click', () => { ifClicked = false; node .transition(500) .style('opacity', 1); link .transition(500) .style("stroke-opacity", 0.5) menuItems.attr('visibility', "hidden"); }); //invalidation.then(() => layout.stop()); return svg.node(); }32:T5da,html ``33:[] 2f:{"id":"46d7d784e8070b10","slug":"active-compound-intersection-pattern-network","title":"Active compound intersection -> Pattern Network","thumbnail":"7ccca75356c6387ac7354fef2cb85ec03842a896eb372ed925b8c68f2acfc7c2","access_level":"public","create_time":"$D2019-09-18T17:22:53.504Z","update_time":"$D2019-10-02T15:53:51.865Z","view_time":null,"first_public_time":"$D2019-09-18T17:23:04.922Z","fork":true,"stars":2,"starred":false,"owner":{"type":"team","id":"550720cff471c380","login":"ravengao","name":"Raven Gao","avatar_url":"https://avatars-next.observableusercontent.com/5f95938c702e6ef5d89873688b85b0127a0d966e072f7fc1a7758b79c59cd4da","tier":"starter_2024"},"version":708,"publish_version":708,"role":null,"authored":false,"authors":[{"type":"individual","id":"cef5006b7e0fa94d","login":"ravengao","name":"Raven Gao","avatar_url":"https://avatars-next.observableusercontent.com/5f95938c702e6ef5d89873688b85b0127a0d966e072f7fc1a7758b79c59cd4da","tier":null}],"members":[{"type":"individual","id":"cef5006b7e0fa94d","login":"ravengao","name":"Raven Gao","avatar_url":"https://avatars-next.observableusercontent.com/5f95938c702e6ef5d89873688b85b0127a0d966e072f7fc1a7758b79c59cd4da","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Active compound intersection -> Pattern Network","cells":[{"id":1,"value":"md`# Active compound intersection -> Pattern Network \n\nThis network is created from all active compound intersection. In total, there are almost 20k patterns calculated from intersection, 7k links between them that indicates parent-child relationship. However, only 5k patterns have links going through. To increase the render performance, I remove those nodes that has no links connected.\n\nIn the future, we can\n 1. filter out pattern node that has low frequence. (e.g. freq > 2)\n 2. filter by aiScore_diff ?\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":7,"value":"$31","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":473,"value":"tooltip = d3.select(\"body\").append(\"div\")\n .attr(\"class\", \"svg-tooltip\")\n .style(\"position\", \"absolute\")\n .style(\"visibility\", \"hidden\")\n .text(\"I'm a circle!\");","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":3,"value":"// filter by: support > 0.4\ndata = d3.json(\"https://gist.githubusercontent.com/ravengao/a548cc4a7dd38f1afe0fe4b31ba8901b/raw/fd86a4e94e31ca2497ee78e1006dbed798f62e67/sample_data_supp%253E0.4_new.json\")\n// data = d3.json(\"https://gist.githubusercontent.com/ravengao/5b65551b7a0199e01380ddc1b13248a0/raw/d31bd24ef9286cb5a6eb4520f99f6a3c6b68c330/sample_v2.json\")\n\n// filter by: support > 0.3\n//data = d3.json(\"https://gist.githubusercontent.com/ravengao/3a6deb4f4add94eb485b570d04128c81/raw/02b60190a410f2143ccdc13c24b614073bb592a7/sample_v2%253E0.3.json\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":677,"value":"//data1 = d3.json(\"https://gist.githubusercontent.com/ravengao/43eb814f9ce881b97db9c217a75aa144/raw/b8caa387af0489ceba6ba531296008ce8ad6c205/intersection_patterns.json\")\n// filtered out nodes with no links\ndata1 = d3.json(\"https://gist.githubusercontent.com/ravengao/96a4f992a7afeb3409e3f0a6b3f79d24/raw/253b69bea13bb982723184e669e10e90f3c6e3b8/intersection_patterns_filtered.json\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":32,"value":"height = 600","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":266,"value":"// calculate node color with aiScore, in a range of (0.3, 0.6)\nnodeColor = {\n const scale = d3.scaleLinear().domain([0.3, 0.6]).range([0, 1]);\n return d => d3.interpolateRdYlGn(scale(d.aiScore || 0));\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":76,"value":"drag = simulation => {\n \n function dragstarted(d) {\n if (!d3.event.active) simulation.alphaTarget(0.3).restart();\n d.fx = d.x;\n d.fy = d.y;\n }\n \n function dragged(d) {\n d.fx = d3.event.x;\n d.fy = d3.event.y;\n }\n \n function dragended(d) {\n if (!d3.event.active) simulation.alphaTarget(0);\n d.fx = null;\n d.fy = null;\n }\n \n return d3.drag()\n .on(\"start\", dragstarted)\n .on(\"drag\", dragged)\n .on(\"end\", dragended);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":11,"value":"d3 = require(\"d3@5\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":134,"value":"cola = require(\"webcola@3/WebCola/cola.min.js\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":211,"value":"$32","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 30:"$2f:body"