2b:null 2c:["$","title",null,{"children":"Element Substitution and Compatibility Network | Substitution Graphs | Observable"}] 31:Tc65,chart = { const svg = d3.create("svg") .attr("viewBox", [0, 0, width, height]); svg.append('rect') .attr('width', '100%') .attr('height', '100%') .attr('fill', 'white') .on('click', function() { // Restore nodes and links to normal opacity. d3.selectAll('.link').style('stroke-opacity', '0.6'); d3.selectAll('.node').style('opacity', '1'); }); var container = svg.append('g'); // Call zoom for svg container. svg.call(zoom(container)); var link = container.append("g") .attr("class", "links") .selectAll("line"); var node = container.append("g") .attr("class", "nodes") .selectAll("circle"); // Make object of all neighboring nodes. var linkedByIndex = {}; json.links.forEach(function(d) { linkedByIndex[d.source.index + ',' + d.target.index] = 1; linkedByIndex[d.target.index + ',' + d.source.index] = 1; }); // A function to test if two nodes are neighboring. function neighboring(a, b) { return linkedByIndex[a.index + ',' + b.index]; } return Object.assign(svg.node(), { update(nodes,links) { link = link.data(links, function(d) { return d.source.index + ", " + d.target.index;}); link.exit().remove(); var linkEnter = link.enter().append("line") .attr('class', 'link') .attr('stroke', 'gray'); link = linkEnter.merge(link); node = node.data(nodes); node.exit().remove(); var nodeEnter = node.enter().append("circle") // Use degree centrality from NetworkX in json. .attr('r', function(d, i) { return degreeSize(d.occurances); }) // Color by group, a result of modularity calculation in NetworkX. .attr("fill", function(d) { return color(d.group); }) .attr('class', 'node') // On click, toggle ego networks for the selected node. .on('click', function(d, i) { // Ternary operator restyles links and nodes if they are adjacent. d3.selectAll('.link').style('stroke-opacity', function (l) { return l.target == d || l.source == d ? 1 : 0.1; }); d3.selectAll('.node').style('opacity', function (n) { return neighboring(d, n) ? 1 : 0.1; }); d3.select(this).style('opacity', 1); }) .call(drag(simulation)); node = nodeEnter.merge(node); node.append("title") // .text(d => d.name); .text(function(d) { return d.name; }); // node.append("text") // .attr("dy", 4) // .attr("dx", -15) // .text(d => d.name); simulation .nodes(nodes) .on("tick", ticked); simulation.force("link") .links(links); simulation.alpha(1).restart(); 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; }); } } }); }32:T481, // A dropdown menu with three different centrality measures, calculated in NetworkX. dropdown2 = { let dropdown = html` Color Nodes By: `; let select = dropdown.querySelector('select'); let label = dropdown.querySelector('label'); for (const element of ["4-", "3-", "2-", "1-", "0", "1+", "2+", "3+", "4+", "5+", "6+", "7+", "8+"]) { let child = document.createElement('option') child.value = element child.innerHTML = element select.appendChild(child) } dropdown.onchange = () => { var grouping = select.value; var coloring = d3.scaleOrdinal() // Color by group, a result of modularity calculation in NetworkX. //.attr("fill", function(d) { return color(d.classification); }) if (grouping == "group") { d3.selectAll(".node").attr("fill", function(d) { return color(d[grouping]); }); } else { d3.selectAll(".node") .attr("fill", function(d) { return color(d["charges"].includes(grouping) ? 5 : 8); }); } } return dropdown; }33:[{"id":"a8a1afd5064642b757e408bfd503b7cbf67a026b2ec351d86362e6a926e31d8e383d184b398a4ced37787c429eb08dd388bc2b0b83d5e04b25e4362d2c24fa8b","href":"https://static.observableusercontent.com/files/a8a1afd5064642b757e408bfd503b7cbf67a026b2ec351d86362e6a926e31d8e383d184b398a4ced37787c429eb08dd388bc2b0b83d5e04b25e4362d2c24fa8b","name":"substitutions_graph@8.json","type":"application/json","lastModified":1733338185361.337,"size":50542}] 2f:{"id":"882b5ea7d7688ee4","slug":null,"title":"Element Substitution and Compatibility Network","thumbnail":"c5c3fd85d50cff5969399e49018c5786742cdea842216a761ef36541270b7529","access_level":"public","create_time":"$D2024-11-26T18:21:45.965Z","update_time":"$D2024-12-19T15:04:18.259Z","view_time":null,"first_public_time":"$D2024-11-26T18:21:45.965Z","has_unpublished_edits":null,"fork":{"id":"f6f8041968f51125","slug":"all-chondrite-network-based-on-chemical-compositions","title":"All Chondrite Network based on chemical compositions","owner":{"id":"97c619b9c7f7a2cd","login":"anirudhprabhu","name":"Anirudh Prabhu"}},"stars":0,"starred":false,"owner":{"type":"team","id":"0e68c82ccf9f10c0","login":"workspace-n","name":"Substitution Graphs","avatar_url":"https://avatars-next.observableusercontent.com/1048d53026c292a7319e7b7d9bcc9c79a859ee0a0b5607d463b1ecc7e20833c2","tier":"starter_2024"},"version":186,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"05cb99b6873a2857","login":"kate-hendrickson","name":"kate-hendrickson","avatar_url":"https://avatars-next.observableusercontent.com/769c344dbe730c71272114ea21285e071a0428888ef3f8f93e635921d5b48961","tier":null}],"members":[{"type":"individual","id":"05cb99b6873a2857","login":"kate-hendrickson","name":"kate-hendrickson","avatar_url":"https://avatars-next.observableusercontent.com/769c344dbe730c71272114ea21285e071a0428888ef3f8f93e635921d5b48961","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":4,"collection":null,"type":"notebook","body":{"title":"Element Substitution and Compatibility Network","cells":[{"id":0,"value":"# Element Substitution and Compatibility Network\n\n### From RRUFF Microprobe Data across all minerals","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"EvolSysPart7_Unipartite","database":"$undefined"},{"id":76,"value":"# Full Network","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":3,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"// Create form for search (see function below).\nsearch = {\n let search = html`\n Search by Element Symbol:\n `;\n let label = search.querySelector('label');\n let input = search.querySelector('input');\n search.onkeyup = () => {\n var term = input.value;\n var selected = d3.selectAll('.node').filter(function (d, i) {\n return d.name.toLowerCase().search(term.toLowerCase()) == -1;\n });\n selected.style('opacity', '0');\n d3.selectAll('.link').attr('stroke-opacity', '0');\n d3.selectAll('.node').transition()\n .duration(10000)\n .style('opacity', '1');\n d3.selectAll('.link').transition().duration(10000).style('stroke-opacity', '0.6');\n }\n return search\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"\t// A dropdown menu with three different centrality measures, calculated in NetworkX.\n\ndropdown = {\n let dropdown = html`\n Size Nodes By:\n `;\n let select = dropdown.querySelector('select');\n let label = dropdown.querySelector('label');\n dropdown.onchange = () => {\n var centrality = select.value;\n var centralitySize = d3.scaleLinear()\n .domain([d3.min(json.nodes, function(d) { return d[centrality]; }), d3.max(json.nodes, function(d) { return d[centrality]; })])\n .range([8,25]);\n d3.selectAll(\".node\").attr(\"r\", d => centralitySize(d[centrality]));\n }\n return dropdown;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":117,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8,"value":" \t// A slider (using only d3 and HTML5) that removes nodes below the input threshold.\nslider = {\n\n let min = d3.min(json.links, function(d) {return d.weight; });\n let max = d3.max(json.links, function(d) {return d.weight; })\n let slider = html`\n Edge Weight Threshold: ${min}\n `;\n let label = slider.querySelector('label');\n let range = slider.querySelector('input');\n range.value = min\n range.oninput = () => {\n let threshold = range.valueAsNumber\n label.innerHTML = `Edge Weight Threshold: ${threshold}`\n let newLinks = json.links.filter(l => l.weight > threshold);\n chart.update(json.nodes,newLinks);\n };\n return slider;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"height=1000;","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"simulation = d3.forceSimulation()\n .force(\"link\", d3.forceLink().id(function(d) { return d.index; }))\n .force(\"charge\", d3.forceManyBody().strength([-250]).distanceMax([500]))\n .force(\"center\", d3.forceCenter(width / 2, height / 2))\n .force(\"collide\", d3.forceCollide().radius( function (d) { return degreeSize(d.degree); }));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"color = d3.scaleOrdinal(d3.schemeCategory10);\n// d3.schemeCategory10","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"// Linear scale for degree centrality.\ndegreeSize = d3.scaleLinear()\n .domain([d3.min(json.nodes, function(d) {return d.occurances; }),d3.max(json.nodes, function(d) {return d.occurances; })])\n .range([8,25]);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":21,"value":"drag = simulation => {\n \n function dragstarted(d) {\n if (!d3.event.active) simulation.alphaTarget(0.3).restart();\n d.fx = d.x;\n d.fy = d.y;\n }\n\n function dragged(d) {\n d.fx = d3.event.x;\n d.fy = d3.event.y;\n }\n\n function dragended(d) {\n if (!d3.event.active) simulation.alphaTarget(0);\n d.fx = null;\n d.fy = null;\n }\n \n return d3.drag()\n .on(\"start\", dragstarted)\n .on(\"drag\", dragged)\n .on(\"end\", dragended);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"zoom = container => {\n // Zooming function translates the size of the svg container.\n function zoomed() {\n container.attr(\"transform\", \"translate(\" + d3.event.transform.x + \", \" + d3.event.transform.y + \") scale(\" + d3.event.transform.k + \")\");\n }\n \n return d3.zoom().scaleExtent([0.5,3]).on('zoom', zoomed)\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"json = FileAttachment(\"substitutions_graph@8.json\").json();","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":"chart.update(json.nodes,json.links)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":32,"value":"d3 = require(\"d3@4\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"Adapted from Code: `https://observablehq.com/@jrladd/marvel-network`","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 30:"$2f:body"