2c:null 2d:["$","title",null,{"children":"SARS-CoV-2 Lineage Tree | CVR Bioinformatics | Observable"}] 32:T590,function filter_tree_data(text_input,node_list,root_node) { console.log("Starting!") const lineage_list = text_input.replace(/\s+/g,"").split(',') const nodes = node_list.filter((d,i)=> {if(lineage_list.includes(d.name) === true){return d}}) const minimal_path = [] let path for (const node of nodes) { path = get_path_to_root(node,node_list) minimal_path.push(node) minimal_path.push(path) } const set = new Set(minimal_path.flat()) const minimal_set = Array.from(set).sort(node_compare).reverse() const root_node_copy = Object.assign({}, root_node) const minimal_set_with_root = minimal_set.concat([root_node_copy]) // Remove nodes not in the minimal set const minimal_set_rewritten = [] for (const [index, node] of minimal_set_with_root.entries()){ const duplicate_node = Object.assign({}, node ) if (!lineage_list.find(a =>a === duplicate_node.name)){ duplicate_node.children = filterByList(minimal_set_with_root,duplicate_node.children) minimal_set_rewritten.push(duplicate_node) }else{ minimal_set_rewritten.push(duplicate_node) } } for (let i = 0; i < minimal_set_rewritten.length; i++){ const children_names = replaceObjectInArrayByName(minimal_set_rewritten[i].children, minimal_set_rewritten) minimal_set_rewritten[i].children = children_names } return minimal_set_rewritten[minimal_set_rewritten.length-1] } 33:T4e2,function group_numbers(number){ if (number <1000){ return d3.color(interpolate_colours[0]).formatHex() }else if (number >1001 && number <=5000){ return d3.color(interpolate_colours[1]).formatHex() }else if (number >5001 && number <=10000){ return d3.color(interpolate_colours[2]).formatHex() }else if (number >10001 && number <=20000){ return d3.color(interpolate_colours[3]).formatHex() }else if (number >20001 && number <=30000){ return d3.color(interpolate_colours[4]).formatHex() }else if (number >40001 && number <=50000){ return d3.color(interpolate_colours[5]).formatHex() }else if (number >50001 && number <=10000){ return d3.color(interpolate_colours[6]).formatHex() }else if (number > 100001 && number <=500000){ return d3.color(interpolate_colours[7]).formatHex() }else if (number > 500001 && number <=600000){ return d3.color(interpolate_colours[8]).formatHex() }else if (number > 600001 && number <=700000){ return d3.color(interpolate_colours[9]).formatHex() }else if (number > 800001 && number <=900000){ return d3.color(interpolate_colours[10]).formatHex() }else if (number >900001 && number <=1000000){ return d3.color(interpolate_colours[11]).formatHex() } }34:T17d1,// Copyright 2021 Observable, Inc. // Released under the ISC license. // https://observablehq.com/@d3/force-directed-graph function ForceGraph( { nodes, // an iterable of node objects (typically [{id}, …]) links // an iterable of link objects (typically [{source, target}, …]) }, { nodeId = (d) => d.id, // given d in nodes, returns a unique identifier (string) nodeGroup, // given d in nodes, returns an (ordinal) value for color nodeGroups, // an array of ordinal values representing the node groups nodeTitle, // given d in nodes, a title string nodeFill = "currentColor", // node stroke fill (if not using a group color encoding) nodeStroke = "#fff", // node stroke color nodeStrokeWidth = 0.8, // node stroke width, in pixels nodeStrokeOpacity = 1, // node stroke opacity nodeRadius = 5, // node radius, in pixels nodeStrength, linkSource = ({ source }) => source, // given d in links, returns a node identifier string linkTarget = ({ target }) => target, // given d in links, returns a node identifier string linkStroke = "#999", // link stroke color linkStrokeOpacity = 0.6, // link stroke opacity linkStrokeWidth = 1.5, // given d in links, returns a stroke width in pixels linkStrokeLinecap = "round", // link stroke linecap linkStrength, colors = d3.schemeTableau10, // an array of color strings, for the node groups width = 640, // outer width, in pixels height = 400, // outer height, in pixels invalidation // when this promise resolves, stop the simulation } = {} ) { // Compute values. const N = d3.map(nodes, nodeId).map(intern); const LS = d3.map(links, linkSource).map(intern); const LT = d3.map(links, linkTarget).map(intern); if (nodeTitle === undefined) nodeTitle = (_, i) => N[i]; const T = nodeTitle == null ? null : d3.map(nodes, nodeTitle); const G = nodeGroup == null ? null : d3.map(nodes, nodeGroup).map(intern); const W = typeof linkStrokeWidth !== "function" ? null : d3.map(links, linkStrokeWidth); const L = typeof linkStroke !== "function" ? null : d3.map(links, linkStroke); console.log(N) // Replace the input nodes and links with mutable objects for the simulation. nodes = nodes; links = d3.map(links, (_, i) => ({ source: LS[i], target: LT[i] })); // Compute default domains. if (G && nodeGroups === undefined) nodeGroups = d3.sort(G); // Construct the scales. const color = nodeGroup == null ? null : d3.scaleOrdinal(nodeGroups, ["#4E79A7","#F28F2B","#E15759",]); // Construct the forces. const forceNode = d3.forceManyBody(); const forceLink = d3.forceLink(links).id(({ index: i }) => N[i]); if (nodeStrength !== undefined) forceNode.strength(nodeStrength); if (linkStrength !== undefined) forceLink.strength(linkStrength); const simulation = d3 .forceSimulation(nodes) .force("link", forceLink) .force("charge", forceNode).force("y", d3.forceY(function(d){ console.log(d) if(d.colour == "Parent Lineage"){ return height/3 } else if (d.colour == "Child Lineage"){ return 2*height/3 } else if (d.colour == "Recombinant Lineage") { return height/2 } })) .force("center", d3.forceCenter()) .on("tick", ticked); const svg = d3 .create("svg") .attr("width", width) .attr("height", height) .attr("viewBox", [-width / 2, -height / 2, width, height]) .attr("style", "max-width: 100%; height: auto; height: intrinsic;"); const link = svg .append("g") .attr("stroke", typeof linkStroke !== "function" ? linkStroke : null) .attr("stroke-opacity", linkStrokeOpacity) .attr("distance", 230) .attr( "stroke-width", typeof linkStrokeWidth !== "function" ? linkStrokeWidth : null ) .attr("stroke-linecap", linkStrokeLinecap) .selectAll("line") .data(links) .join("line"); const node = svg .append("g") .attr("fill", nodeFill) .attr("stroke", nodeStroke) .attr("stroke-opacity", nodeStrokeOpacity) .attr("stroke-width", nodeStrokeWidth) // SM: change // .selectAll("circle") .selectAll("g") .data(nodes) // SM: change // .join("circle") .join("g") // SM: change // .attr("r", nodeRadius) .call(drag(simulation)); // SM: change // append circle and text to node (selection of all elements corresponding to each node) node.append("circle").attr("r", nodeRadius); node .append("text") .text(({ index: i }) => T[i]) .attr("fill", "gray") .attr("stroke", "none") .attr("font-size", "1em"); if (W) link.attr("stroke-width", ({ index: i }) => W[i]); if (L) link.attr("stroke", ({ index: i }) => L[i]); if (G) node.attr("fill", ({ index: i }) => color(G[i])); if (T) node.append("title").text(({ index: i }) => T[i]); if (invalidation != null) invalidation.then(() => simulation.stop()); function intern(value) { return value !== null && typeof value === "object" ? value.valueOf() : value; } function ticked() { link .attr("x1", (d) => d.source.x) .attr("y1", (d) => d.source.y) .attr("x2", (d) => d.target.x) .attr("y2", (d) => d.target.y); node.attr("transform", (d) => `translate(${d.x} ${d.y})`); // SM: change // instead of moving the circle centers we transform the whole // .attr("cx", d => d.x) // .attr("cy", d => d.y); } function drag(simulation) { function dragstarted(event) { if (!event.active) simulation.alphaTarget(0.3).restart(); event.subject.fx = event.subject.x; event.subject.fy = event.subject.y; } function dragged(event) { event.subject.fx = event.x; event.subject.fy = event.y; } function dragended(event) { if (!event.active) simulation.alphaTarget(0); event.subject.fx = null; event.subject.fy = null; } return d3 .drag() .on("start", dragstarted) .on("drag", dragged) .on("end", dragended); } return Object.assign(svg.node(), { scales: { color } }); }35:T1090,chart = function(rooted_tree){ const root = d3.hierarchy(rooted_tree); root.x0 = dy / 2; root.y0 = 0; root.descendants().forEach((d, i) => { d.id = i; d._children = d.children; if (d.depth && d.data.name.length !== 7) d.children = null; }); const svg = d3.create("svg") .attr("viewBox", [-margin.left, -margin.top, width, dx]) .style("font", "10px sans-serif") .style("user-select", "none"); const gLink = svg.append("g") .attr("fill", "none") .attr("stroke", "#555") .attr("stroke-opacity", 0.4) .attr("stroke-width", 1.5); const gNode = svg.append("g") .attr("cursor", "pointer") .attr("pointer-events", "all"); function update(source) { const duration = d3.event && d3.event.altKey ? 2500 : 250; const nodes = root.descendants().reverse(); const links = root.links(); // Compute the new tree layout. tree(root); let left = root; let right = root; root.eachBefore(node => { if (node.x < left.x) left = node; if (node.x > right.x) right = node; }); const height = right.x - left.x + margin.top + margin.bottom; const transition = svg.transition() .duration(duration) .attr("viewBox", [-margin.left, left.x - margin.top, width, height]) .tween("resize", window.ResizeObserver ? null : () => () => svg.dispatch("toggle")); // Update the nodes… const node = gNode.selectAll("g") .data(nodes, d => d.id); // Enter any new nodes at the parent's previous position. const nodeEnter = node.enter().append("g") .attr("transform", d => `translate(${source.y0},${source.x0})`) .attr("fill-opacity", 0) .attr("stroke-opacity", 0) .on("click", (event, d) => { d.children = d.children ? null : d._children; update(d); }); nodeEnter.append("circle") .attr("r", 2.5) .attr("fill", d =>group_numbers(d.data.estimated_count)) .attr("stroke", "black") .on("mouseover", function(){return tooltip.style("visibility", "visible");}) .on("mousemove", function(){return tooltip.style("top", (event.pageY)+"px").style("left",(event.pageX)+"px");}) .on("mouseout", function(){return tooltip.style("visibility", "hidden");}); nodeEnter.append("text") .attr("dy", "0.31em") .attr("x", d => d._children ? -6 : 6) .attr("text-anchor", d => d._children ? "end" : "start") .text(d => d.data.name) .clone(true).lower() .attr("stroke-linejoin", "round") .attr("stroke-width", 3) .attr("stroke", "white"); // Transition nodes to their new position. const nodeUpdate = node.merge(nodeEnter).transition(transition) .attr("transform", d => `translate(${d.y},${d.x})`) .attr("fill-opacity", 1) .attr("stroke-opacity", 1); // Transition exiting nodes to the parent's new position. const nodeExit = node.exit().transition(transition).remove() .attr("transform", d => `translate(${source.y},${source.x})`) .attr("fill-opacity", 0) .attr("stroke-opacity", 0); // Update the links… const link = gLink.selectAll("path") .data(links, d => d.target.id); // Enter any new links at the parent's previous position. const linkEnter = link.enter().append("path") .attr("d", d => { const o = {x: source.x0, y: source.y0}; return diagonal({source: o, target: o}); }); // Transition links to their new position. link.merge(linkEnter).transition(transition) .attr("d", diagonal); // Transition exiting nodes to the parent's new position. link.exit().transition(transition).remove() .attr("d", d => { const o = {x: source.x, y: source.y}; return diagonal({source: o, target: o}); }); // Stash the old positions for transition. root.eachBefore(d => { d.x0 = d.x; d.y0 = d.y; }); } // create a tooltip var tooltip = d3.select("#tooltip") .append("div") .style("position", "absolute") .style("visibility", "hidden") .text("I'm a circle!"); update(root); return svg.node(); 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30:{"id":"6475ff63fc3ebfb3","slug":null,"title":"SARS-CoV-2 Lineage Tree","thumbnail":"005b79a0faa66cfc6dc0a4a72f3614d33e44c07817c584f78d3ed462a83e9363","access_level":"public","create_time":"$D2022-11-25T02:46:38.179Z","update_time":"$D2023-08-16T16:29:04.682Z","view_time":null,"first_public_time":"$D2022-11-25T17:06:24.961Z","has_unpublished_edits":null,"fork":{"id":"e257f81c745be447","slug":"collapsible-tree","title":"Collapsible tree","owner":{"id":"863951e3ebe4c0ae","login":"d3","name":"D3"}},"stars":0,"starred":false,"owner":{"type":"team","id":"1157d8a0e7ace7c6","login":"cvr-bioinfo","name":"CVR Bioinformatics","avatar_url":"https://avatars-next.observableusercontent.com/022d43de01273d3d19941f51b9b2c412d919f4a74262d41e14c5379b08c7d5f2","tier":"education_2026","bio":""},"version":3061,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"1c0f023b5e4ac4b5","login":"kieran12lamb","name":"Kieran 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\nThe corresponding files used to generate the tree can be found here:
https://github.com/cov-lineages/pango-designation
\n\nLineage tips are coloured by estimated sequence counts retrieved from COG-UK and can be accessed here: https://www.cogconsortium.uk/priority-areas/data-linkage-analysis/public-data-analysis/ \n
\nThe Tree is built using the collapsable tree template which can be found here: https://observablehq.com/@d3/collapsible-tree","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2924,"value":"- - -","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":455,"value":"## Select Node to Root From\n\nThe PANGO lineage tree is very large, so often it's desirable to root the tree from a convenient sub-lineage to minimise the number of unnecessary nodes visualised. You can type the lineage to root by below:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":502,"value":"viewof text = Inputs.text({label: \"Lineage to Root from\",value:\"Root\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2922,"value":"If an alternative root has been selected you can view the parental lineage tree by clicking the box below and selecting the parent of interest:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":894,"value":"viewof parent_toggle = Inputs.toggle({label: \"View Parent Tree\", value: false})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":606,"value":"viewof parent_select = Inputs.radio(parent_list, {label: \"Parent lineages are \", value: parent_list[0]})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2963,"value":"- - -","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1973,"value":"Plot.legend({\n label:\"Estimated Lineage Counts\",\n width:1200,\n color: {\n domain:[0,1000,5000,10000,20000,30000,40000,50000,60000,70000,80000,90000,1000000],\n scheme:\"YlOrRd\",\n // type:\"linear\",\n // nice:true\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":652,"value":"tree_plot = {\n if (parent_toggle == false){\n return chart(rooted_tree)\n }else{\n return chart(parent_tree)\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2912,"value":"Click on each node to expand its descendants","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":404,"value":"DOM.download(() => serialize(tree_plot), '_pango_tree.svg', \"Save as SVG\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2930,"value":"DOM.download(\n new Blob(['Children lineages of ' + text + ':\\n' + children_list.join(',')], {type: \"text/csv\"}), 'children_lineages.txt', \"Save list of children lineages\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2926,"value":"- - -","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2014,"value":"## Build your own Tree Subset\n\nYou can also build a custom subset tree by selecting a lineage to root by and providing a comma-separated list of descendant lineages to include below:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2781,"value":"viewof subset_root = Inputs.text({label: \"Lineage to Root from\",value:\"Root\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2102,"value":"viewof lineage_text_area = Inputs.text({label: \"Enter lineages\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2368,"value":"subset_chart = chart(filter_tree_data(lineage_text_area,query_data,subset_rooted_tree))\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2979,"value":"DOM.download(() => serialize(subset_chart), 'subset_pango_tree.svg', \"Save as SVG\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2971,"value":"- - -","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":729,"value":"## Recombinant Graph","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2866,"value":"For lineages that have arisen through a recombination event (i.e. any X based lineage), you can use this graph to see recombination points between parental and descendant lineages. Simply type a recombinant lineage of interest below:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2881,"value":"viewof recombinant_selection = Inputs.text({label: \"Select Recombinant To View\",value:\"XBB\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1121,"value":"recombinant_graph= { if (filtered_recombinant_graph_data.links.length!=0){\n return Swatches(d3.scaleOrdinal(new Set(filtered_recombinant_graph_data.nodes.map(function(d){return d.colour})), [\"#4E79A7\",\"#F28F2B\",\"#E15759\",]), {\n // columns: \"150px\",\n // swatchWidth: 120,\n // swatchHeight: 10,\n marginLeft: 60 }) \n }\n return \"No recombinant lineage given\"\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1086,"value":"recombinant_plot = {\n if (filtered_recombinant_graph_data.links.length==0){\n return ForceGraph(filtered_recombinant_graph_data, {\n nodeId: (d) => d.id, // node identifier, to match links\n nodeGroup: (d) => d.colour, // group identifier, for color\n nodeTitle: (d) => d.id, // hover text\n nodeLabel: (d) => d.id, // hover text\n linkStrength:0.015,\n width:0,\n height: 0,\n invalidation // stop when the cell is re-run\n }) \n }else{\n return ForceGraph(filtered_recombinant_graph_data, {\n nodeId: (d) => d.id, // node identifier, to match links\n nodeGroup: (d) => d.colour, // group identifier, for color\n nodeTitle: (d) => d.id, // hover text\n nodeLabel: (d) => d.id, // hover text\n linkStrength:0.015,\n width:400,\n height: 300,\n invalidation // stop when the cell is re-run\n })\n \n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2869,"value":"DOM.download(() => serialize(recombinant_plot), 'recombinant_graph.svg', \"Save as SVG\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2957,"value":"
\n- - -","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1598,"value":"# Bibliography","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1613,"value":"bibliography","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":542,"value":"# Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2812,"value":"### Tree Subset Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2785,"value":"subset_rooted_tree = {\n let filter_data = query_data.filter(d=> d.name == subset_root )[0]\n if (typeof(filter_data) === 'undefined'){\n return data\n }\n return filter_data\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2541,"value":"function filterByList(array1, array2) {\n // create a new array to store the filtered items\n const filteredList = [];\n\n // iterate through the original list\n for (let i = 0; i < array1.length; i++) {\n // if the current item is also in the filter list, add it to the filtered list\n if(array2.find(obj => obj.name === array1[i].name)){\n filteredList.push(array1[i]);\n }\n }\n // return the filtered list\n return filteredList;\n}\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2534,"value":"function replaceObjectInArrayByName(array1, array2) {\n // Create a new array that will hold the modified objects.\n const newArray = [];\n\n // Loop over the first array.\n for (let i = 0; i < array1.length; i++) {\n // Get the name of the current object.\n const name = array1[i].name;\n\n // Find the corresponding object in the second array.\n const matchingObject = array2.find(obj => obj.name === name);\n\n // If a matching object was found, replace the object in the first array with it.\n if (matchingObject) {\n newArray.push(matchingObject);\n } else {\n newArray.push(array1[i]);\n }\n }\n\n // Return the new array.\n return newArray;\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2187,"value":"function get_path_to_root(node,node_list){\n let last_node = node\n let array_of_parents = []\n console.log(node)\n if (node.alias_parent !== \"Recombinant\"){\n while (node.alias_parent != \"Root\") {\n const parent_node = node_list.filter((d,i)=> {if(d.name == node.alias_parent){return d}})[0]\n array_of_parents.push(parent_node)\n node = parent_node\n }\n }else{\n console.log(node)\n }\n \n return array_of_parents\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2316,"value":"function node_compare(a,b) {\n if (a.full_name.split(\".\").length < b.full_name.split(\".\").length)\n return -1;\n if (a.full_name.split(\".\").length > b.full_name.split(\".\").length)\n return 1;\n return 0;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2184,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":644,"value":"children_list = {\n if (parent_toggle == false){\n let children = []\n d3.hierarchy(rooted_tree).descendants().forEach((d,i) => {if (i!=0){children.push(d.data.name)}})\n return children\n }else{\n let children = []\n d3.hierarchy(parent_tree).descendants().forEach((d,i) => {if (i!=0){children.push(d.data.name)}})\n return children\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2814,"value":"## Main Tree Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2840,"value":"#### URLs","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1499,"value":"pango_tree_url = \"https://raw.githubusercontent.com/kieran12lamb/PangoTreeFiles/master/julia_lineages.json\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1533,"value":"node_list_url = \"https://raw.githubusercontent.com/kieran12lamb/PangoTreeFiles/master/node_list.json\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1549,"value":"recombinant_graphs_url = \"https://raw.githubusercontent.com/kieran12lamb/PangoTreeFiles/master/recombinant_graphs.json\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1616,"value":"variables_url = \"https://raw.githubusercontent.com/kieran12lamb/PangoTreeFiles/master/variables.json\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1620,"value":"variables = fetch(variables_url)\n .then(response => {\n return response.json();\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2862,"value":"### Datasets","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1497,"value":"data = fetch(pango_tree_url)\n .then(response => {\n return response.json();\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":492,"value":"rooted_tree = {\n let filter_data = query_data.filter(d=> d.name == text )[0]\n if (typeof(filter_data) === 'undefined'){\n return data\n }\n return filter_data\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":963,"value":"parent_tree = {\n if (parent_toggle == true){\n let parent_filter_data = query_data.filter(d=> d.name == parent_select )[0]\n if (typeof(parent_filter_data) === 'undefined'){\n return data\n }\n return parent_filter_data\n }\n return rooted_tree\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":806,"value":"parent_list = {\n if (rooted_tree.name == \"Root\" ){\n return [\"Root\"]\n }\n if (recombinant_list.has(rooted_tree.name) ){\n let recombinant_parents = [] \n query_data.forEach((d,i) => {if (( d.name == rooted_tree.name) && (d.parent != \"Recombinant\")){recombinant_parents.push(d.alias_parent)}})\n return recombinant_parents\n }\n return [rooted_tree.alias_parent]\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":448,"value":"query_data = fetch(node_list_url)\n .then(response => {\n // if (!response.ok) throw new Error(response.status);\n return response.json({typed: true});\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2856,"value":"### Colour","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1707,"value":"function log_scale_domain(value) {\n let max_log_value = Math.log(value)\n let min = Math.log(value)/10\n let array = []\n for (let index = 1; index <= 10; ++index) {\n array.push(Math.round(Math.exp(min*index)))\n }\n return array\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1390,"value":"function colorLegend(colorScale, options = {}) {\n let { tickPadding = 5, width = 110, marginRight = 80 } = options;\n return Plot.plot({\n marks: [\n Plot.cellX(colorScale.domain(), {\n y: colorScale.domain(),\n x: 0,\n color: colorScale.range()\n })\n ],\n y: {\n axis: \"right\",\n tickSize: 0,\n tickPadding\n },\n x: {\n axis: null\n },\n width,\n marginRight\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1908,"value":"interpolate_colours = d3.quantize(d3.interpolateHcl(\"#ffffbf\", \"#9e0142\"), 12)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1940,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2852,"value":"### Recombination Plot","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":996,"value":"recombinant_graph_data = fetch(recombinant_graphs_url)\n .then(response => {\n return response.json();\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1020,"value":"filtered_recombinant_graph_data = {\n if (recombinant_selection.includes(\".\")){\n return{\n \"links\":[],\n \"nodes\":[]}\n }\n let approved_links = recombinant_graph_data.links.filter(d => d.source == recombinant_selection || d.target == recombinant_selection)\n let approved_nodes = []\n for (let node in recombinant_graph_data.nodes){\n let contains_node = false\n node = recombinant_graph_data.nodes[node]\n for (let link in approved_links){\n link = approved_links[link]\n if (node.id == link.source || node.id == link.target){\n contains_node = true \n } \n }\n if (contains_node == true){\n approved_nodes.push(node)\n }\n }\n return{\n \"links\":approved_links.sort(function(a, b) {\n return a.target.localeCompare(b.target);\n }),\n \"nodes\":[...new Map(approved_nodes.map(item => [item.id, item])).values()].sort(function(a, b) {\n return a.colour.localeCompare(b.colour);\n })}\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":785,"value":"recombinant_list = new Set(query_data.map(d=> {if(d.name.includes(\"X\") && (d.name.includes(\".\") == false) ){return d.name}}).sort())","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":978,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2850,"value":"### Tree Chart Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":3,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":323,"value":"diagonal = d3.linkHorizontal().x(d => d.y).y(d => d.x)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":327,"value":"// tree = d3.tree().nodeSize([dx, dy])\ntree = d3.tree().nodeSize([dx, dy])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":275,"value":"dx =12","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":277,"value":"dy = width / 10","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":224,"value":"margin = ({top: 10, right: 120, bottom: 10, left:50})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":10,"value":"d3 = require(\"d3@6\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":402,"value":"serialize = {\n const xmlns = \"http://www.w3.org/2000/xmlns/\";\n const xlinkns = \"http://www.w3.org/1999/xlink\";\n const svgns = \"http://www.w3.org/2000/svg\";\n return function serialize(svg) {\n svg = svg.cloneNode(true);\n const fragment = window.location.href + \"#\";\n const walker = document.createTreeWalker(svg, NodeFilter.SHOW_ELEMENT);\n while (walker.nextNode()) {\n for (const attr of walker.currentNode.attributes) {\n if (attr.value.includes(fragment)) {\n attr.value = attr.value.replace(fragment, \"#\");\n }\n }\n }\n svg.setAttributeNS(xmlns, \"xmlns\", svgns);\n svg.setAttributeNS(xmlns, \"xmlns:xlink\", xlinkns);\n const serializer = new window.XMLSerializer;\n const string = serializer.serializeToString(svg);\n return new Blob([string], {type: \"image/svg+xml\"});\n \n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2858,"value":"### Various Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":2021,"value":"import {Pack} from \"@d3/pack\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2038,"value":"import {Sunburst} from \"@d3/sunburst\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1127,"value":"import {Legend, Swatches} from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1557,"value":"import {Treemap} from \"@d3/treemap\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":2837,"value":"### Bibliography","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":1604,"value":"cite = viewof bibliography","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1596,"value":"viewof bibliography = bib({\n Rambaut2020: 'Rambaut, A., Holmes, E.C., O’Toole, Á. et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 5, 1403–1407 (2020). https://doi.org/10.1038/s41564-020-0770-5',\n OToole2022: \"O'Toole Á, Pybus OG, Abram ME, Kelly EJ, Rambaut A. Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. BMC Genomics. 2022 Feb 11;23(1):121. doi: 10.1186/s12864-022-08358-2. PMID: 35148677; PMCID: PMC8832810.\",\n \n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1588,"value":"import { bib } from \"@stardisblue/citations\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W36","stdlib":"1"}} 31:"$30:body"