29:null 2a:["$","title",null,{"children":"Exploring SARS-CoV-2 intrahost variation in Omicron lineages. | Sergei Pond | Observable"}] 2f:T593,html`

${results.N} isolates analyzed	${results.S} NGS samples	${floatFormat(results.V / results.N)} AV per sample ${summaryH (results.VARS)}
${floatFormat(d3.sum(results.F) / results.N)} fixed AV per sample ${summaryH (results.F)}	${floatFormat(d3.sum(results.LF) / results.N)} low frequency AV per sample ${summaryH (results.LF)}	${floatFormat(results.SYN/results.N)} : ${floatFormat(results.NONSYN/results.N)} mean Syn : mean Non-Syn per sample

`30:T53d,vegalite ({ "$schema": "https://vega.github.io/schema/vega-lite/v4.json", "data": { "values": bySample[variantToView] ? bySample[variantToView] : [] }, "layer" : [ { "width": 800, "height": 80, "transform":[{ "density": "AF", //"bandwidth": 0.01 }], "mark": {type: "area", "opacity" : 0.2, tooltip : true, line : true}, "encoding": { "x": { "field": "value", "grid" : null, "title": "Allele Frequency", "type": "quantitative", "axis": {"grid": false} }, "y": { "field": "density", "type": "quantitative", "title" : "", "axis": {"grid": false} }, "color" : {"value" : "grey"}, } }, { "mark": {type: "tick", "opacity" : 0.5, tooltip : true, size : 10, thickness: 2}, "transform":[{ "calculate": "-0", "as": "placement" }], "encoding": { "x": { "field": "AF", "grid" : null, "title": "Allele Frequency", "type": "quantitative", "axis": {"grid": false} }, "y" : { "type": "quantitative", "field" : "placement" }, "color" : {"field" : "EFFECT"}, } }, ] }) 31:T80b,genomicDist = vegalite ({ "$schema": "https://vega.github.io/schema/vega-lite/v4.json", "config" : { "bar": {continuousBandSize : 3} }, "data": { "values": bySample [variantToView], }, "vconcat" : [ { "width": 800, "height" : 100, "selection": { "brush": {"type": "interval", "encodings": ["x"]} }, "mark": {"type": "bar", "tooltip": {"content": "data"}, "filled": true, "clip" : true}, "encoding": { "y": { "field": "AF", "type": "quantitative", "axis" : {"grid" : false, "title" : "Variant frequency", "orient" : "left"}, "scale" : {"type" : "linear", domain: [0,1]} }, "x" : { "field": "POS", "type": "quantitative", "axis" : {"grid" : false, "title" : "Genomic Position"}, "scale" : {zero:false, domainMin: 1, domainMax : 29903} }, "color" : { "field" : "cluster", "type" : "nominal", } } }, { "width": 800, "height" : 100, "selection": { "brush": {"type": "interval", "encodings": ["x"]} }, "mark": {"type": "bar", "tooltip": {"content": "data"}, "filled": true, "clip" : true}, "encoding": { "y": { "field": "AF", "type": "quantitative", "axis" : {"grid" : false, "title" : "Variant frequency", "orient" : "left"}, "scale" : {"type" : "linear", domain: [0,1]} }, "x" : { "field": "POS", "type": "quantitative", "axis" : {"grid" : false, "title" : "Genomic Position"}, "scale" : {"domain": {"selection": "brush"}, zero:false, domainMin: 1, domainMax : 29903} }, "color" : { "field" : "cluster", "type" : "nominal", } } //"shape": {"field": "species", "type": "nominal"} }] //"resolve": {"scale": {"y": "independent"}} })32:T429,aggregateByIsolate = { let variants_by_isolate = {}; _.each (accessions_by_isolate, (acc, iso)=> { let my_variants = {}; let valid_acc = _.filter (acc, (a)=>annotationData[a].collection_date >= date_range.range[0] && annotationData[a].collection_date <= date_range.range[1]); if (valid_acc.length == 0) return; variants_by_isolate [iso] = {}; variants_by_isolate [iso].tech = _.map (valid_acc, (a)=>annotationData[a].instrument_platform); variants_by_isolate [iso].date = annotationData[valid_acc[0]].collection_date.getTime(); _.each (valid_acc, (accn,i)=> { _.each (variantsBySample[accn], (v)=> { let vc = variantKey (v); if (!my_variants[vc]) { my_variants[vc] = _.clone (v); my_variants[vc].tech = []; } my_variants[vc].tech.push ([variants_by_isolate [iso].tech[i], v.DP4]); }); }); variants_by_isolate[iso].v = _.map (my_variants); }); return variants_by_isolate; }33:T72b,AV_presets = [["Empty list" , []], ["501Y metasignature" , pad_array(["nsp2/85","nsp2/501","nsp3/183","nsp3/370","nsp3/837","nsp3/890","nsp6/107","nsp6/260","exonuclease/496","helicase/47","helicase/599","E/71","S/18","S/26","S/69","S/98","S/138","S/144","S/215","S/243","S/417","S/484","S/501","S/655","S/681","S/701","S/716","S/1027","S/1118","S/1176","S/1264","ORF3a/57","ORF3a/171","N/205","N/235"])], ["alpha (B.1.1.7)" , pad_array (["913","ORF1a/1001","ORF1a/1708","5986","ORF1a/2230","ORF1a/3675","14676","15279","16176","S/69","S/144","S/501","S/570","S/681","S/716","S/982","S/1118","ORF8/27","ORF8/52","ORF8/73","N/3","N/235"])], ["beta (B.1.351)" , pad_array (["nsp2/85","ORF1ab/1655","ORF1ab/3353","S/80","S/215","S/484","S/501","S/701","ORF3a/57","ORF3a/171","E/71","N/205","22280","11287"])], ["gamma (P.1)" , pad_array (["733","2749","ORF1a/1118","ORF1a/1795","11287","12778","13860","S/20","S/26","S/417","S/484","S/501","S/1027","ORF8/92","N/80"])], ["delta (B.1.617.2)" , pad_array (["S/19","S/142","S/452","S/478","S/681","S/950","ORF3a/26","M/82","ORF7a/82","ORF7a/120","N/63","N/203","N/377"])], ["mu (B.1.621)" , pad_array (["3037","ORF1a/1055","ORF1a/1538","6037","ORF1a/3255","ORF1a/3729","13057","ORF1b/314","ORF1b/1342","18877","19035","20148","S/95","S/145","S/346","S/484","S/501","S/614","S/681","S/950","ORF3a/57","ORF8/11","ORF8/38","ORF8/67","N/205"])], ["omicron (B.1.1.529)" , pad_array (["NSP3/38", "NSP3/1069", "NSP3/1266", "NSP3/1892","NSP4/492","3C/132","NSP6/189","RDRP/323","exonuclease/42","S/67","S/95","S/142","S/212","S/339","S/371","S/373","S/375","S/417","S/440","S/446","S/477","S/478","S/484","S/493","S/496","S/498","S/501","S/505","S/547","S/614","S/655","S/679","S/681","S/764","S/796","S/856","S/954","S/969","S/981","E/9","M/3","M/19","M/63","N/13","N/203","N/204"])]]34:T7f5,spark = (data, range = { low: 0, high: 0}, margin = {left: 5, right: 20, top: 5, bottom: 5}, style = ({ line: { stroke: "#444", strokeWidth: 0.7 }, circle: { fill: "#f00", stroke: "none" }, margin: { left: 5, right: 20, top: 5, bottom: 5 }, dim: { width: 100, height: 30 } })) => { let x = d3.scaleLinear(); let y = d3.scaleLinear(); const width = style.dim.width; const height = style.dim.height; const xScale = x .range([margin.left, width - margin.right]) .domain(d3.extent(data, d => d.x)); const yScale = y .range([height - margin.bottom, margin.top]) .domain(d3.extent(data, d => d.y)); const last = { x: xScale(data[data.length - 1].x), y: yScale(data[data.length - 1].y) }; const svg = d3 .create("svg") .attr("width", width) .attr("height", height) .attr("viewBox", [0, 0, width, height]); const g = svg.append("g"); const line = d3 .line() .curve(d3.curveMonotoneX) .x(d => xScale(d.x)) .y(d => yScale(d.y)); const band = g .append("rect") .attr("x", margin.left) .attr("y", yScale(range.high)) .attr("width", width - margin.right) .attr("fill", style.line.stroke) .attr("opacity", 0.3) .attr("height", yScale(range.low) - yScale(range.high)); const path = g .append("path") .datum(data) .attr("d", line) .style("fill", "none") .style("stroke", style.line.stroke) .style("stroke-width", style.line.strokeWidth); const current = g .append("g") .attr("transform", d => `translate(${last.x},${last.y})`); const curr_circle = current .append("circle") .attr("r", 1.5) .style("fill", style.circle.fill) .style("stroke", style.circle.stroke); const curr_label_n = current .append("text") .attr("text-anchor", "right") .attr("dy", ".35em") .attr("pointer-events", "none") .attr("x", 5) .style("fill", style.circle.fill) .style("font", ".5em sans-serif") .text(`${data[data.length - 1].y}`); return svg.node(); }35:Td4d,html` `36:[] 2d:{"id":"eca281041a9a7ec2","slug":"exploring-sars-cov-2-intrahost-variation-in-omicron-lineag","title":"Exploring SARS-CoV-2 intrahost variation in Omicron lineages.","thumbnail":"be2c22ef579cc717ae37b8607a8bc9ab63296c3f017dd2034548cfb348e312ef","access_level":"public","create_time":"$D2021-12-07T11:32:07.075Z","update_time":"$D2021-12-17T14:54:58.371Z","view_time":null,"first_public_time":"$D2021-12-17T14:40:29.127Z","has_unpublished_edits":null,"fork":{"id":"dfca5ad82dd13a90","slug":"exploring-sars-cov-2-intrahost-variation-individual-sampl","title":"Exploring SARS-CoV-2 intrahost variation (individual samples)","owner":{"id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond"}},"stars":0,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024"},"version":1929,"publish_version":1929,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null}],"members":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Exploring SARS-CoV-2 intrahost variation in Omicron lineages.","cells":[{"id":0,"value":"md`# Exploring SARS-CoV-2 intrahost variation in Omicron lineages.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1257,"value":"md`All result processing takes place in the browser. \nYou can select a date range to restrict the analysis to using the widget below. Current date range : ${timeFmt(date_range.range[0])} - ${timeFmt(date_range.range[1])}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1336,"value":"md`**Figure 1**. Sample collection dates`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1288,"value":"viewof date_range = rs(samplesForSlider, d=>d.date, value=>d3.sum(value.values.map(d=>d.count)), {height: 140, yTicks:2,yScale:d3.scalePow().exponent(0.5),rangeFmt : (a,b)=>\"Recompute for \" + timeFmt(a) + \" : \" + timeFmt (b)})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1236,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1341,"value":"md`**Figure 2**. Diversity and divergence of allelic variation within samples`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1473,"value":"vegalite ({\n \"data\": {\"values\": dnd},\n \"width\" : 600,\n \"height\" : 150,\n \"layer\" : [{\n \"mark\": {\"type\" : \"line\", \"color\" : \"grey\"},\n \"encoding\": {\n \"x\": {\"field\": \"time\", \"type\": \"temporal\", \"axis\" : {\"grid\" : false, \"titleFontSize\" : 18, \"labelFontSize\" : 14}},\n \"y\": {\"field\": \"divergence\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, \"title\" : \"Divergence\", \"titleFontSize\" : 18, \"labelFontSize\" : 14}}\n }\n },\n {\n \"mark\": {\"type\" : \"circle\", \"fill\" : false, \"stroke\" : \"firebrick\"},\n \"encoding\": {\n \"x\": {\"field\": \"time\", \"type\": \"temporal\", \"axis\" : {\"grid\" : false, \"title\" : \"Sample Collection\", \"titleFontSize\" : 18, \"labelFontSize\" : 14}},\n \"y\": {\"field\": \"divergence\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, \"title\" : \"Divergence\", \"titleFontSize\" : 18, \"labelFontSize\" : 14}},\n \"size\" : {\"field\" : \"diversity\", \"type\": \"quantitative\"}\n }\n }\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1584,"value":"md`**Table 1.** Display the distribution of selected AVs in the samples`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1620,"value":"viewof AVpreset = Inputs.select(AV_presets, {label: \"Preset AVs\", format: x => x[0]})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1593,"value":"viewof AVs4table = Inputs.textarea({label: \"AVs to view\", \"value\" : AVpreset[1], submit: \"View\", placeholder: \"1023,S/18,S/440,ORF1a/5000\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1578,"value":"viewof search = Inputs.search(table1Data)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1581,"value":"viewof avtable = Inputs.table(search, {\n rows : 20,\n format : {\n AF : (d)=> html`${float_format (d3.mean (d))} ${summaryAF (d)}`,\n DP : (d)=> html`${float_format (d3.mean (d))} ${summaryDP (d)}`,\n Dates : (d)=>timeFmtT1 (d[0]) + \"-\" + timeFmtT1 (d[1])\n \n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1840,"value":"md`**Figure 2** Patterns of co-occurrence of selected AVs (rows: AVs, columns : samples) [select some in Table 1 to filter down]`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1845,"value":"Legend(AFcolor, {\n title: \"Allele Frequency\",\n ticks: 10,\n //tickFormat: \".2f\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1792,"value":"canvas = {\n const w = table1Image.length;\n if (w) {\n const h = table1Image[0].length;\n const R = 4;\n const context = DOM.context2d(h*R, w*R, 1);\n for (let i = 0; i < w; i++) {\n for (let j = 0; j < h; j++) {\n context.fillStyle = AFcolor (table1Image[i][j]);\n context.fillRect( j*R, i*R, R, R );\n }\n }\n return context.canvas;\n }\n return DOM.context2d(1,1,1).canvas;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":858,"value":"table2label = md`**Table 2**. Summary of all allelic variants found in the **${results.N}** samples. Mean AF : mean frequency of the variant in samples where it found; ≥50%, 10-50%, <10% : number of AVs within this AF range in the sample. Subpopulations counts the number of AF clusters with more than one AV based on OPTICS clustering.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":835,"value":"viewof table2 = Inputs.table (_.sortBy (_.map (aggregateByIsolate, (d,k)=>{\n let c = cov (_.map (d.v, (dd)=>dd.AF));\n let vc = _.countBy (_.map (d.v, (dd)=>dd.AF >= 0.5 ? \"≥50%\" : (dd.AF >= 0.1 ? \"10-50%\" : '<10%')));\n return ({'Sample' : k, 'AVs' : d.v.length, 'Runs' : d.tech.length, 'Mean AF' : c[0], '≥50%' : vc[\"≥50%\"], '10-50%' : vc[\"10-50%\"], '<10%' : vc[\"<10%\"], 'Subpopulations' : _.filter (fClusters[k], (d)=>d.length > 1).length});\n }), (d)=>-d.AVs), { \n rows : 15\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":149,"value":"viewof variantToView = autoSelect({\n options: _.keys (bySample),\n title: \"Select a sample to expore further\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":39,"value":"md`**Figure 4.** Distribution of allele frequencies for ${variantToView} and its smoothed kernel density`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":63,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":695,"value":"md`**Figure 5.** Allelic variants found in ${variantToView} and their inferred population clusters`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":675,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":962,"value":"viewof table3 = Inputs.table (_.sortBy (_.map (bySample[variantToView], (d)=>{\n return (_.extend ({'Position' : d.POS, 'AV' : variantKey(d, true), 'AF' : d.AF, 'Cluster' : d.cluster}, annotate_variant(d)));\n }), (d)=>d.POS), { \n rows : 15,\n format : {\n 'HaploRelRank' : (d)=>d.toFixed (6)\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":742,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1246,"value":"results = {\n let r = {};\n r.N = _.size (aggregateByIsolate);\n r.S = d3.sum (_.map (aggregateByIsolate, (d)=>d.tech.length));\n r.VARS = _.map (aggregateByIsolate, (d)=>d.v.length);\n r.V = d3.sum (r.VARS);\n r.F = _.map (aggregateByIsolate, (d)=>_.filter (d.v, v=>v.AF >= 0.8).length);\n r.SYN = d3.sum (_.map (aggregateByIsolate, (d)=>_.filter (d.v, v=>v.EFFECT=='SYNONYMOUS_CODING').length));\n r.NONSYN = d3.sum (_.map (aggregateByIsolate, (d)=>_.filter (d.v, v=>v.EFFECT=='NON_SYNONYMOUS_CODING').length))\n r.LF = _.map (aggregateByIsolate, (d)=>_.filter (d.v, v=>v.AF <= 0.15).length);\n return r;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1384,"value":"roundToDays = (date, d)=> {\n const F = (d*24*3600*1000);\n let dd = Math.floor ((date - epochStart)/F);\n return epochStart + F*dd ;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1345,"value":"computeDiversityAndDivergence = (data, variant_filter, bin_date) => {\n variant_filter = variant_filter || ((d)=>true);\n bin_date = bin_date || ((d)=> roundToDays (d.date, bin_date));\n let V = _.groupBy (_.map (data, d=> [d.date, _.filter (d.v, (v)=>variant_filter (v))]),(v)=>v[0]);\n let dvr = _.mapValues (V, (d)=>({'divergence' : d3.mean (d, (v)=>v[1].length)}));\n \n _.each (V, (vars, d)=> {\n let S = 0;\n if (vars.length > 1) {\n for (let i = 0; i < vars.length; i++) {\n let my_variants = new Set (_.map (vars[i][1], (v)=>variantKey (v,true)));\n for (let j = i + 1; j < vars.length; j++) {\n let mv2 = vars[j][1];\n let shared = _.filter (mv2, (v)=>my_variants.has (variantKey (v, true))).length;\n S += (my_variants.size + mv2.length - 2*shared);\n }\n }\n S = 2*S / (vars.length) / (vars.length - 1);\n }\n dvr[d]['diversity'] = S;\n });\n \n return _.map (dvr, (d, k)=>{d.time = +k; return d;});\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1422,"value":"dnd = computeDiversityAndDivergence (aggregateByIsolate)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":21,"value":"variantTable = _.filter (await obtainSourceData(null, {'url' : 'https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/intrahost/data/omicron.tsv.gz', 'tsv' : true}), (d)=>d.FILTER == \"PASS\" || (\"FILTER\" in d == false))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1166,"value":"variantsBySample = _.groupBy (variantTable, (d)=>d.Sample)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1223,"value":"tech = _.map (aggregateByIsolate, (d)=>_.map (d.tech, (dd)=>dd))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1355,"value":"epochStart = new Date(Date.UTC(2020, 0, 1, 0, 0, 0)).getTime()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1135,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1123,"value":"accessions_by_isolate = _.mapValues(_.groupBy (_.map (_.countBy (variantTable, (d)=>d.Sample), (v,k)=>[k, isolates_for_accessions[k]]), (d)=>d[1]), (a)=>_.map (a, (aa)=>aa[0]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1137,"value":"isolates_for_accessions = _.fromPairs (_.map (annotationData, (d)=>[d.run_accession, d.isolate]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1119,"value":"annotationData = _.fromPairs (_.map (_.filter (await obtainSourceData(null, {'url' : 'https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/intrahost/data/omicron-meta.tsv.gz', 'tsv' : true})), (d)=>[d.run_accession,d]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"byVariant = _.fromPairs (_.sortBy (_.toPairs (_.groupBy (variantTable, (v)=>variantKey(v))), (d)=>+d[0].split (\"|\")[0]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1925,"value":"_.filter (byVariant, (d)=>d[0].POS>23000&d[0].POS<24000)\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":173,"value":"equiv_map = {\n return {\n 'SYNONYMOUS_CODING' : 'Synonymous',\n 'NON_SYNONYMOUS_CODING' : 'Non-synonymous',\n '.' : 'Non-coding',\n 'STOP_GAINED' : 'Stop'\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":620,"value":"N = {\n return {\n samples : _.size (bySample) \n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":615,"value":"bySample = _.groupBy (variantTable, (d)=>d.Sample);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":944,"value":"fClusters = {\n let c = {};\n _.each (aggregateByIsolate, (s,v)=> {\n c[v] = dbscan.run(_.map (s.v, (d)=>[d.AF]), 0.1, 2);\n _.each (c[v], (vv, ci)=> {\n if (vv.length > 1) {\n _.each (vv, (idx)=> {\n s.v[idx].cluster = ci + 1;\n });\n } else {\n s.v[vv[0]].cluster = null;\n }\n });\n })\n return c;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":178,"value":"map2key = (d)=> {return d in equiv_map ? equiv_map[d] : \"Indel\"};","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":749,"value":"orderedSampleNames = _.fromPairs (_.map (_.sortBy (_.keys (bySample)), (d,i)=>[d,i]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":981,"value":"variantAnnotation = _.fromPairs (_.map (await d3.csv (\"https://raw.githubusercontent.com/spond/SARS-CoV-2-variation/master/variation/variant-annotation.csv\", d3.autoType), (d)=>[d.Coord + \"/\" + d.Codon,d]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1268,"value":"samplesForSlider = _.map (_.countBy (_.map (accessions_by_isolate, (d,k)=>annotationData[accessions_by_isolate[k][0]].collection_date.getTime())), (v,k)=>{return {'date' : new Date(+k), 'count' : v}})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1604,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1572,"value":"nuc_coordinates = {\n let equiv = {};\n _.each (site_equiv, (d,k)=> {\n _.each (d, (s)=> {\n equiv[s[0]] = s[1];\n })\n });\n return equiv;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1645,"value":"coordinates4table = {\n let nuc_coords = new Set ();\n _.each (AVs4table.replace (\" \",\"\").split (\",\"), (d)=>{\n let n = +nuc_coordinates [d];\n nuc_coords.add (n);nuc_coords.add (n+1); nuc_coords.add (n+2);\n });\n return nuc_coords;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1801,"value":"table1Image = {\n let selectedAVs = [];\n let sampleN = {};\n let N = 0;\n let letmein = new Set (_.map (avtable, (d)=>\"\" + d.Loc + d.AV + d.AA));\n _.each (byVariant, (v, k)=> { \n if (letmein.has (v[0].POS+v[0].REF + \">\" + v[0].ALT+v[0].TRID + \"/\" + v[0].AA)) {\n let AFs = _.map (v, (d)=>[d.Sample, d.AF]);\n let dates = _.map (v, (d)=>new Date (aggregateByIsolate[isolates_for_accessions[d.Sample]].date));\n _.each (AFs, (a)=> {\n if (! (a[0] in sampleN)) {\n sampleN [a[0]] = N++;\n }\n });\n let my_record = {\n 'Loc' : v[0].POS,\n 'T' : k,\n 'AFs' : AFs\n }\n selectedAVs.push (my_record);\n }\n });\n \n return _.map (_.sortBy (selectedAVs, (d)=>d.Loc), (d)=> {\n let afs = Array(N).fill(0);\n _.each (d.AFs, (a)=> {\n afs[sampleN[a[0]]] = a[1];\n });\n return afs;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1655,"value":"table1Data = {\n let selectedAVs = [];\n _.each (byVariant, (v, k)=> {\n let myN = +(k.split ('|')[0]);\n if (coordinates4table.has (myN)) {\n let AFs = _.map (v, (d)=>d.AF);\n let dates = _.map (v, (d)=>new Date (aggregateByIsolate[isolates_for_accessions[d.Sample]].date));\n let my_record = {\n 'Loc' : v[0].POS,\n 'AV' : v[0].REF + \">\" + v[0].ALT,\n 'AA' : v[0].TRID + \"/\" + v[0].AA,\n 'N' : AFs.length,\n 'AF' : AFs,\n 'DP' : _.map (v, (d)=>d.DP),\n 'Dates' : [d3.min (dates), d3.max (dates)]\n }\n selectedAVs.push (my_record);\n }\n });\n return _.sortBy (selectedAVs, (d)=>d.Loc);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":24,"value":"md`### Utility functions`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1847,"value":"import {Legend} from \"@d3/color-legend\"\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1692,"value":"summaryH = (d)=>histogram(d, {\n thresholds: 20,\n width : 60,\n height : 18,\n color: { fill: 'firebrick'},\n domainline: { size: 0.5, stroke: \"lightgrey\"},\n margin: { vertical: 0, horizontal: 0 }\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1754,"value":"summaryAF = (d)=>histogram(d, {\n thresholds: 20,\n domain : [0,1],\n width : 80,\n height : 20,\n color: { fill: 'firebrick'},\n domainline: { size: 0.5, stroke: \"lightgrey\"},\n margin: { vertical: 0, horizontal: 0 }\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1772,"value":"summaryDP = (d)=>histogram(d, {\n thresholds: 20,\n width : 80,\n height : 20,\n color: { fill: 'firebrick'},\n domainline: { size: 0.5, stroke: \"lightgrey\"},\n margin: { vertical: 0, horizontal: 0 }\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1260,"value":"timeFmt = d3.timeFormat (\"%Y/%m/%d\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1780,"value":"timeFmtT1 = d3.timeFormat (\"%Y%m%d\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":988,"value":"annotate_variant = (v)=> {\n if (v.CODON.length > 1) {\n let cdn = v.CODON.split ('/')[1].toUpperCase();\n for (let i = v.POS-1; i >= v.POS - 3; i--) {\n let tg = \"\" + i + \"/\" + cdn;\n if (tg in variantAnnotation) {\n let va = variantAnnotation[tg];\n return {\n 'Global Freq' : va['GlobalF'],\n 'Clades' : va['Clade0.75'] ? va['Clade0.75'].replace (/;/gi, ', ', true) : null,\n 'Predicted' : _.isNumber (va['Pred']) ? (va['Pred'] >= 0.001 ? 'Yes' : (va['Pred'] > 0 ? 'LF' : 'No')) : null,\n 'HaploRelRank' : _.isNumber (va['Haplo']) ? va['Haplo'] : '',\n 'LastSel' : va['LastSel']\n }\n }\n }\n }\n return {'Global Freq' : null, 'Clades' : null, 'Predicted' : null};\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1238,"value":"floatFormat = d3.format (\".2f\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":748,"value":"variantFreqBySample = (v)=> {\n let f = new Array (N.samples);\n for (let i = 0; i < N.samples; i++) f[i] = 0.;\n _.each (byVariant[v], (d)=>f[orderedSampleNames[d.Sample]] = d.AF);\n return f;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":476,"value":"generate_summary_stats = (counts)=> {\n return _.map (_.groupBy (counts, (d)=>d.kind), (c,k)=> {\n return {'kind' : k, \n 'mean' : d3.mean (c, (cc)=>cc.count), \n 'median' : d3.median (c, (cc)=>cc.count), \n 'range' : [d3.min (c, (cc)=>cc.count),d3.max (c, (cc)=>cc.count)],\n 'IQR' : [d3.quantile (c, 0.25, (cc)=>cc.count),d3.quantile (c, 0.75, (cc)=>cc.count)]\n };\n })\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":124,"value":"variantKey = (d, short)=> {return \"\" + (short ? \"\" : d.POS + \"|\") + d.REF + \">\" + d.ALT + \" \" + d.TRID + \" \" + d.AA}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":36,"value":"collision_entropy = (dist)=> {\n return -Math.log (dist, (sum,p)=> sum + p*p);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":251,"value":"cov = (freqs)=> {\n let sum = 0,\n sum2 = 0,\n n = freqs.length;\n \n _.each (freqs, (f)=> {sum += f; sum2 += f*f;});\n let mean = sum/n;\n let variance = sum2/n - mean*mean;\n return [mean,variance,Math.sqrt (variance)/mean,n];\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":439,"value":"float_format = d3.format (\".2f\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":485,"value":"frac_format = d3.format (\".2p\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":913,"value":"dbscan = new clustering.OPTICS()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1546,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1636,"value":"pad_array = (arr)=>_.map (arr, (d)=>d.toUpperCase())","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1850,"value":"AFcolor = d3.scaleSequentialSqrt([0, 1], d3.interpolateBlues)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"md`### Libraries/Modules`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1663,"value":"import {line, bar, area, histogram, ticks, range} from \"@hamzaamjad/tiny-charts\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1265,"value":"import {barRangeSlider as rs} from \"@spond/selector-with-confirmation\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1539,"value":"import {parseSiteList, site_equiv} from \"@spond/sars-cov-2-selected-sites\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":904,"value":"clustering = require('https://bundle.run/density-clustering@1.3.0')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":134,"value":"import {autoSelect, radio} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":415,"value":"import {table} from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":717,"value":"import {multiAutoSelect} from \"@spond/untitled/3\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":797,"value":"import {obtainSourceData} from \"@spond/exploring-sars-cov-2-intrahost-variation-descriptive\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1243,"value":"html``","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1241,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W36","stdlib":"1","titling":"auto"}} 2e:"$2d:body"