2d:null 2e:["$","title",null,{"children":"Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes | Sergei Pond | Observable"}] 33:T875,trends = vegalite ({ "config": { "style": { "cell": { "stroke": "transparent" } } }, "data": {"values": _.filter (plotData, (t)=>t.type != 'total' /*&& t.value >= 0.001*/)}, "columns" : 2, "facet": { "field": "type", "sort": {"field" : "site"}, "header": { "title" : "Global Prevalence During Analysis Period", "titleOrient" : "left", "titleFontSize": 20, "labelFontSize": 15, "labelOrient" : "right" } }, "spec": { "width": 300, "height": 60, "layer": [{ "mark": { "type": "area", "size": 2, "interpolate": "linear", "opacity" : 0.7, "color" : "gray" }, "encoding": { "x": { "field": "date", //timeUnit: "yearmonth", "type": "temporal", "axis": { "grid": 0, "titleFontSize": 18, "labelFontSize": 14, "labelAngle" : 30 }, "title": ""//"End of a three-month analysis window" }, "y": { "scale": { "type": "sqrt", "domain": [0, 1] }, "field": "value", "type": "quantitative", "title": "", "axis": { "grid": false, "titleFontSize": 18, "labelFontSize": 11 } } } }, { "transform": [ {"calculate": "datetime(2020,11,0)", "as": "detect"} ], "mark": { "type": "rule", "color" : "lightgrey", }, "encoding": { "size": {"value": 5}, "opacity" : {"value" : 0.1}, "x": { "field": "detect", "type": "temporal", } } }, { "mark": { "type": "point", "filled" : true, "tooltip" : true }, "encoding": { "x": { "field": "date", "type": "temporal", }, "y": { "scale": { "type": "sqrt", "domain": [0, 1] }, "field": "value" }, "color" :{ "condition": { "test": "datum['kind'] == '-'", "value": "darkblue" }, "value" : "darkred", }, "size" : {"field" : "pv", "type": "quantitative", "title" : " -log10(p)", "scale" : {"domain" : [1,15]}} } }] } })34:T53f,computeRR = (clade, cutoff, set)=> { let byMutation = {}; let total = [0,0]; _.each (data.duplicates, (haplo, id)=> { if (data.annotation.values[5] [data.annotation.meta[id][5]] == clade) { const beforeOrAfter = data.annotation.values[0] [data.annotation.meta[id][0]]; if (beforeOrAfter) { let before = beforeOrAfter <= cutoff ? 0 : 1; total [before] ++; _.each (data.variants.aa_variants[haplo], (aa, position)=> { if (aa != '?') { let tag = ("" + (+position+1)) + aa; if (tag in byMutation == false) { byMutation[tag] = [0,0]; } byMutation[tag][before] += 1; } }); } } }); byMutation = _.mapValues (byMutation, (value, mut)=> { return [value[0], value[1], value[0]/total[0], value[1]/total[1], value[1]*total[0] / (value[0]*total[1]), twoByTwo (value[0], value[1], total[0], total[1])]; }); if (set) byMutation = _.chain (byMutation).toPairs().filter (d=>set.has (d[0])).fromPairs().value() else byMutation = _.chain (byMutation).toPairs().filter (d=>Math.max (d[1][2],d[1][3]) >=minF && d[1][4]>=minRR && d[1][5] < 1e-6).fromPairs().value(); byMutation["total"] = total; return byMutation; }35:T49d,sharedRR = { let mutations = {}; _.each ([RR,RR2,RR3,RR4], (d,i)=> { _.each (d, (ddd, dd)=> { if (dd == 'total') return; if (dd in mutations) { mutations[dd].push (i); } else { mutations[dd] = [i]; } }); }); let shared = _.chain (mutations).toPairs ().filter ((d)=>d[1].length >= minClades).value(); let table_rows = []; _.each (shared, (d)=> { _.each ([RR,RR2,RR3,RR4], (r, i)=> { if (d[0] in r) { const rd = r[d[0]]; let row = { "Clade" : "V" + (i+1), "Codon" : parseInt (d[0]), "Mutation" : d[0], "Early" : fracFormat (rd[2]), "Late": fracFormat(rd[3]), "RR" : rd[4].toFixed (3), "p" : rd[5] < 1e-8 ? "*" : "", "Shared by" : d[1].length }; const coord = gene.toUpperCase() + "/" + parseInt (d[0]); if (coord in map2ORF1) { row["Coord"] = map2ORF1[coord]; } table_rows.push ( row ); } }); }); return table_rows; }36:[] 31:{"id":"ad245ab27afc7659","slug":"sars-cov-2-gene-trends","title":"Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes","thumbnail":"dd4d303ce1da9be14bf921e740e5eed9747c2599981fbc7007ac33fd4858a06e","access_level":"public","create_time":"$D2021-05-23T13:07:37.911Z","update_time":"$D2021-12-03T18:50:17.620Z","view_time":null,"first_public_time":"$D2021-06-08T21:05:12.366Z","fork":false,"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":880,"publish_version":880,"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":1,"collection":null,"type":"notebook","body":{"title":"Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes","cells":[{"id":0,"value":"# Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":625,"value":"viewof gene = select ({\n options: [\"S\",\"3C\",\"E\",\"endornase\",\"exonuclease\",\"helicase\",\"leader\",\"M\",\"methyltransferase\",\"N\",\"nsp2\",\"nsp3\",\"nsp4\",\"nsp6\",\"nsp7\",\"nsp8\",\"nsp9\",\"nsp10\",\"ORF3a\",\"ORF6\",\"ORF7a\",\"ORF8\",\"RdRp\"],\n description: \"Use this gene\",\n value: \"S\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":84,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":702,"value":"viewof signaturesToTrack = textarea({\n title: \"Mutations to plot (gene coordinates)\", \n spellcheck: false,\n value: \"5F,18F,26RS,67VS,80ASY,98F,138HY,215GHV,417NT,427N,484KQ,501Y,520S,655Y,681LHR,701V,716I,1027I,1117I,1118H,1176F,1219VC,1264L\",\n width: \"100%\",\n rows: 4,\n submit: \"Update\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":650,"value":"md`#### RR > 2 and frequency of ≥ 0.05% in **at least** two clades`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":744,"value":"viewof minRR = text({value: \"2\", description: \"Mininum relative risk\", submit: \"Update\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":747,"value":"viewof minF = text({value: \"0.0005\", description: \"Mininum frequency [0-1]\", submit: \"Update\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":750,"value":"viewof minClades = text({value: \"2\", description: \"Mininum clades sharing a mutation\", submit: \"Update\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":539,"value":"table (sharedRR)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":"### Data and libraries","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":74,"value":"plotData = _.chain (tabulated).map((d,i)=>_.map (d, (v,k)=>{\n if (k == \"total\") {\n return {'value' : v, 'type' : k , 'date' : unique_ranges[i][1]}\n }\n const CI = wilsonCI (v, d['total']-v);\n const site = parseInt (k);\n let pv = null;\n let kind = null;\n if (site in S_selection) {\n const P = _.find (S_selection[site], (ss)=>ss.to.getTime () == unique_ranges[i][1].getTime());\n if (P) {\n pv = -Math.log (P.p)/Math.log (10);\n kind = P.alpha > P.beta ? \"-\" : \"+\";\n }\n }\n return {'N' : d['total'], 'value' : v/d['total'], 'lb' : CI[0], 'ub' : CI[1], 'type' : gene + \" \" + (k.length >= 5? k : (k.length ==4 ? \" \" + k : \" \" + k)) , 'date' : unique_ranges[i][1], 'site' : site, 'pv' : pv, kind : kind};\n} )).flatten().value()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"wilsonCI = (S,F) => {\n const Z = 1.96;\n const CP = (S + 0.5 * Z * Z) / (S+F+Z*Z);\n const TERM = Z / (F+S+Z*Z) * Math.sqrt (S*F/(S+F) + Z*Z*0.25);\n return [CP - TERM, CP + TERM];\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"\ntabulated = {\n let tabulated = _.map (unique_ranges, (d)=>{return {'total' : 0}});\n _.each (_.groupBy (data.duplicates, (d)=>data.annotation.values[0][data.annotation.meta[d][0]]), (sd)=> {\n const myRecord = data.annotation.meta[sd[0]];\n const myDate = data.annotation.values[0][myRecord[0]];\n if (!myDate) return;\n _.each (unique_ranges, (ur,i)=> {\n if (myDate >= ur[0] && myDate <= ur[1]) {\n tabulated[i].total += sd.length;\n _.each (sd, (dupid)=> {\n const myVariants = data.variants.aa_variants[dupid];\n if (!myVariants) return;\n _.each (sites2track, (s2t)=> {\n if ((s2t[2] in myVariants) && (s2t[1].has ('?') || s2t[1].has (myVariants[s2t[2]]))) {\n tabulated[i][s2t[3]] = 1 + (tabulated[i][s2t[3]] ? tabulated[i][s2t[3]] : 0);\n }\n });\n });\n }\n });\n})\n return tabulated;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"unique_ranges = _.map (_.mapValues (_.groupBy (siteHistory, (d)=>d.from), d => [d[0].from, d[0].to]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":63,"value":"sites2track = _.map (mutsToTrack, (d)=>{\n return [d[0],new Set (_.map (d[1])),+d[0]-1,d[0]+d[1]]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":585,"value":"sigForRR = {\n let SSR = new Set();\n _.each (sites2track, (d)=> {\n _.each ([...d[1]], (r)=> {\n SSR.add ((+d[0]) + r);\n })\n });\n return SSR;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":711,"value":"mutsToTrack = _.map (signaturesToTrack.split (/,[\\s]*/), (d)=> {\n let m = d.match (/([0-9]+)(.+)/);\n \n if (m) {return [m[1], m[2]]};\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":278,"value":"shafer1 = [[\"18\",\"F\"],[\"26\",\"S\"],[\"95\",\"I\"],[\"144\",\"T\"],[\"215\",\"G\"],[\"246\",\"IM\"],[\"346\",\"K\"],[\"417\",\"N\"],[\"439\",\"K\"],[\"452\",\"RQ\"],[\"477\",\"N\"],[\"478\",\"R\"],[\"484\",\"KQ\"],[\"490\",\"S\"],[\"494\",\"P\"],[\"501\",\"Y\"],[\"655\",\"Y\"],[\"681\",\"HR\"]]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":339,"value":"set1 = [[\"5\",\"F\"],[\"18\",\"F\"],[\"26\",\"RS\"],[\"67\",\"VS\"],[\"80\",\"ASY\"],[\"98\",\"F\"],[\"138\",\"HY\"],[\"215\",\"GHV\"],[\"417\",\"NT\"],[\"427\",\"N\"],[\"484\",\"KQ\"],[\"501\",\"Y\"],[\"520\",\"S\"],[\"655\",\"Y\"],[\"681\",\"LHR\"],[\"701\",\"V\"],[\"716\",\"I\"],[\"1027\",\"I\"],[\"1117\",\"I\"],[1118,\"H\"],[\"1176\",\"F\"],[\"1219\",\"VC\"],[\"1264\",\"L\"]]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":284,"value":"predicted = _.map (recentS, (d)=>[d[0].site, '?'])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":856,"value":"predictedString = _.map (_.map (predicted, (d)=>d[0]+d[1])).join (\",\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":252,"value":"recentS = {\n const maxdate = new Date (2021,7,1).getTime();\n const subsetS = {};\n _.each (S_selection, (d, s)=> {\n let ss = _.filter (d, (dd)=>dd.to.getTime() <= maxdate && dd.alpha < dd.beta);\n if (ss.length) {\n subsetS [s] = ss;\n }\n });\n \n const latest = d3.max (_.filter (unique_ranges, (d)=>d[1].getTime() <= maxdate), (d)=>d[1]);\n \n return _.filter (_.map (_.filter (subsetS, (d)=>d.length >= 1 && _.find (d, (e)=>e.to.getTime()==latest.getTime())), (dd)=>_.sortBy (dd, (ddd)=>ddd.p)), (d)=> {\n let pass = true;\n for (let i = 1; i < d.length && pass; i++) {\n pass = d[i].to.getTime() < d[i-1].to.getTime();\n }\n return pass;\n });\n //_.filter (S_selection\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":194,"value":"S_selection = _.groupBy (_.filter (siteHistory, (d)=>d.gene == gene), (d)=>d.site)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":549,"value":"fracFormat = d3.format (\".3p\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":432,"value":"N = _.size (data.duplicates)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":633,"value":"data = loadVariantData (getVariantFileNames (gene))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":437,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":496,"value":"twoByTwo = (r11, r12, r21, r22)=> {\n const r1 = r11 +r12;\n const r2 = r21 +r22;\n const c1 = r11 + r21;\n const c2 = r12 + r22;\n const N = c1 + c2;\n \n let T = 0;\n let e = r1*c1/N;\n T += (r11-e)*(r11-e)/e;\n e = r1*c2/N;\n T += (r12-e)*(r12-e)/e;\n e = r2*c1/N;\n T += (r21-e)*(r21-e)/e;\n e = r2*c2/N;\n T += (r22-e)*(r22-e)/e;\n return chisqrprob(1,T);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":673,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":543,"value":"RR_table = (data)=>_.chain (data).toPairs().filter ((d)=>d[0] != 'total').sortBy ((d)=>parseInt(d[0])).map ((d)=> {\n return {\n \"Mutation\" : d[0], \n \"Early\" : fracFormat (d[1][2]), \n \"Late\": fracFormat(d[1][3]), \n \"RR\" : d[1][4].toFixed (3),\n \"p\" : d[1][5] < 1e-8 ? \"*\" : \"\"\n };\n}).value();","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":441,"value":"RR = computeRR (\"B.1.1.7\", new Date (2021,2,15))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":637,"value":"RR2 = computeRR (\"B.1.351\", new Date (2021,2,15))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":639,"value":"RR3 = computeRR (\"P.1\", new Date (2021,2,15))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":737,"value":"RR4 = computeRR (\"B.1.617.2\", new Date (2021,5,1))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":40,"value":"siteHistory = _.filter (await d3.csv (\"https://raw.githubusercontent.com/spond/SARS-CoV-2-variation/master/windowed-sites-fel-2021-07.csv\", d3.autoType), (d)=>true || d.alpha < d.beta)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":777,"value":"map2ORF1 = _.chain (reverseLookup).map ((d)=>[d.length > 1 ? d[1][0] : null,d[0][0]]).fromPairs().value()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"data","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"import {loadVariantData,getVariantFileNames} from \"@spond/spike-trends\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"d3 = require(\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":20,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":630,"value":"import {checkbox, radio, text, textarea,select,autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":536,"value":"import { table } from '@gnestor/table'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":774,"value":"import {reverseLookup} from \"@spond/sc2-genes\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":502,"value":"import {chisqrprob} from \"@jazztap/chi-squared-test\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W36","stdlib":"1","titling":"auto"}} 32:"$31:body"