30:Ta77,html`

${analysisSummary[lastDate].N} sequences ${trendAreaChart(_.map (analysisDates, (d)=>analysisSummary[d].N))}	${analysisSummary[lastDate].HA} haploptypes ${trendAreaChart(_.map (analysisDates, (d)=>analysisSummary[d].HA))}	${analysisDates.length} analyses ${timeFormat (analysisDatesConverted[0])} : ${timeFormat (analysisDatesConverted[analysisDatesConverted.length-1])}
${floatFormat (analysisSummary[lastDate].NNN)} NNN codons/haplo ${trendAreaChart(_.map (analysisDates, (d)=>analysisSummary[d].NNN))}	${analysisSummary[lastDate].issues.problematic.length} Problematic sites ${trendAreaChart(_.map (analysisDates, (d)=>analysisSummary[d].issues.problematic.length))}	${analysisSummary[lastDate].issues["N rich"].length} Sites with >10% NNN ${trendAreaChart(_.map (analysisDates, (d)=>analysisSummary[d].issues["N rich"].length))}
${selectionByDate[lastDate].P.size} positively selected sites (MEME) ${trendAreaChart(_.map (analysisDates, (d)=>selectionByDate[d].P.size))}	${selectionByDate[lastDate].N.size} negatively selected sites (FEL) ${trendAreaChart(_.map (analysisDates, (d)=>selectionByDate[d].N.size))}	${analysisSummary.pairs.length} Co-evolving pairs

`31:T4d1,md`

Column descriptions

**Site** : codon in S-gene **Note** : New (new in this analysis compared to the previous one); N-rich (this site has >5% NNN in the analyzed subsample); Problematic (this site has alignment/homology issues) **Selection** : what kind of selective pressure is this site under in the most recent analysis. **P-value** : Most recent analysis p-value on internal branches; MEME for positive; FEL for negative; chart shows p-values over all analyses; red line == significance level **Mean dN/dS** : Most recent abnalysis dN/dS (internal branches) estimated by FEL (100=infinity); chart shows this over all analyses. **Branches** : #of branches under selection (MEME) in the most recent analysis; chart shows this over all analyses. **Syn** : #synonymous subs along internal tree branches (SLAC) in the most recent analysis; chart shows this over all analyses. **NonSyn** : #non-synonymous subs along internal tree branches (SLAC) in the most recent analysis; chart shows this over all analyses. **Composition** : Top three codons found at this site in the analyzed subsample; the number of distinct other codons (plus their total count) are also shown.

`32:Tc9a,genomicDist = vegalite ({ "$schema": "https://vega.github.io/schema/vega-lite/v4.json", "data": { "values": _.flatten (_.map ( analysisSummary.subs.subs, (d,i)=> { let r = []; if (rate_options.indexOf ("S leaves") >= 0) r.push ({ 'POS' : +i+1, 'count' : d[0][0], 'type' : 'S leaves' }); if (rate_options.indexOf ("NS leaves") >= 0) r.push ({ 'POS' : +i+1, 'count' : d[0][1], 'type' : 'NS leaves' }); if (rate_options.indexOf ("S internal") >= 0) r.push ({ 'POS' : +i+1, 'count' : d[0][2], 'type' : 'S internal' }); if (rate_options.indexOf ("NS internal") >= 0) r.push ({ 'POS' : +i+1, 'count' : d[0][3], 'type' : 'NS internal' }); return r; } )), }, "vconcat" : [ { "width": 800, "height" : 100, "selection": { "brush": {"type": "interval", "encodings": ["x"]} }, "mark": {"type": "circle", "tooltip": {"content": "data"}, "filled": true, "clip" : true, 'interpolate' : 'monotone'}, "encoding": { "y": { "field": "count", "type": "quantitative", "axis" : {"grid" : false, "title" : "Count", "orient" : "left"}, "scale" : {"type" : rate_options.indexOf ("Sqrt") >= 0? "sqrt" : "linear"} }, "x" : { "field": "POS", "type": "quantitative", "axis" : {"grid" : false, "title" : "Genomic Position"}, "scale" : {zero:false, domainMin: 1} }, "color" : { "title" : "Substitution", "field" : "type", "type" : "nominal", } } }, { "width": 800, "height" : 100, "selection": { "brush": {"type": "interval", "encodings": ["x"]} }, "mark": {"type": "circle", "tooltip": {"content": "data"}, "filled": true, "clip" : true, 'interpolate' : 'step'}, "encoding": { "y": { "field": "count", "type": "quantitative", "axis" : {"grid" : false, "title" : "Count", "orient" : "left"}, "scale" : {"type" : rate_options.indexOf ("Sqrt") >= 0? "sqrt" : "linear"} }, "x" : { "field": "POS", "type": "quantitative", "axis" : {"grid" : false, "title" : "Genomic Position"}, "scale" : {"domain": {"selection": "brush"}, zero:false, domainMin: 1} }, "color" : { "field" : "type", "type" : "nominal", } } //"shape": {"field": "species", "type": "nominal"} }] //"resolve": {"scale": {"y": "independent"}} })33:T66c,settings = ({ 'BA.1 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA1.json', 'sig' : signaturesitesBA1} , 'BA.2 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA2.json', 'sig' : signaturesitesBA2} , 'BA.1 Jan 5th 2022' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/current-20220105.json', 'sig' : signaturesitesBA1} , 'BA.1 (to 03/01/22)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/current.json', sig : signaturesitesBA1}, 'BA.4 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA4.json', 'sig' : signaturesitesBA4}, 'BA.5 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA5.json', 'sig' : signaturesitesBA5}, 'BA.2.12.1 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA2.12.1.json', 'sig' : signaturesitesBA2121}, 'BA.2.75 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA275.json', 'sig' : signaturesitesBA275}, 'BA.2.75.2 (latest)' : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA2.75.2.json', 'sig' : signaturesitesBA2752}, "BA.5.1 (latest)" : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/BA5.1.json', 'sig' : signaturesitesBA51}, "Last 2 weeks" : {'url' : 'https://raw.githubusercontent.com/veg/omicron-selection/master/summaries/last2.json', 'sig' : signaturesitesBA2} })34:T93c,selectedSitesTable = { let ss = []; const resolved = new Set (['A','C','G','T']); const hc = analysisSummary[lastDate]['H']; const lastSel = selectionByDate [lastDate]; const in_last = table_filter.indexOf ("Selected in last analysis")>=0; const dateBeforeLast = analysisDates[analysisDates.length-2]; _.each (analysisSummary.sites, (info, s)=> { // filter here let site_object = {}; site_object ["Site"] = +s; site_object ["Note"] = ""; if (siteLabels[s]) { if (siteLabels[s].P && ! do_problematic) return; if (siteLabels[s].N && ! do_nrich) return; site_object ["Note"] = siteLabels[s].P ? "Problematic " : (siteLabels[s].N ? "N-rich " : ""); } site_object ["Selection"] = lastSel.P.has (s) ? "Positive" : lastSel.N.has (s) ? "Negative" : "Neutral"; if (site_object ["Selection"] == "Neutral") { if (in_last) return; } if (site_object ["Selection"] == "Positive") { site_object ["P-value"] = _.map (analysisSummary.sites[s].meme, (d)=>d[0]); if (s in signatureSites) site_object ["Note"] += "Signature"; if (dateBeforeLast) if (!selectionByDate[dateBeforeLast].P.has (s)) site_object ["Note"] += "New"; } else { if (dateBeforeLast) if (site_object ["Selection"] == "Negative" && !selectionByDate[dateBeforeLast].N.has (s)) site_object ["Note"] += "New"; if (s in signatureSites) site_object ["Note"] += "Signature"; site_object ["P-value"] = _.map (analysisSummary.sites[s].fel, (d)=>d[0]); } site_object ["Mean dN/dS"] = _.map (analysisSummary.sites[s].fel, (d)=>Math.min (d[5],100)); if (_.some (analysisSummary.sites[s].meme, (d)=>d[0] <= pval)) { site_object ["Branches"] = _.map (analysisSummary.sites[s].meme, (d)=>d[1]); } else { site_object ["Branches"] = []; } site_object ["Syn"] = _.map (analysisSummary.sites[s].slac, (d)=>d[0]); site_object ["NonSyn"] = _.map (analysisSummary.sites[s].slac, (d)=>d[1]); site_object ["Composition"] = analysisSummary.haplos[s-1]; //site_object ["NNN/Gaps"] = 1-d3.sum(_.filter (analysisSummary.haplos[s-1], (count, codon)=> _.every (codon, (c)=>resolved.has (c))))/hc; ss.push (site_object); }); return ss; }35:T4f9,haploRanks = { const N = analysisSummary[lastDate].N; const H = analysisSummary[lastDate].HA; let muts = []; let nucs = new Set (['A','C','G','T']); _.each (analysisSummary.counts, (d,i)=> { let siteN = 0; _.each (d, (count, codon)=> { if (_.every (codon, (ch)=>nucs.has (ch))) siteN += count; else if (codon == '---') siteN += count; }); _.each (d, (count, codon)=> { const F = count / siteN; if (F >= 0.0025) { if (_.every (codon, (ch)=>nucs.has (ch))) { let globalA = globalAnnotation[1][(i+1)]; if (globalA) {if (globalA == codon) return;} else {if (F>=0.5) return;} muts.push ([i,codon,count,F,analysisSummary.haplos_all[i][codon]]); } } }); }); let last_rank = muts.length + 1; let last_score = H+1; let current_rank = muts.length; return _.map (_.sortBy (muts, (d)=>-d[4]), (d,i)=> { if (d[4] < last_score) { last_score = d[4]; last_rank = current_rank; } d.push (Math.pow (10,last_rank/muts.length)); current_rank -= 1; return d; }); }36:T961,metaSigData = { let direct_counts = {}; _.each (meta501, (sig)=> { let wt = sig[1]; let om = sig[2]; let site = sig[0]; let states = _.toPairs (analysisSummary.counts[site-1]); let N = d3.sum (states, (d)=>d[1]); let counts = _.groupBy (states, (codon) => { return translate_ambiguous_codon ( codon[0] ); }); direct_counts[site] = {}; direct_counts[site]['Pos'] = +site; direct_counts[site]['WT'] = wt; direct_counts[site]['N501Y sig.'] = [...sig[2]].join ("/"); direct_counts[site]['Missing, %'] = 100*d3.sum (_.chain (counts).toPairs().filter ((d)=>d[0] == '?' || d[0].length > 1).map (d=>d[1]).map ((d)=>d3.sum(_.map (d, (c)=>c[1]))).value())/N; direct_counts[site]['Total mut., %'] = 100*d3.sum (_.sortBy (_.chain (counts).toPairs().filter ((d)=>d[0] != '?' && d[0].length == 1 && d[0] != sig[1]).map (d=>d[1]).map ((d)=>d3.sum(_.map (d, (c)=>c[1]))).value(), (d)=>-d).slice(0))/N; direct_counts[site]['Sig.mut, %'] = 100*d3.sum(_.map ([...sig[2]], (sigs)=> d3.sum (_.map (counts[sigs], (d)=>[d[0], d[1]/N]), (d)=>d[1]))); let sd = analysisSummary.subs.map[(+site)-1]; let RC = 0; let SC = 0; let TS = 0; let siteStates = {}; function recurse_node (node) { if (node.data.name in sd) { siteStates[node.data.name] = sd[node.data.name]; if (tree_object.isLeafNode (node)) return; if (node.parent) { let PS = translate_ambiguous_codon(siteStates[node.parent.data.name]); let MS = translate_ambiguous_codon (siteStates[node.data.name]); if (PS == sig[1]) { if (MS == sig[1]) { SC ++; } if (sig[2].has (MS)) { RC ++; } } if (MS.length == 1 && PS.length == 1 && MS != '?' && PS != '?' && MS != '-' && PS != '-') { TS ++; } } } else { siteStates[node.data.name] = siteStates[node.parent.data.name]; } _.each (node.children, (c)=>recurse_node(c)); } recurse_node(tree_object.nodes); direct_counts[site]['Total subs'] = TS; direct_counts[site]['Syn. subs'] = SC; direct_counts[site]['Sig. subs'] = RC; }); return _.map (direct_counts); }37:T992,reversionData = { let direct_counts = {}; _.each (signatureSites, (sig, site)=> { let wt = site[0]; let om = site[1]; let states = _.toPairs (analysisSummary.counts[(+site)-1]); let N = d3.sum (states, (d)=>d[1]); let counts = _.groupBy (states, (codon) => { return translate_ambiguous_codon ( codon[0] ); }); direct_counts[site] = {}; direct_counts[site]['Pos'] = +site; direct_counts[site]['WT'] = sig[0]; direct_counts[site]['Signature'] = sig[1]; direct_counts[site]['Missing, %'] = 100*d3.sum (_.chain (counts).toPairs().filter ((d)=>d[0] == '?' || d[0].length > 1).map (d=>d[1]).map ((d)=>d3.sum(_.map (d, (c)=>c[1]))).value())/N; direct_counts[site]['Total mut., %'] = 100*d3.sum (_.sortBy (_.chain (counts).toPairs().filter ((d)=>d[0] != '?' && d[0].length == 1 && d[0] != '-').map (d=>d[1]).map ((d)=>d3.sum(_.map (d, (c)=>c[1]))).value(), (d)=>-d).slice(1))/N; direct_counts[site]['Rev., %'] = 100*d3.sum (_.map (counts[sig[0]], (d)=>[d[0], d[1]/N]), (d)=>d[1]); direct_counts[site]['Syn. mut, %'] = 100*d3.sum (_.sortBy (counts[sig[1]], (c)=>-c[1]).slice (1), (d)=>d[1]/N); let sd = analysisSummary.subs.map[(+site)-1]; let RC = 0; let SC = 0; let TS = 0; let siteStates = {}; function recurse_node (node) { if (node.data.name in sd) { siteStates[node.data.name] = sd[node.data.name]; if (tree_object.isLeafNode (node)) return; if (node.parent) { let PS = translate_ambiguous_codon(siteStates[node.parent.data.name]); let MS = translate_ambiguous_codon (siteStates[node.data.name]); if (PS == sig[1]) { if (MS == sig[1]) { SC ++; } if (MS == sig[0]) { RC ++; } } if (MS.length == 1 && PS.length == 1 && MS != '?' && PS != '?' && MS != '-' && PS != '-') { TS ++; } } } else { siteStates[node.data.name] = siteStates[node.parent.data.name]; } _.each (node.children, (c)=>recurse_node(c)); } recurse_node(tree_object.nodes); direct_counts[site]['Total subs'] = TS; direct_counts[site]['Syn. subs'] = SC; direct_counts[site]['Rev. subs'] = RC; }); return _.map (direct_counts); }38:T434,consecutiveMutations = (ms, do_shuffle) => { let lookup = _.range (ms[0].length); if (do_shuffle) lookup = _.shuffle (lookup); let computeRepeats = (d, minL)=> { let lastR = -5; let currentRun = 0; let R4 = 0; for (let i = 0; i < d.length; i++) { if (d[lookup[i]]) { if (i == lastR + 1) { currentRun ++; lastR ++; } else { currentRun = 1; lastR = i; } } else { if (currentRun >= minL) { R4++; currentRun = 0; } } } if (currentRun >= minL) R4++; return R4; }; let bb = []; _.each (ms, (d,i)=> { let T = d3.sum (d); const minL = 3; let R4 = 0; if (T >= minL) { R4 = computeRepeats (d,minL); } bb.push ([T,R4,d]); }); return _.filter (bb, (d)=>d[1]); }39:T863,mutationPatterns = { let siteStates = {}; let si = []; _.each (signatureSites, (states, site)=> { let sidx = (+site)-1; let sd = analysisSummary.subs.map[sidx]; si.push (site); function recurse_node (node) { if (! (node.data.name in siteStates)) { siteStates [node.data.name] = []; } if (node.data.name in sd) { siteStates[node.data.name].push (sd[node.data.name]); } else { siteStates[node.data.name].push (siteStates[node.parent.data.name][si.length-1]); } _.each (node.children, (c)=>recurse_node(c)); } recurse_node(tree_object.nodes); }); let signature_vectors = {}; let node_names = []; function recurse_node2 (node) { if (tree_object.isLeafNode (node)) return; node_names.push (node.data.name); if (node.parent) { let sig = []; let mv = siteStates[node.data.name]; let pv = siteStates[node.parent.data.name]; //signature_vectors [node.data.name] = pv.length; for (let i = 0; i < pv.length; i++) { let codon = pv[i]; if (translate_ambiguous_codon (codon) == signatureSites[si[i]][1] && translate_ambiguous_codon (mv[i]) == signatureSites[si[i]][0]) { sig.push (1); continue; } sig.push (0); } signature_vectors [node.data.name] = sig; } _.each (node.children, (c)=>recurse_node2(c)); } recurse_node2(tree_object.nodes); signature_vectors = _.map (signature_vectors); signature_vectors.sort ((a,b)=> { for (let i = 0; i < a.length; i++) { if (a[i] < b[i]) return -1; if (b[i] > a[i]) return 1; } return 0; }); return [signature_vectors, node_names]; return _.flatten (_.map (signature_vectors, (d, j)=>_.map (d, (c,i)=> { return {'Pos' : si[i], 'REV' : c, 'Branch' : j} }))); }3a:T63b,plotPie = (values)=>{ return vegalite ({ "columns": 3, "hconcat": _.map ([[values.internal,"ω internal"],[values.leaves,"ω leaves"], [values.srv,"Syn rates"]], (d) => { return { "title" : d[1], "data" : {"values" : d[0]}, "encoding": { "theta": {"field": "1", "type": "quantitative", "stack": true}, "color": {"field": "0", "type": "quantitative", "title" : "Rate", "legend" : {"titleFontSize" : 14, "orient" : "right"}, "scale": { "domain" : [0,1,4], "type" : "sqrt", "clamp" : true, "scheme": "blueorange" } }}, "layer" : [ { "mark": {"type": "arc", "innerRadius": 50, "outerRadius" : 70, tooltip : true, padAngle : 0.0, strokeWidth : 1, strokeOpacity: 1}, "encoding" : { "stroke" : {value : "black"}, } }, { "mark": {"type": "text", "outerRadius" : 80, "fontSize" : 10}, "encoding": { "color" : {"value" : "black"}, "text": { "field": "0", "type": "nominal", "format" : ".2f", "condition": {"test": "datum['0'] <= 1.", "value": ""}, } } }, { "mark": {"type": "text", "outerRadius" : 40, "fontSize" : 10}, "encoding": { "color" : {"value" : "black"}, "text": { "field": "1", "type": "nominal", "format" : ".2p", "condition": {"test": "datum['0'] <= 1.", "value": ""} } } } ]} }), "view": {"stroke": null} }) }3b:T4da,plotD = (c)=>({ "data": {"values": _.filter (motifPlot (c), (d)=>d.t && d.t >= minDate2Display)}, "width" : 600, "height" : 300, "transform": [{ "joinaggregate": [{ "op": "sum", "field": "count", "as": "T", }], "groupby" : ["motif"] }, { "window": [{ "op": "sum", "field": "count", "as": "CC", }], "groupby" : ["motif"], "ignorePeers": false, "frame": [null, 0] }], "layer" : [{ "mark": {"type" : "line", "opacity" : 0.5, "size" : 4, "point" : {"size" : 32}, tooltip : true}, "encoding": { "x": { "field": "t", "type" : "temporal", "timeUnit": "monthdateyear", "scale" : {"zero" : false}, "axis" : {"grid" : false, "title" : "Sample Date", "titleFontSize" : 16} }, "y": {"field": clusters_cumulative ? "CC" : "count","type" : "quantitative", "axis" : {"grid" : false, "title" : "Sequences with motif", "titleFontSize" : 16}, "scale" : {"type" : clusters_log ? "symlog" : "linear"}}, "color" : {"field" : "motif", "title" : "Sequence Motif", legend : {"titleFontSize" : 16, "labelFontSize" : 12}, "sort" : {"field" : "T", "order" : "descending"}} } }] })3c:T1e97,display_tree = (T) => { let dim = treeDim.length ? _.map (treeDim.split ("x"), (d)=>+d) : null; let showAA = doAA.indexOf ("amino-acids") >= 0; let showInternal = doAA.indexOf ("show internal") >= 0; let showDifferences = doAA.indexOf ("differences from most common") >= 0; let showSYN = doAA.indexOf ("show syn. subs") >= 0; let showNONSYN = doAA.indexOf ("show non-syn. subs") >= 0; let showMUL = doAA.indexOf ("show only multiple subs") >= 0; var t = T.render({ height:dim && dim[0] || tree_object.getTips().length * 14, width:dim && dim[1] || 600, 'show-scale' : true, 'is-radial' : false, 'left-right-spacing': 'fit-to-size', 'top-bottom-spacing': 'fit-to-size', 'node_circle_size' : (n)=>0, 'draw-size-bubbles' : true, 'internal-names' : showInternal, 'node-span': bubbleSize } ); let node_labels = {}; let changesByBranch = null; let most_common = null; let S_subs = {}; let NS_subs = {}; let siteID = null; let subsB2 = null; t.label_counts = null; if (_.isArray (site4tree) && site4tree.length) { siteID = _.map (site4tree, (s)=>analysisSummary.subs.map [s]); subsB2 = _.map (site4tree, (s)=>analysisSummary.subs.SB2 [s]); } if (siteID) { if (!_.isArray (siteID)) { siteID = [siteID]; } _.each (siteID, (sd,idx)=> { let siteStates = {}; function recurse_node (node) { if (node.data.name in sd) { if (subsB2[idx] && (node.data.name in subsB2[idx])) { S_subs[node.data.name] = (subsB2[idx][node.data.name][0][0]) + (S_subs[node.data.name] ? S_subs[node.data.name] : 0); NS_subs[node.data.name] = (subsB2[idx][node.data.name][0][1]) + (NS_subs[node.data.name] ? NS_subs[node.data.name] : 0); } siteStates[node.data.name] = sd[node.data.name]; } else { siteStates[node.data.name] = siteStates[node.parent.data.name]; } _.each (node.children, (c)=>recurse_node(c)); } recurse_node(tree_object.nodes); _.each (siteStates, (s,n)=> { if (! (n in node_labels)) { node_labels [n] = []; } node_labels[n].push (s); }); }); let label_counts = {}; if (showAA) { for (let node in node_labels) { node_labels[node] = _.map (node_labels[node], (c)=> (c in translation_table ? translation_table[c] : '?')).join (""); if (!isRefSeq (node)) { label_counts[node_labels[node]] = (getCopyNumber (node)||1) + (label_counts[node_labels[node]] ? label_counts[node_labels[node]] : 0); } } } else { for (let node in node_labels) { node_labels[node] = node_labels[node].join (""); if (!isRefSeq (node)) { label_counts[node_labels[node]] = (getCopyNumber (node)||1) + (label_counts[node_labels[node]] ? label_counts[node_labels[node]] : 0); } } } t.label_counts = _.chain(label_counts).toPairs().sortBy ((d)=>-d[1]).map((d)=>({'pattern': d[0], 'count' : d[1]})).value(); if (showDifferences) { most_common = t.label_counts[0].pattern; } } else { // compute all substitutions per branch changesByBranch = {}; _.each (_.range (_.size(analysisSummary.subs.map)), (s)=> { let sd = analysisSummary.subs.map [s]; let siteStates = {}; function recurse_node (node) { if (node.data.name in sd) { siteStates[node.data.name] = sd[node.data.name]; if (node.parent) { if (! (node.data.name in changesByBranch)) { changesByBranch [node.data.name] = {}; } changesByBranch [node.data.name][s+1] = [siteStates[node.parent.data.name], sd[node.data.name]]; } } else { siteStates[node.data.name] = siteStates[node.parent.data.name]; } _.each (node.children, (c)=>recurse_node(c)); } recurse_node(tree_object.nodes); }); } //console.log (changesByBranch); S_subs; NS_subs; let name_text = (d)=> { if (d) { if (most_common) { return _.map (d, (c,i) => {if (c == most_common[i]) return '.'; return c}).join (""); } } return d; } t.nodeLabel ((n)=> isRefSeq (n.data.name) ? n.data.name : (name_text(node_labels[n.data.name]) || "" + (getCopyNumber(n.data.name) || ""))); let c10_2 = d3.scaleOrdinal(d3.schemeDark2); const is_gap = (d)=> { let is_gap = _.countBy (d, (c)=>c); if (_.size (is_gap) == 1 && (_.keys(is_gap)[0] == '-' || _.keys(is_gap)[0] == 'N') ) return true; return false; } t.c10 = (d)=> { if (is_gap (d)) { return '#999'; } return c10_2 (d); } function sort_nodes (asc) { T.traverse_and_compute (function (n) { var d = 1; if (n.children && n.children.length) { d += d3.max (n.children, function (d) { return d["count_depth"];}); } n["count_depth"] = d; }); T.resortChildren (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); t.style_nodes ((e,n) => { if (isRefSeq (n.data.name)) return; let isint = (n.children && n.children.length); e.style ('fill', t.c10 (node_labels[n.data.name])); e.selectAll ("circle").style ('fill', t.c10 (node_labels[n.data.name])); e.selectAll ("title").data ([isint ? "" : n.data.name + ". Copies = " + getCopyNumber (n.data.name)]).join ("title").text ((d)=>d); }); t.style_edges ((e,n) => { if (node_labels) { let hilite = 0; if (showSYN) hilite += S_subs[n.target.data.name]; if (showNONSYN) hilite += NS_subs[n.target.data.name]; if (showMUL) hilite = hilite > 1; if (hilite) { e.style ('stroke', is_gap (node_labels[n.target.data.name]) ? 'grey' : 'firebrick').style ('stroke-width',5); } else { e.style ('stroke-width',null); } e.selectAll ("title").data (["" + S_subs[n.target.data.name] + " syn subs, " + NS_subs[n.target.data.name] + " non-syn subs"]).join ("title").text ((d)=>d); } if (changesByBranch) { if (changesByBranch[n.target.data.name]) { let non_gap = _.filter (_.toPairs (changesByBranch[n.target.data.name]), (d)=>!is_gap (d[1][1])); e.style ('stroke', null).style ('stroke-width',non_gap.length <= 8 ? non_gap.length : 8 ); e.selectAll ("title").data ([_.map (non_gap, (d)=> "" + d[0] + ":" + d[1][0] + "(" + translate_ambiguous_codon(d[1][0]) + ")" + "→" + d[1][1] + "(" + translate_ambiguous_codon(d[1][1]) + ")").join (", ")]).join ("title").text ((d)=>d); } else { e.style ('stroke-width',null); } } }); t.placenodes(); t.update(); return t; }3d:Td4d,html` `3e:[] 2e:{"title":"Selection analysis of Omicron S-gene sequences enabled by data from ","cells":[{"id":0,"value":"# Selection analysis of Omicron S-gene sequences enabled by data from $\"gisaid-logo\"$
","pinned":false,"hidden":false,"mode":"md"},{"id":1677,"value":"viewof analysis2view = Inputs.select ([\"BA.1 Jan 5th 2022\", \"BA.1 (to 03/01/22)\",\"BA.1 (latest)\", \"BA.2 (latest)\", \"BA.4 (latest)\", \"BA.5 (latest)\", \"BA.2.12.1 (latest)\", \"BA.5.1 (latest)\",\"BA.2.75 (latest)\", \"BA.2.75.2 (latest)\", \"Last 2 weeks\"], {\"label\" : \"Analysis to view\", \"value\" : \"Last 2 weeks\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":243,"value":"md`#### Sequence count by sampling dates`","pinned":false,"hidden":false,"mode":"ojs"},{"id":217,"value":"sampling_chart = {\n let definition = {};\n definition.data = samplingDates;\n definition.width = 800;\n definition.height = 120;\n definition.legendValues = [\n \"Min\",\n \"Max\",\n \"Avg\",\n \"Last\"\n ];\n definition.series = [\n {\n \"label\": \"Sequences\",\n \"metric\": \"count\",\n \"legend\": true,\n \"tooltip\": true,\n \"negativeY\": false,\n \"lineColor\": \"black\",\n \"fillColor\": \"firebrick\"\n }\n ];\n const c = new TimeSeriesChart(definition);\n return c.svg;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":248,"value":"md`#### Selection analysis overview`","pinned":false,"hidden":false,"mode":"ojs"},{"id":258,"value":"viewof table_filter = Inputs.checkbox([\"Problematic\", \"N-rich\", \"Selected in last analysis\"], {value: [\"N-rich\",\"Selected in last analysis\" ], label: html`Include sites`, format: x => html`${x}`})","pinned":false,"hidden":false,"mode":"ojs"},{"id":63,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":152,"value":"md`>_Values are based on the most recent analysis (${timeFormat (analysisDatesConverted[analysisDatesConverted.length-1])}). Line charts show trends over successive analyses runs (~daily)_`","pinned":false,"hidden":false,"mode":"ojs"},{"id":162,"value":"md`#### Selected site report`","pinned":false,"hidden":false,"mode":"ojs"},{"id":165,"value":"viewof search = Inputs.search(selectedSitesTable)","pinned":false,"hidden":false,"mode":"ojs"},{"id":566,"value":"viewof table_composition = Inputs.checkbox([\"Composition as AA\"], {value: [], label: \"\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":173,"value":"viewof avtable = Inputs.table(search, {\n rows : 20,\n format : {\n \"Type\" : (d)=> {\n return d;\n },\n \"Note\" : (d)=>html`${d}`,\n \"Composition\" : (d)=>html`${compositionString(d)}`,\n \"P-value\" : (d)=>html`${pvFormat(d[d.length-1])} ${trendPVChart(d)}`,\n \"Mean dN/dS\" : (d)=>html`${floatFormat(d[d.length-1])} ${trendOmegaChart(d)}`,\n \"Branches\" : (d)=>d.length ? html`${d[d.length-1]} ${trendOmegaChart(d)}` : \"\",\n \"Syn\" : (d)=>html`${floatFormat(d[d.length-1])} ${trendOmegaChart(d)}`,\n \"NonSyn\" : (d)=>html`${floatFormat(d[d.length-1])} ${trendOmegaChart(d)}`,\n //\"Composition\" : (d)=> plotComposition (_.map (d, (d,k)=>({'Codon' : k, 'Count' : d})))\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":816,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":717,"value":"md`#### Co-evolving site report`","pinned":false,"hidden":false,"mode":"ojs"},{"id":743,"value":"mermaid`\n %%{init: {'theme': 'base', 'themeVariables': { 'clusterBkg' : '#FFF', 'clusterBorder' : '#000', 'primaryColor': 'lightgrey', 'edgeLabelBackground':'white', 'tertiaryColor': '#fff0f0', 'fontSize' : \"16px\", 'fontFamily' : 'arial', 'lineColor' : 'rgba(0,0,0,0.25)'}}}%%\n ${coevolvingPairs}\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":826,"value":"md`Sites found to be co-evolving thorough a [Bayesian Graphical Model](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732215/) analysis. PP == posterior probability of conditional non-independence of sites (i.e. substitutions at one site along internal branches coincide with substitutions along the second site).`","pinned":false,"hidden":false,"mode":"ojs"},{"id":579,"value":"md`#### Predicting mutations that can spread.\n\nBased on a simpler version of the epi.score featured developed in [Maher et al](https://www.medrxiv.org/content/10.1101/2021.06.21.21259286v1.abstract). All resolved codons occuring at ≥0.5% are considered. We then compute how many unique haplotypes each mutation occurs in, rank them, compute rank percetile p and transform it to 10^p. High score is interpreted as more likely to spread (close 10); it is reported only for mutations that are currently sub-consensus (<50%). Other clade columns refer to mutation frequency and score in pre-Omicron data\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":677,"value":"viewof searchHT = Inputs.search(haploTable)","pinned":false,"hidden":false,"mode":"ojs"},{"id":681,"value":"viewof httable = Inputs.table(searchHT, {\n rows : 20,\n format : {\n \n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":847,"value":"md`#### Atypical site cluster evolution.\n\nTemporal trends of amino-acid motifs found at Clusters 1, 2, and 3 [defined in Martin et al](https://virological.org/t/selection-analysis-identifies-significant-mutational-changes-in-omicron-that-are-likely-to-influence-both-antibody-neutralization-and-spike-function-part-1-of-2/771). These clusters did not experience positive selection prior to the emergence of Omicron and were interpreted as contributing to adaptive/functional features of the Spike protein in Omicron. Cluster 1 = 339,371,373,375. Cluster 2 = 493,496,498,505. Cluster 3 = 764,856,954,969,981. \n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":857,"value":"viewof cluster_options = Inputs.checkbox([\"Only resolved\",\"Cumulative\",\"Log-scale\"], {\"value\" : [\"Only resolved\", \"Cumulative\",\"Log-scale\"], label: \"\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":863,"value":"viewof which_cluster = Inputs.select(_.keys (analysisSummary.clusters), {label: \"Show\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":873,"value":"vegalite (plotD(analysisSummary.clusters[which_cluster]))","pinned":false,"hidden":false,"mode":"ojs"},{"id":926,"value":"md`#### Evolutionary history of specific sites.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":912,"value":"viewof treeDim = text({placeholder : \"1024 x 800\", description: \"Tree dimension (height x width in pixels), leave blank to auto-scale\", submit: \"Resize\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":965,"value":"viewof site2viewIDX = multiAutoSelect ({\n options : _.map (analysisSummary.subs.map, (d,k)=>\"S/\" + (+k+1)),\n title: \"View these sites\",\n value : \"\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1253,"value":"Inputs.table (tree_rendering.label_counts || [], {\n format: {\n \"pattern\" : (d)=>html`${d}`\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":995,"value":"viewof doAA = Inputs.checkbox(\n [\"amino-acids\",\"differences from most common\",\"show internal\",\"show syn. subs\",\"show non-syn. subs\",\"show only multiple subs\"],{\"value\" : [\"amino-acids\",\"show non-syn. subs\"], label: \"Display options\" }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":933,"value":"tree_figure = tree_rendering.show()","pinned":false,"hidden":false,"mode":"ojs"},{"id":1836,"value":"md`#### Haplotype frequencies \nThe distribution of the number of sequences sharing the same nucleotide S hapolytpe (identical sequence up to missing data)`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1797,"value":"vegalite ({\n \"width\" : 300,\n \"height\" : 300,\n \"data\" : {\"values\" : haplotypeCounts},\n \"transform\": [{\n \"calculate\": \"log(datum.count)/log(10)\", \"as\": \"log_x\"\n }, {\n \"bin\": {\"maxbins\" : 30},\n \"field\": \"log_x\",\n \"as\": \"bin_log_x\",\n \"maxbins\" : 10\n }, {\n \"calculate\": \"pow(10, datum.bin_log_x)\", \"as\": \"x1\"\n }, {\n \"calculate\": \"pow(10, datum.bin_log_x_end)\", \"as\": \"x2\"\n }],\n \"mark\": {\"type\" : \"bar\", \"stroke\" : 1, \"color\" : \"firebrick\"},\n \"encoding\": {\n \"x\": {\n \"field\": \"x1\",\n \"scale\": {\"type\": \"log\", \"base\": 10},\n \"axis\": {\"tickCount\": 5, \"title\" : \"Sequences / haplotype\", \"titleFontSize\" : 16, \"grid\" : false}\n },\n \"x2\": {\"field\": \"x2\"},\n \n \"y\": {\"aggregate\": \"count\", \"scale\" : {\"type\" : \"symlog\"}, \"axis\": {\"tickCount\": 5, \"title\" : \"Count\", \"titleFontSize\" : 16, \"grid\" : false}}\n }})","pinned":false,"hidden":false,"mode":"ojs"},{"id":558,"value":"md`#### Gene-wide selection \nThe distribution of ω ratio estimates and site-to-site synonymous rates inferred with BUSTED[S]. The test p-value for positive diversifying selection on **internal** tree branches is **${pvFormat(analysisSummary.busted.p)}**`","pinned":false,"hidden":false,"mode":"ojs"},{"id":546,"value":"plotPie (analysisSummary.busted)","pinned":false,"hidden":false,"mode":"ojs"},{"id":806,"value":"md`The distribution of tree wide ω values estimated over internal and terminal (leaf) branches`","pinned":false,"hidden":false,"mode":"ojs"},{"id":772,"value":"omega_chart = {\n let definition = {};\n definition.data = dNdSTrends;\n definition.width = 700;\n definition.height = 120;\n definition.legendValues = [\n \"Min\",\n \"Max\",\n \"Avg\",\n \"Last\"\n ];\n definition.series = [\n {\n \"label\": \"ω internal\",\n \"metric\": \"omega_internal\",\n \"legend\": true,\n \"tooltip\": true,\n \"negativeY\": false,\n \"lineColor\": \"firebrick\",\n \"fillColor\": \"#b2222220\",\n },\n {\n \"label\": \"ω leaves\",\n \"metric\": \"omega_leaves\",\n \"legend\": true,\n \"tooltip\": true,\n \"negativeY\": false,\n \"lineColor\": \"#006400\",\n \"fillColor\": \"#00640040\",\n }\n ];\n const c = new TimeSeriesChart(definition);\n return c.svg;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1092,"value":"md`Distribution of different types of substitutions across S-gene sites`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1140,"value":"viewof rate_options = Inputs.checkbox([\"S leaves\",\"S internal\", \"NS leaves\", \"NS internal\", \"Sqrt\"], {\"value\" : [\"S internal\", \"NS internal\"], label: \"\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1089,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":1337,"value":"md`#### Reversion patterns at signature S-gene sites`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1398,"value":"viewof revtable = Inputs.table(reversionData, {\n rows : 20,\n format : {\n \n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1652,"value":"md`#### Evolutionary patterns at N501Y metasignature S-gene sites`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1657,"value":"viewof metatable = Inputs.table(metaSigData, {\n rows : 20,\n format : {\n \n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":14,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1704,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":27,"value":"analysisSummary = d3.json (settings[analysis2view].url)","pinned":false,"hidden":false,"mode":"ojs"},{"id":211,"value":"samplingDates = _.filter (_.map (analysisSummary.dates, (d,k)=> {\n return {'date' : timeParser (k), 'count' : d};\n}), (d)=>d.date >= minDate2Display);","pinned":false,"hidden":false,"mode":"ojs"},{"id":1164,"value":"minDate2Display = new Date (2021,9,15)","pinned":false,"hidden":false,"mode":"ojs"},{"id":777,"value":"dNdSTrends = {\n return _.map (analysisSummary[\"analysis dates\"], (d)=> {\n return {'date' : timeParser(d), 'omega_internal' : analysisSummary[d].omega.internal, 'omega_leaves' : analysisSummary[d].omega.leaves};\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":506,"value":"cautionByDate = {\n return _.fromPairs (_.map (analysisDates, (d)=> {\n return [d,{'Problematic' : new Set (analysisSummary[d].issues.problematic), 'N-rich' : new Set (analysisSummary[d].issues[\"N rich\"])}];\n }));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":118,"value":"selectionByDate = {\n let sbd = {};\n _.each (analysisDates, (d)=> {\n sbd[d] = {'P' : new Set(), 'N' : new Set ()};\n });\n \n _.each (analysisSummary.sites, (info, site)=> {\n _.each (info.fel, (d,i)=> {\n if (d[0] <= pval && d[1] > d[2]) {\n if (useSite (site-1, analysisDates[i])) {\n sbd[analysisDates[i]].N.add (site);\n }\n }\n });\n _.each (info.meme, (d,i)=> {\n if (d[0] <= pval) {\n if (useSite (site-1, analysisDates[i])) {\n sbd[analysisDates[i]].P.add (site);\n }\n }\n });\n });\n return sbd;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":38,"value":"analysisDates = analysisSummary[\"analysis dates\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":51,"value":"analysisDatesConverted = _.map (analysisDates, (d)=>d3.timeParse(\"%Y%m%d\")(d).getTime())","pinned":false,"hidden":false,"mode":"ojs"},{"id":253,"value":"siteLabels = {\n let sl = {};\n _.each (analysisSummary [lastDate].issues.problematic, (d)=>{\n if (! (d in sl)) {\n sl[d] = {};\n }\n sl[d] = {'P' : true};\n });\n _.each (analysisSummary [lastDate].issues[\"N rich\"], (d)=>{\n if (! (d in sl)) {\n sl[d] = {};\n }\n sl[d] = {'N' : true};\n });\n return sl\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":37,"value":"lastDate = analysisDates[analysisDates.length-1]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1771,"value":"haplotypeCounts = _.map (_.filter (_.map (analysisSummary.subs.L, (d,k)=>k), (k)=>k.split ('_').length > 2), (d)=> {let p = d.split ('_'); return {'count' : +p[p.length-1]};\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":167,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":604,"value":"haploTable = {\n return _.map (_.filter (haploRanks, (d)=>d[3] < 0.5), (d)=> {\n const gd = globalAnnotation [0][\"\" + (d[0] + 1) + d[1]];\n return {\n 'Site' : d[0] + 1,\n 'Codon' : d[1],\n 'AA' : translate_ambiguous_codon (d[1]),\n 'Freq' : d[3],\n 'Score' : d[5],\n 'Other clades freq' : gd ? gd [\"GlobalF\"] : null,\n 'Other clades score' : gd ? Math.pow (10, 1-gd [\"Haplo\"]): null,\n };\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":585,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":123,"value":"pval = analysisSummary.p","pinned":false,"hidden":false,"mode":"ojs"},{"id":488,"value":"do_problematic = table_filter.indexOf (\"Problematic\")>=0\n ","pinned":false,"hidden":false,"mode":"ojs"},{"id":492,"value":"do_nrich = table_filter.indexOf (\"N-rich\")>=0","pinned":false,"hidden":false,"mode":"ojs"},{"id":611,"value":"globalAnnotation = {\n let rd = await d3.csv (\"https://raw.githubusercontent.com/spond/SARS-CoV-2-variation/master/variation/variant-annotation.csv\", d3.autoType);\n return [\n _.fromPairs (_.map (rd, (d)=>[\"\" + ((d.Coord-21562)/3+1) + d.Codon,d])),\n _.fromPairs (_.map (rd, (d)=>[((d.Coord-21562)/3+1),d.Ref]))];\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":885,"value":"clusters_resolved = cluster_options.indexOf (\"Only resolved\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":893,"value":"clusters_cumulative = cluster_options.indexOf (\"Cumulative\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":902,"value":"clusters_log = cluster_options.indexOf (\"Log-scale\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":724,"value":"coevolvingPairs = {\n let included = _.filter (analysisSummary.pairs, (d)=>useSite (d[0], lastDate) && useSite (d[1], lastDate));\n let nodes = new Set ();\n _.each (included, (d)=>{nodes.add (d[0]); nodes.add (d[1]);});\n let graph = [\"graph LR;\"];\n _.each ([...nodes], (n)=> {\n graph.push (\" \" + n +\";\");\n });\n _.each (included, (d)=> {\n graph.push (\" \" + d[1] + \"-->|PP = \" + floatFormat (d[4]) + \"|\" + d[0] + \";\");\n graph.push (\" \" + d[0] + \"-->|SUBS = \" + d[5] + \",\" + d[6] + \",\" + d[7] + \" |\" + d[1] + \";\");\n });\n graph.push (\"\");\n return graph.join (\"\\n\");\n /*\n Ref(\"Reference Clade (K=1)\");\\\n G1(\"Group 1 (K=12.9)\");\\\n G2(\"Group 2 (K=0.64)\");\\\n \\\n G1-->|INT p = 0.03|Ref;\\\n G1-->|INT p = 0.007|G2;\\ '\n return nodes;*/\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":937,"value":"tree_object = {\n \n let T = new phylotree.phylotree (analysisSummary.subs.T);\n T.branch_length_accessor = (n)=>analysisSummary.subs.L[n.data.name];\n return T;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":983,"value":"site4tree = _.map (site2viewIDX, (d)=>parseInt(d.split (\"/\")[1])-1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1040,"value":"copyNumbers = _.filter (_.map (analysisSummary.subs.L, (d,k)=>getCopyNumber(k)))","pinned":false,"hidden":false,"mode":"ojs"},{"id":1233,"value":"tree_rendering = display_tree(tree_object)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1747,"value":"signaturesitesBA1 = ({\"67\" : \"AV\", \"95\" : \"TI\", \"142\" : \"GD\", \"339\" : \"GD\", \"371\" : \"SL\", \"373\" : \"SP\", \"375\" : \"SF\", \"417\" : \"KN\", \"440\" :\"NK\", \"446\" : \"GS\", \"477\" : \"SN\", \"478\" : \"TK\", \"484\" : \"EA\", \"493\" : \"QR\", \"496\" : \"GS\", \"498\" : \"QR\", \"501\" : \"NY\", \"505\" : \"YH\", \"547\" : \"TK\", \"614\" : \"DG\", \"655\" : \"HY\", \"679\" : \"NK\", \"681\" : \"PH\", \"764\" : \"NK\", \"796\" : \"DY\", \"856\" : \"NK\", \"954\": \"QH\", \"969\" : \"NK\", \"981\" : \"LF\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1751,"value":"signaturesitesBA2 = ({\"19\":\"TI\", \"24\" : \"LS\", \"142\" : \"GD\", \"339\" : \"GD\", \"371\" : \"SF\", \"372\" : \"SP\", \"375\" : \"SF\", \"376\" : \"TA\", \"405\" : \"DN\", \"408\" : \"RS\", \"417\" : \"KN\", \"440\" : \"NK\", \"477\" : \"SN\", \"478\" : \"TK\", \"484\" : \"EA\", \"493\" : \"QR\", \"498\" : \"QR\", \"501\" : \"NY\", \"505\" : \"YH\", \"614\" : \"DG\", \"655\" : \"HY\", \"679\" : \"NK\", \"681\" : \"PH\", \"764\" : \"NK\", \"796\" : \"DY\", \"954\" : \"QH\", \"969\" : \"NK\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1869,"value":"signaturesitesBA275 = ({\"19\":\"TI\", \"24\" : \"LS\", \"147\" : \"KE\", \"152\" : \"WR\", \"157\" : \"FL\", \"210\": \"IV\", \"213\" : \"VG\", \"257\": \"GS\", \"339\" : \"GD\", \"371\" : \"SF\", \"372\" : \"SP\", \"375\" : \"SF\", \"376\" : \"TA\", \"405\" : \"DN\", \"408\" : \"RS\", \"417\" : \"KN\", \"440\" : \"NK\", \"477\" : \"SN\", \"478\" : \"TK\", \"484\" : \"EA\", \"498\" : \"QR\", \"501\" : \"NY\", \"505\" : \"YH\", \"614\" : \"DG\", \"655\" : \"HY\", \"679\" : \"NK\", \"681\" : \"PH\", \"764\" : \"NK\", \"796\" : \"DY\", \"954\" : \"QH\", \"969\" : \"NK\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1879,"value":"signaturesitesBA2752 = ({\"19\":\"TI\", \"24\" : \"LS\", \"147\" : \"KE\", \"152\" : \"WR\", \"157\" : \"FL\", \"210\": \"IV\", \"213\" : \"VG\", \"257\": \"GS\", \"339\" : \"GD\", \"346\" : \"RT\", \"371\" : \"SF\", \"372\" : \"SP\", \"375\" : \"SF\", \"376\" : \"TA\", \"405\" : \"DN\", \"408\" : \"RS\", \"417\" : \"KN\", \"440\" : \"NK\", \"477\" : \"SN\", \"478\" : \"TK\", \"484\" : \"EA\", \"486\" : \"FS\", \"498\" : \"QR\", \"501\" : \"NY\", \"505\" : \"YH\", \"614\" : \"DG\", \"655\" : \"HY\", \"679\" : \"NK\", \"681\" : \"PH\", \"764\" : \"NK\", \"796\" : \"DY\", \"954\" : \"QH\", \"969\" : \"NK\", \"1199\" : \"DN\"})","pinned":true,"hidden":false,"mode":"ojs"},{"id":1843,"value":"signaturesitesBA4 = ({\"19\":\"TI\", \"24\" : \"LS\", \"142\" : \"GD\", \"339\" : \"GD\", \"371\" : \"SF\", \"372\" : \"SP\", \"375\" : \"SF\", \"376\" : \"TA\", \"405\" : \"DN\", \"408\" : \"RS\", \"417\" : \"KN\", \"440\" : \"NK\", \"452\" : \"LR\", \"477\" : \"SN\", \"478\" : \"TK\", \"484\" : \"EA\", \"486\" : \"FV\", \"498\" : \"QR\", \"501\" : \"NY\", \"505\" : \"YH\", \"614\" : \"DG\", \"655\" : \"HY\", \"679\" : \"NK\", \"681\" : \"PH\", \"764\" : \"NK\", \"796\" : \"DY\", \"954\" : \"QH\", \"969\" : \"NK\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1846,"value":"signaturesitesBA5 = signaturesitesBA4","pinned":false,"hidden":false,"mode":"ojs"},{"id":1864,"value":"signaturesitesBA51 = signaturesitesBA5","pinned":false,"hidden":false,"mode":"ojs"},{"id":1849,"value":"signaturesitesBA2121 = ({\"19\":\"TI\", \"24\" : \"LS\", \"142\" : \"GD\", \"339\" : \"GD\", \"371\" : \"SF\", \"372\" : \"SP\", \"375\" : \"SF\", \"376\" : \"TA\", \"405\" : \"DN\", \"408\" : \"RS\", \"417\" : \"KN\", \"440\" : \"NK\", \"452\" : \"LQ\", \"477\" : \"SN\", \"478\" : \"TK\", \"484\" : \"EA\", \"493\" : \"QR\", \"498\" : \"QR\", \"501\" : \"NY\", \"505\" : \"YH\", \"614\" : \"DG\", \"655\" : \"HY\", \"679\" : \"NK\", \"681\" : \"PH\", \"704\" : \"SL\", \"764\" : \"NK\", \"796\" : \"DY\", \"954\" : \"QH\", \"969\" : \"NK\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1342,"value":"signatureSites = settings [analysis2view].sig","pinned":false,"hidden":false,"mode":"ojs"},{"id":1617,"value":"meta501 = _.map ([\"L18F\",\"P26RLS\",\"DEL69\",\"S98F\",\"D138HY\", \"DEL144\",\"D215GHVY\",\"DEL241\",\"K417NT\",\"E484K\",\"N501Y\",\"H655Y\",\"P681LRH\",\"A701V\",\"T716I\",\"T1027I\",\"D1118H\",\"V1176F\",\"V1264L\"], (d)=>{\n var matches = [];\n d.replace(/([A-Z]+)([0-9]+)([A-Z]*)/g, function(m, a, b, c) {\n matches.push([a, b, c])\n });\n matches = matches[0];\n if (matches[0].length > 1) {\n return [+matches[1], \"\", new Set ('-')];\n }\n return [+matches[1],matches[0], new Set (matches[2])];\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1635,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":1357,"value":"$37","pinned":false,"hidden":false,"mode":"ojs"},{"id":1531,"value":"clusterSites = new Set ([3,4,5,6,13,14,15,17,22,24,25,26,27])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1563,"value":"//_.filter (_.map (_.range (10000), (d)=>consecutiveMutations (mutationPatterns[0], true).length >= 4))","pinned":false,"hidden":false,"mode":"ojs"},{"id":1504,"value":"$38","pinned":false,"hidden":false,"mode":"ojs"},{"id":1445,"value":"$39","pinned":false,"hidden":false,"mode":"ojs"},{"id":22,"value":"md`### Code`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1043,"value":"getCopyNumber = (n)=>{\n if (n.substr (0,3) == \"REF\") return 0;\n let p = n.split (\"_\");\n return +p[p.length-1];\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1037,"value":"bubbleScale = d3.scaleSqrt()\n .domain([1, d3.max(copyNumbers)])\n .range([1, 8])","pinned":false,"hidden":false,"mode":"ojs"},{"id":503,"value":"useSite = (site, date)=> {\n if (!do_problematic && cautionByDate[date][\"Problematic\"].has (site)) return false;\n if (!do_nrich && cautionByDate[date][\"N-rich\"].has (site)) return false;\n return true;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":290,"value":"async function plotComposition (d) {\n let vg = await vegalite ({\n \"data\": {\"values\" : d},\n \"mark\": {\"type\" : \"bar\", \"tooltip\" : true, \"size\" : 10},\n \"width\" : 100,\n \"height\" : 10,\n \"encoding\": {\n \"x\": {\n \"field\": \"Count\",\n \"type\": \"quantitative\",\n \"scale\" : {\"type\" : \"linear\", \"domain\" : [0, d3.sum (d, (c)=>c.Count)]},\n \"stack\": true,\n \"axis\" : null\n },\n \"color\": {\n \"field\": \"Codon\",\n \"type\": \"nominal\",\n \"legend\" : null\n }\n }}\n );\n return vg;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":363,"value":"compositionString = (d)=>{\n const translate = table_composition.indexOf (\"Composition as AA\") >= 0;\n let codons = _.chain(d).toPairs().sortBy ((d)=>-d[1]).value();\n let ann = [];\n _.each (codons.slice (0,3), (d)=> {\n ann.push ((translate ? translate_ambiguous_codon(d[0]) : d[0]) + \"_{\" + (d[1]) + \"}\");\n });\n if (codons.length > 3) ann.push (\" +\" + (codons.length - 3) + \"(\" + d3.sum (codons.slice (3,codons.length), (d)=>d[1]) + \")\");\n return \"\" + ann.join(\"\") + \"\";\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"timeFormat = d3.timeFormat(\"%Y-%m-%d\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":101,"value":"floatFormat = d3.format (\".2f\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":421,"value":"pvFormat = d3.format (\".3f\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":212,"value":"timeParser = d3.timeParse(\"%Y%m%d\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":90,"value":"trendAreaChart = (d)=> {\n return area(\n d,\n {\n \"width\" : 125,\n \"height\" : 25,\n \"color\" : {\"line\" : \"black\", \"fill\" : \"silver\"},\n \"highlights\" : {\"start\" : null, \"end\" : null, \"min\" : null, \"max\" : null},\n \"datum\" : null,\n \"scaling\" : \"zero\",\n \"margin\" : {\"horizontal\" : .04, \"vertical\" : .125}\n }\n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":427,"value":"trendPVChart = (d)=> {\n return area(\n d,\n {\n \"width\" : 80,\n \"height\" : 20,\n \"color\" : {\"line\" : \"black\", \"fill\" : \"silver\"},\n \"highlights\" : {\"start\" : null, \"end\" : null, \"min\" : null, \"max\" : null},\n \"datum\" : {\"value\" : pval, \"color\" : \"firebrick\"},\n \"scaling\" : \"zero\",\n \"margin\" : {\"horizontal\" : .04, \"vertical\" : .125}\n }\n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":474,"value":"trendOmegaChart = (d)=> {\n return area(\n d,\n {\n \"width\" : 80,\n \"height\" : 20,\n \"color\" : {\"line\" : \"black\", \"fill\" : \"blue\"},\n \"highlights\" : {\"start\" : null, \"end\" : null, \"min\" : \"steelblue\", \"max\" : \"firebrick\"},\n \"datum\" : null,\n \"scaling\" : \"zero\",\n \"margin\" : {\"horizontal\" : .04, \"vertical\" : .125}\n }\n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":532,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs"},{"id":855,"value":"motifPlot = (cluster)=>_.chain (_.toPairs (cluster)).filter ((d)=>clusters_resolved ? d[0].indexOf ('?') < 0 : true).map ((c)=>_.flatten (_.map(c[1], (cnt, dt)=>({'motif' : c[0], 't' : timeParser(dt), 'count' : cnt})))).flatten().value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":853,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs"},{"id":1035,"value":"bubbleSize = (n)=> {\n let s = bubbleScale (getCopyNumber(n.data.name));\n return Math.min (s||1,10);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1272,"value":"isRefSeq = (d)=>d.substr (0,3) == \"REF\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":909,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs"},{"id":19,"value":"md`### Libraries and imports`","pinned":false,"hidden":false,"mode":"ojs"},{"id":205,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":906,"value":"phylotree=require (\"phylotree\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":918,"value":"import {select, text, input, autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":208,"value":"import {TimeSeriesChart} from \"@geofduf/simple-dashboard-line-charts\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":87,"value":"import {line, bar, area, histogram, ticks, range} from \"@hamzaamjad/tiny-charts\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":572,"value":"import {translate_ambiguous_codon} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":721,"value":"import {mermaid} from \"@matthewkenny/mermaid-js\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":967,"value":"import {multiAutoSelect} from \"@spond/untitled/3\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1003,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":943,"value":"html`\n `","pinned":false,"hidden":false,"mode":"ojs"},{"id":70,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":191,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":72,"value":"$3d","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W3e","stdlib":"1","titling":"auto"}