30:Ta76,html`

${analysisSummary[lastDate].N} sequences ${trendAreaChart(_.map (analysisDates, (d)=>analysisSummary[d].N))}	${analysisSummary[lastDate].HA} haplotypes ${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:T4d0,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 analysis 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:Tc9e,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"]} }, // First figure "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"]} }, // Second Figure "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:T494,settings = ({ 'BA.2 (05-15-2022)' : {'url': 'https://data.hyphy.org/web/RASCL_HEAVY/BA.2-05152022.json', 'sig': signaturesitesBA2}, '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} })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 ([\n \"BA.1 Jan 5th 2022\", \n \"BA.1 (to 03/01/22)\",\n \"BA.1 (latest)\", \n \"BA.2 (latest)\", \n \"BA.4 (latest)\", \n \"BA.5 (latest)\", \n \"BA.2.12.1 (latest)\"], \n {\"label\" : \"Analysis to view\", \n \"value\" : \"BA.1 (latest)\"})","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). SUBS is the amount of substitutions inferred for site 1, the amount of substitutions inferred for site 2, and the number of shared substitutions. `","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":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`## Parse 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":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":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\")\n\ntimeFormat = d3.timeFormat(\"%m-%d-%Y\")","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\" : \"silver\"},\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":"$3d","pinned":false,"hidden":false,"mode":"ojs"},{"id":1872,"value":"### Experimental Viz.","pinned":false,"hidden":false,"mode":"md"},{"id":1874,"value":"omega_chart = {\n let definition = {};\n definition.data = dNdSTrends;\n definition.width = 700;\n definition.height = 120;\n definition.legendValues = [\n \"Min\",\n \"Max\",\n \"Avg\",\n \"Last\"\n ];\n definition.series = [\n {\n \"label\": \"ω internal\",\n \"metric\": \"omega_internal\",\n \"legend\": true,\n \"tooltip\": true,\n \"negativeY\": false,\n \"lineColor\": \"firebrick\",\n \"fillColor\": \"#b2222220\",\n },\n {\n \"label\": \"ω leaves\",\n \"metric\": \"omega_leaves\",\n \"legend\": true,\n \"tooltip\": true,\n \"negativeY\": false,\n \"lineColor\": \"#006400\",\n \"fillColor\": \"#00640040\",\n }\n ];\n const c = new TimeSeriesChart(definition);\n return c.svg;\n}","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W3e","stdlib":"1","titling":"auto"}