31:T7f7,loaderParagraph = { let params = new URLSearchParams(location.search); let base_loader = params.get ("base"); const base_url = base_loader || "https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/"; const base_dir = params.get ("dir") || "data/fasta/2021-02-10"; const title = params.get ("title") || "global"; const temporal_dir = base_url + "/" + (params.get ("temporal") || (base_loader ? "" : "data/")); let loader = html`

Loading ${title} analysis data...

`; loader.value = [{},{"reference" : "20191201", "values" : [[]]},base_dir,title,temporal_dir]; yield loader loader = html`

Loading ${title} analysis data...

`;; loader.value = [{},{"reference" : "20191201", "values" : [[]]},base_dir,title,temporal_dir]; let rd = await d3.json (base_url + "/" +base_dir+"/report.json"); loader = html`

Loading sequence annotation data..

`; loader.value = [{},{"reference" : "20191201", "values" : [[]]},base_dir,title,temporal_dir]; yield loader let at = await d3.json (base_loader ? base_loader + "/" + base_dir + "/sequence-info.json" : (base_dir ? base_url + "/" +base_dir+"/sequence-info.json" : " https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/data/db/sequence-info.json")); let rdc = d3.timeParse ("%Y%m%d")(at.reference).getTime(); let daysSince2Date = (d)=>new Date (rdc + 24*3600000*d) let dr = _.map (d3.extent (at.values[0]), daysSince2Date); let sc = _.map (rd, (d)=>d["total sequences"]); let retValue = md`Includes data sampled between **${d3.timeFormat ("%B %d%, %Y")(dr[0])} and ${d3.timeFormat ("%B %d%, %Y")(dr[1])}**, with a median of **${d3.median(sc)}** sequences per gene/ORF.
View searchable and downloadable detailed site-level reports [here](https://observablehq.com/@spond/evolutionary-annotation-of-sars-cov-2-covid-19-genomes-enab?collection=@spond/sars-cov-2). `; retValue.value = [rd,at,base_dir,title,temporal_dir]; yield retValue; }32:T519,md`

Analysis details

Which positions in the [SARS-CoV-2 genome](https://www.ncbi.nlm.nih.gov/nuccore/?term=COVID) **may be** subject to **positive** selection, i.e., involved in adaptation, or **negative** selection, i.e. conserved during evolution? We used several statistical techniques and other sources of information to identify potential candidates using unique genomic sequences ([details](https://github.com/veg/SARS-CoV-2/tree/compact)), to identify sets of sites that might merit a deeper look. The genome below shows the location of sites identified as having one or more of the features of interest. You may select a site in the drop-down menu below and view its inferred properties, trends over time, and evolution on the phylogenetic tree.

Starting on **2020-11-18** we have begun employing a probabilistic low frequency variant filtering sequence preprocessing to reduce the number of (dead-end) lineages that are going into selection analyses. This means that some (but not all) low frequency mutations will not be reflected in counts or shown on trees

Data usage notes

GISAID data provided on this page is subject to GISAID’s [Terms and Conditions](https://www.gisaid.org/registration/terms-of-use/).

`33:T14a8,genome_view = vegalite({ "config": { "view": { "stroke": null }, }, "vconcat": [ { "layer": [ { "height": 40, "width": 800, "data": { "values": gene_coordinates }, "transform": [{ "calculate": "(datum['3'] % 2) ? -1 : 1", "as": "coloring" }, { "calculate": "(datum['3'] % 2) ? -1 : 0", "as": "y" }, { "calculate": "(datum['3'] % 2) ? 14 : 15", "as": "y2" }, { "calculate": "'https://observablehq.com/@spond/sc2-genes?segment='+(datum['1'])+'&dir='" + "+'"+ _timeDirectory + "'", "as": "url" } ], "mark": { "type": "bar", "stroke": "#000", "tooltip" : null, }, "encoding": { "x": { "field": "0", "type": "quantitative", "axis": null }, "x2": { "field": "2" }, "y": { "field": "y", "type": "quantitative", "axis": null }, "y2": { "field": "y2" }, "fill": { "condition": {"test": "datum['coloring'] < 0", "value": "lightgrey"}, "value" : "white" }, "href": {"field": "url"}, "opacity": { "value": "0.5" } } }, { "height": 40, "width": 800, "data": { "values": gene_coordinates }, "transform": [ { "lookup": "1", "from": { "data": {"values": _.toPairs (_.countBy (filteredListOfSites, (d)=>d[0].split ("/")[0]))}, "key": "0", "fields": ["1"], }, "default" : "0", "as" : "count" }, { "calculate": "datum['0'] + (datum['2']-datum['0'])*(datum['count'])/(datum['2']-datum['0'])*3", "as": "extent" }, { "calculate": "-20", "as": "y" }, { "calculate": "-22", "as": "y2" } ], "mark": { "type": "bar", "fill": "steelblue", "stroke" : null, "tooltip" : {"field": "extent", "type": "quantitative"}, }, "encoding": { "x": { "field": "0", "type": "quantitative", "axis": null }, "x2": { "field": "extent", "type": "quantitative", "axis": null }, "y": { "field": "y", "type": "quantitative", "axis": null }, "y2": { "field": "y2", "type": "quantitative", "axis": null } } }, { "data" : {"values" : _.map (filteredListOfSites, (d)=>d[1])}, "transform": [{ "calculate": "3", "as": "y" }, { "calculate": "12", "as": "y2" }], "mark": { type: "rule", "tooltip": [ {"field": "coord", "type": "quantitative", "title" : "Nucleotide coordinate"} ], }, "encoding": { "x": { "field": "coord", "type": "quantitative", "axis": null, }, "y": { "field": "y", "type": "quantitative", "axis": null, }, "y2": { "field": "y2", "type": "quantitative", "axis": null, }, "size" : {"value" : 1.}, "color" : { "condition": [ {"test": "datum['fel-positive'] || datum['meme']", "value": "red"}, ], "value" : "darkgrey" }, "opacity" : {"value" : 1.} } }, { "data": { "values": gene_coordinates }, "transform": [ { "calculate": "-15 + ((datum['3'] % 2) ? 30 : 0) ", "as": "y" }, { "calculate": "(datum['0'])+50 + (datum['3'] == 22 ? 300 : 0) + (datum['3'] == 19 ? -300 : 0)", "as": "x" }], "mark": { "type": "text", "fontSize": 9, "baseline": "bottom", "tooltip" : false, "align" : "left" }, "encoding": { "x": { "field": "x", "type": "quantitative", }, "y": { "field": "y", "type": "quantitative" }, "text": { "field": "1", "legend" : null, }, } }, ] }, ], }, {loader: {target: '_blank'}})34:T8bc,selectionHistoryPlot = vegalite({ "title" : "Selection detection history of " + site2view[0] + "/" + site2view[1], width : 800, height: 60, data: {values: dataForSelectionHistoryPlot}, mark: {type:"line", tooltip: true}, encoding: { x: {field: "date", type: "temporal", axis: {"title": "Analysis Date", titleFontSize : 14}, "timeUnit" : "datemonthyear", "scale": { "nice" : "month" }}, "tooltip": [ {"field": "date", "type": "temporal", "title" : "Analysis Date"}, {"field": "p", "type": "quantitative", "title" : "MEME p-value"}, {"field": "fel", "type": "quantitative", "title" : "FEL p-value"}, {"field": "kind", "type": "nominal", "title" : "FEL selection kind"}, {"field": "branches", "type": "quantitative", "title" : "Selected branches (MEME)"} ] }, "layer": [{ "layer" : [{ "mark": {"type": "bar", "opacity" : 0.5, "color" : "steelblue"}, "encoding": { "y": {"field": "p", "type": "quantitative", axis: { "title": "MEME p-value", "titleFontSize" : 14, "tickCount" : 4, "grid" : false, "orient": "left", }, "scale": { "type": "symlog", }}, }, }, { "mark": {"type": "line", "interpolate" : "monotone", "strokeWidth" : 3, "color" : "steelblue"}, "encoding": { "y": {"field": "p", "type": "quantitative", axis: { "title": "MEME p-value", "titleColor" : "steelblue", "titleFontSize" : 14, "grid" : false, "orient": "left" }, "scale": { "type": "symlog" }}, }, }]}, { "mark": {"type": "line", "interpolate" : "monotone", "strokeWidth" : 3, "color" : "orange"}, "encoding": { "y": {"field": "fel", "type": "quantitative", axis: { "title": "FEL p-value", "titleColor" : "orange", "titleFontSize" : 14, "tickCount" : 4, "orient": "right", }, "scale": { "type": "symlog" }}, }, } ], //"config": {"axisY": {"minExtent": 30}}, "resolve": {"scale": {"y": "shared"}} })35:T70e,temporal_evolution_plot = vegalite({ "title" : "Temporal evolution of " + site2view[0] + "/" + site2view[1] + " composition", width : 600, height: 300, data: {values: dataForTemporalPlot}, transform: [{ "window": [{ "op": "sum", "field": "N", "as": "total_count" }], "groupby": ["T"], "frame" : [null, null] }, { "calculate": "datum.N/datum.total_count * 100", "as": "PercentOfTotal" }], mark: {type:"line", tooltip: true}, encoding: { x: {field: "T", type: "temporal", axis: {"title": "Collection Date", titleFontSize : 14}}, "tooltip": [ {"field": "T", "type": "temporal", "title" : "date"}, {"field": "N", "type": "quantitative", "title" : "count"}, {"field": "R", "type": "nominal", "title" : "character"} ], "color" : { "sort": aminoAcids, "sort": {"op": "min", "field": "R"}, "field" : "R" , "title" : "Character", "scale": {"range" : consistentColorScheme}, } }, "layer": [{ "mark": {"type": "bar", "opacity" : 0.5}, "encoding": { "y": {"field": "N", "type": "quantitative", axis: { "title": "#Sequences with residue", "titleFontSize" : 14 }, "scale": { "type": viewOptionsSqrt ? "sqrt" : "linear" }}, }, }, { "mark": {"type": "line", "interpolate" : "monotone", "strokeWidth" : 3}, "encoding": { "y": {"field": "PercentOfTotal", "type": "quantitative", axis: { "title": "% of total", "titleFontSize" : 14 }, "scale": { "type": viewOptionsSqrt ? "sqrt" : "linear" }}, }, } ], "config": {"axisY": {"minExtent": 30}}, "resolve": {"scale": {"y": "independent"}} })36:T583,distribution_map = vegalite ( { "width": 800, "height": 400, "title" : "Distribution of " + useResidueForMap + " at " + site2view[0] + "/" + site2view[1] + " (" + d3.timeFormat ("%Y-%m-%d")(date_range.range[0]) + " to " + d3.timeFormat ("%Y-%m-%d")(date_range.range[1]) + ")", "data": { "values" : world, "format": { "type": "topojson", "feature": "countries" } }, "transform": [{ "lookup": "id", "default" : "-0.0001", "from": { "data": { "values": dataForMapPlot }, "key": "id", "fields": ["rate","name","total","variant"] } }], "projection": { "type": "mercator", "center" : [5,20], "scale": 110, }, "mark": { type : "geoshape", }, "encoding": { "tooltip": [ {"field": "name", "type": "nominal"}, {"field": "variant", "type": "quantitative"}, {"field": "total", "type": "quantitative"}, {"field": "rate", "type": "quantitative"} ], "color": { "condition": { "test": mapViewOptions.indexOf ("w") >= 0 ? "datum.rate <= 0" : "datum.rate < 0", "value": "#aaa" }, "scale" : { domainMin : 0., type: mapViewOptions.indexOf ("q") >= 0 ? "sqrt" : "linear" }, "legend" : { "title" : "Residue frequency" }, "field": "rate", "type": "quantitative" } } } )37:T14a4,renderTree = (tree, container, nodeStatesRaw, duplicateCount, dim, ebf)=>{ if (tree == null) return null; var t = tree.render(container, dim ? { height:dim[0] || 1024, width: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 } : { //height:1024, width:800, 'show-scale' : true, 'left-right-spacing': 'fit-to-size', //'top-bottom-spacing': 'fit-to-size', 'is-radial' : false, 'node_circle_size' : (n)=>0 }); let nodeStatesAA = translateToAminoAcids (nodeStatesRaw); let nodeStates = treeViewAA ? nodeStatesAA : nodeStatesRaw; let colors = arrayToDict(buildConsistentColorScheme (_.countBy (nodeStates), treeViewAA)); let colorsAA = arrayToDict(buildConsistentColorScheme (_.countBy (nodeStatesAA), true)); let duplicateCountN = _.clone(duplicateCount); const bs = (n) => { if (tree.is_leafnode (n)) { return 2 + Math.pow (duplicateCountN[n.data.name], 0.25); } return 0; }; t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = nodeStates ? true : false; if (!dim) { t.font_size = 10; t.spacing_x (9); } ebf = ebf || {}; t.phylotree.branch_length_accessor = n=> { let bl = +n.data.attribute; if (treeViewCensor && bl > 0.01) { n.data.censored_bl = true; return 0.01; } else { n.data.censored_bl = false; } return bl; } t.node_label ((n)=>{ //return "" + duplicateCountN[n.data.name]; if (nodeStates) { //if (duplicateCount) //return (n.data.name in duplicateCount[n.data.name]) ? duplicateCount[n.data.name] : n.data.name; return nodeStates[n.data.name];// + " (" + n.data.name + ")"; } return n.data.name; //return ""; }); function sort_nodes (asc) { tree.traverse_and_compute (function (n) { var d = 1; if (n.children && n.children.length) { d = d3.min (n.children, function (d) { return d["count_depth"];}); } else { d = -duplicateCount[n.data.name]; } n["count_depth"] = d; }); tree.resort_children (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); tree.traverse_and_compute ((n) => { if ("notshown" in n) { delete n["notshown"]; } //if (treeViewHide) { n.notshown = true; //} if (n.parent) { duplicateCountN[n.parent.data.name] = duplicateCountN[n.data.name] + (duplicateCountN[n.parent.data.name] ? duplicateCountN[n.parent.data.name] : 0); } }); function recurse (n) { n.notshown = false; if (n.children) { return recurse(n.children[0]); //recurse(n.children[n.children.length-1]); } else { return n; } } tree.traverse_and_compute ((n) => { if (n.parent) { if (treeViewHide) { n.notshown = n.notshown && (nodeStates[n.data.name] == nodeStates[n.parent.data.name] || duplicateCount [n.data.name] == 0) && ((n.data.name in ebf) == false) ; } else { n.notshown = n.notshown && (duplicateCount [n.data.name] == 0); } if (n.notshown == false) { let retained = recurse (n); duplicateCountN[retained.data.name] = duplicateCountN[n.data.name]; n.parent.notshown = false; } } else { n.notshown = false; } }); t.style_nodes ((e,n) => { if (n.data.name in nodeStates) { e.style ('fill', colors [nodeStates[n.data.name]]); e.selectAll ("circle").style ('fill', colorsAA [nodeStatesAA[n.data.name]]); e.append ("title").text ("" + duplicateCountN[n.data.name] + " sequences"); } //} }); t.style_edges ((e,d) => { //console.log (site); if (nodeStates) { if (nodeStates[d.target.data.name] != nodeStates[d.source.data.name]) { e.style ('stroke-width',3); e.style ('stroke',nodeStatesAA[d.target.data.name] != nodeStatesAA[d.source.data.name] ? '#E94B3CFF' : '#2D2926FF'); } else { e.style ('opacity', 0.3); } if (d.target.data.name in ebf) { e.style ('stroke','purple'); } } else { /*if (d.target.data.name in tree_object[1]) { let binfo = tree_object[1][d.target.data.name]; if (binfo[0].length) { e.style ('stroke-color', species_colors (binfo[0].length)); } }*/ //e.selectAll("title").text ("p = " + p); } if (d.target.data.censored_bl) { e.style ('stroke-dasharray',10); } }); t.placenodes(); t.update(); return t; }38:T56d,tabulateResiduesByTimeLocation = (labeledNodes, duplicateMaps, meta, stride) => { /* array of {'R' : residue, 'C' : country, 'T' : date, 'N' : count} */ let result = {}; stride = stride || 1; for (let n in labeledNodes) { if (n in duplicateMaps) { let tag = [labeledNodes[n],0,0]; _.each (unpackRangedArray (duplicateMaps[n]), (seqID)=> { if (meta.values[0][meta.meta[seqID][0]]) { tag[1] = Math.floor ((+meta.values[0][meta.meta[seqID][0]])/stride); tag[2] = meta.meta[seqID][2]; if (tag in result) { result[tag] += 1; } else { result[tag] = 1; } let world_tag = [tag[0], tag[1], -1]; if (world_tag in result) { result[world_tag] += 1; } else { result[world_tag] = 1; } } }); } } let refDate = d3.timeParse ("%Y%m%d")(meta.reference).getTime(); //return refDate; let timing = []; _.each (result, (count, key)=> { let key_bits = key.split (","); timing.push ({ "R" : key_bits[0], "T" : new Date (refDate + 24*3600000*stride*(+key_bits[1])), "C" : key_bits[2] == "-1" ? "World" : meta.values[2][key_bits[2]], "N" : count}); }); return timing; }39:T449,selectionData = { //let rawData = await d3.json ("https://dl.dropbox.com/s/0fhgt26ebxzha2y/sequences.report.json"); _.each (rawData, (data, gene)=> { let remappedSelection = {}; _.each (data.selection, (siteInfo, siteIndex)=> { let refIndex = data.map[siteIndex], gIndex; if (refIndex >= 0) { gIndex = refIndex; refIndex += 1; } else { while (siteIndex > 0) { if (data.map[siteIndex] >= 0) { break; } siteIndex --; } if (siteIndex == 0) { refIndex = "INS5'"; gIndex = 0; } else { refIndex = "INS" + ( data.map[siteIndex] + 1); gIndex = data.map[siteIndex]; } } siteInfo.genomic_coordinate = offsetsByGene[gene] + gIndex*3; remappedSelection[refIndex] = siteInfo; }); data.selection = remappedSelection; }); return rawData; }3a:T462,filteredListOfSites = { const recentSite = (site)=> { const siteidx = site.replace ('/',' '); return (recentDateCutoff<=d3.min (_.chain (siteHistory).filter ((d)=>d.coordinate == siteidx).value(), (d)=>d.date)); } return _.chain (annotatedSelectionData) .filter (siteFilteringOptions.indexOf ("s") >= 0 ? ((d)=>_.isNumber (d[1]["fel-positive"]) || _.isNumber (d[1]["meme"])) : (d)=>true) .filter (siteFilteringOptions.indexOf ("n") >= 0 ? ((d)=>_.isNumber (d[1]["fel-negative"])) : (d)=>true) .filter (siteFilteringOptions.indexOf ("m") >= 0 ? (d)=>d[1]["meme-branches"] : (d)=>true) .filter (siteFilteringOptions.indexOf ("t") >= 0 ? (d)=>d[1]["trend"] : (d)=>true) .filter (siteFilteringOptions.indexOf ("f") >= 0 ? (d)=>d[1]["maf"] : (d)=>true) .filter (siteFilteringOptions.indexOf ("u") >= 0 ? (d)=>d[1]["unusual"] > 0 : (d)=>true) .filter (siteFilteringOptions.indexOf ("e") >= 0 ? (d)=>d[1]["hla"] : (d)=>true) .filter (siteFilteringOptions.indexOf ("r") >= 0 ? (d)=>recentSite (d[0]) : (d)=>true) .value(); }3b:T8f8,annotatedSelectionData = { const p = 0.05; const Z = 5; // minimal Z-score for trend const maf = 0.05; let nucs = {'A' : 1, 'C' : 1, 'G' : 1, 'T' : 1}; _.each (selectionData, (record, gene)=> { _.each (record["selection"], (siteRecord, site)=> { siteRecord['annotation'] = { 'fel-negative' : null, 'fel-positive' : null, 'meme' : null, 'meme-branches' : null, 'maf' : null, 'trend' : null, 'unusual' : null, 'coord' : null, 'hla' : null }; if (siteRecord.fel <= p) { if (siteRecord.kind == "negative") { siteRecord['annotation']['fel-negative'] = siteRecord.fel; } else { siteRecord['annotation']['fel-positive'] = siteRecord.fel; } } if (siteRecord.meme <= p) { siteRecord['annotation']['meme'] = siteRecord.meme; siteRecord['annotation']['meme-branches'] = siteRecord["meme-branches"] >= 2; } if (siteRecord.MAF >= maf) { siteRecord['annotation'].maf = true; } if ("hla" in siteRecord) { siteRecord['annotation'].hla = _.size (siteRecord["hla"]); } // scan through non-gap, non-ambig codons and record any that have // low (<1e-6) probability let evo_annotation = {}; if ('evolutionary_predictions' in siteRecord) { _.each (siteRecord['counts'], (support, codon) => { if (_.every (codon, (c)=>c in nucs)) { evo_annotation[codon] = siteRecord['evolutionary_predictions'][codon] || 0.0; } siteRecord['filtered_support'] = evo_annotation; }); siteRecord['annotation']['unusual'] = _.filter (siteRecord['filtered_support'], (c)=>c <= 1e-6).length; } siteRecord['annotation']['trend'] = siteRecord['trend'] >= Z; siteRecord['annotation']['coord'] = siteRecord['genomic_coordinate']; }); }); return _.chain (selectionData).map ((d,k)=>_.chain (d['selection']).map ((s,i)=>[k + "/" + i, s['annotation']]).value()).flatten(false).value(); }3c:T265a,siteHTMLReport = ()=>{ const p = 0.05; const size = (fraction)=>Math.max (6,Math.round (24 + 3*Math.log10 (fraction))); const percentFormat = d3.format ("6.4p"), numberFormat = d3.format ("6.2f"); const nucsG = {'A':1,'C':1,'G':1,'T':1,'-':1}; const nucs = {'A':1,'C':1,'G':1,'T':1}; const kind = (prob) => { if (prob > 0.5) return "consensus"; if (prob > 0.01) return "common"; if (prob > 1e-6) return "accepted"; return "unexpected"; } const reportCodon = (codon, total,ref) => { return (codon[0] == ref ? "" : "") + codon[0] + (codon[0] == ref ? "" : "") + "(" + translate_ambiguous_codon (codon[0]) + ") : " + percentFormat (codon[2]/total) + " / " + kind (codon[1]); }; if (site2view.length > 1) { const codonCounts = _.mapValues (_.groupBy (_.filter (_.toPairs (codonStates), (d)=>d[0][0] != 'N'), (d)=>d[1]), (v)=>d3.sum(_.map (v, (d)=>duplicateCount[d[0]]))); const total = d3.sum (_.map (codonCounts)); const countAA = _.chain (translateToAminoAcids(_.chain (codonCounts).map ((v,k)=>[k,k]).fromPairs().value())).map ((v,k)=>[v, codonCounts[k]]).groupBy ((d)=>d[0]).map ((v,k)=>[k,d3.sum(_.map (v, d=>d[1]))]).fromPairs().value(); const refAA = translate_ambiguous_codon (siteInformationRecord.ref_codon); const hlaReport = (HLA) => { const pos = +_.keys (HLA[1])[0]; const count = HLA[1][pos]; const lookup = hlaData[HLA[0]]; return "

  " 
          + HLA[0].substr (0,pos) 
          + "" 
          + HLA[0].substr (pos,1) 
          + "" 
          + HLA[0].substr (pos+1,HLA[0].length - pos-1) 
          + " (" + count + ")"
          + (lookup.type == 'predicted' ? '' : '')
          + "
    "
          + _.map (_.sortBy (_.toPairs (lookup.score), (d)=>d[1]), (d)=>{
            let short_name = d[0].split ('-')[1].split(':')[0];
            return "" + d[0] + "";
          }).join (", ")
          + "

"; } let gaps = 0, ambigs = 0, fromGenome = siteInformationRecord['genomic_coordinate'], toGenome = fromGenome+2; gaps = d3.sum (_.chain (codonCounts).toPairs().filter ((d)=>d[0].indexOf ('-') >= 0).map ((d)=>d[1]).value()) / siteInformationRecord["total sequences"]; ambigs = d3.sum (_.chain (codonCounts).toPairs().filter ((d)=>_.some (d[0], (c)=>(c in nucsG)==false)).map ((d)=>d[1]).value()) / siteInformationRecord["total sequences"]; let ep = [], lt = []; if (siteInformationRecord.evolutionary_predictions) { ep = _.chain (codonCounts).toPairs().filter ((d)=>_.every (d[0], (c)=>c in nucs)).map ((d)=>[d[0],siteInformationRecord.evolutionary_predictions[d[0]]|| 0,d[1]]).sortBy ((d)=>-d[2]).value(); //lt = _.chain (siteInformationRecord.evolutionary_predictions).toPairs().filter ((d)=>d[1] >= 0.01).sortBy (d=>-d[1]).value(); } let report_blob = `

Codon ${site2view[1]} in ${site2view[0]}, genomic coordinate ${siteInformationRecord.genomic_coordinate}

${siteInformationRecord.counts ? '' + siteInformationRecord["sequences"] + ' haplotypes, ' + numberFormat(siteInformationRecord["L"]) + ' subs/site (internal branches)' : ""}.
${_.chain (countAA).toPairs().filter ((d)=>d[0].length == 1).sortBy (d=>-d[1]).map ((d)=>(d[0] == refAA ? '' : '') + "" + d[0] + "_{" + d[1] + "}"+(d[0] == refAA ? '' : '')).value().join ("")}
${percentFormat(siteInformationRecord.MAF)} cumulative minor alleles, ${percentFormat(ambigs)} mixed bases, ${percentFormat(gaps)} complete or partial gaps.
${numberFormat(siteInformationRecord.substitutions[0])} synonymous, ${numberFormat(siteInformationRecord.substitutions[1])} non-synonymous substitutions.
Pervasive negative selection (internal branches). FEL p-value '+numberFormat(siteInformationRecord.fel)+'
Pervasive positive diversifying selection (internal branches). FEL p-value '+numberFormat(siteInformationRecord.fel)+'
Episodic positive diversifying selection (internal branches). MEME p-value '+numberFormat(siteInformationRecord.meme)+'.
'+percentFormat(siteInformationRecord['meme-fraction'])+' internal branches in the selected class; '+siteInformationRecord['meme-branches']+' individual internal branches with strong signal for selection.
${numberFormat(siteInformationRecord.trend)} Z-score for frequency trend.
Evolutionary predictions (codon : observed/predicted)
" + reportCodon (d, total, siteInformationRecord.ref_codon) + "
Likely evolutionary targets (codon : predicted prob)
" + d[0] + " (" + translate_ambiguous_codon (d[0]) + ") :" + percentFormat(d[1]) + "
CTL Epitopes overlapping this site

`; return report_blob; } else { return ``; } }3d:[] 2f:{"title":"Natural selection analysis of global SARS-CoV-2/COVID-19 enabled by data from ","cells":[{"id":0,"value":"md`# Natural selection analysis of ${_analysisTitle} SARS-CoV-2/COVID-19 enabled by data from $\"gisaid-logo\"$ `\n\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":2105,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":1624,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":924,"value":"md`There are **${annotatedSelectionData.length}** sites with at least one feature of interest and **${filteredListOfSites.length} sites** having all of the features selected below`","pinned":false,"hidden":false,"mode":"ojs"},{"id":939,"value":"viewof siteFilteringOptions = checkbox({\n options: [\n { value: \"s\", label: \"+ sel.\" },\n { value: \"n\", label: \"- sel.\" },\n { value: \"m\", label: \"Multiple sel. events\" },\n { value: \"f\", label: \"High frequency\" },\n { value: \"t\", label: \"Trending up\" },\n { value: \"u\", label: \"Unexpected codons\" },\n { value: \"e\", label: \"CTL epitope\" },\n { value: \"r\", label: \"≥\" + d3.timeFormat (\"%Y/%m/%d\")(recentDateCutoff) }\n\n ],\n value: [\"s\", \"m\", \"t\"],\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1694,"value":"trendLegend = swatches({\n color: d3.scaleOrdinal(['red','darkgrey']).domain (['Positively selected','Other']),\n swatchSize: 10\n //tickFormat: \"%\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1037,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":2308,"value":"md`Click on a gene/segment above to display summary information about selected sites`","pinned":false,"hidden":false,"mode":"ojs"},{"id":197,"value":"viewof render_site = autoSelect({\n options: _.map (filteredListOfSites, (d)=>d[0]),\n title: `View a site among the ${filteredListOfSites.length} with the selected properties (SARS-CoV-2 reference coordinates)`,\n value: _.find (filteredListOfSites, (d)=>d[0]==\"S/501\")? \"S/501\" : (filteredListOfSites.length ? _.sample (filteredListOfSites)[0] : undefined),\n placeholder: \"Select a site to view\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1186,"value":"html`${siteHTMLReport()}`\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":1986,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":220,"value":"viewof country2view = select({\n options: sequenceCountByLocation,\n title: `Limit to this location`,\n placeholder: \"Select a location\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":328,"value":"viewof temporalViewOptions = checkbox({\n options: [\n { value: \"a\", label: \"Amino-acids\" },\n { value: \"w\", label: \"By week\" },\n { value: \"b\", label: \"Include ambiguous bases\" },\n { value: \"q\", label: \"Sqrt y-axis scale\" }\n ],\n value: [\"a\", \"w\", \"b\", \"q\"],\n //submit: true\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":192,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":750,"value":"viewof useResidueForMap = select({\n options: _.map (availableResidues, (k, v)=> {return {'label' : v + \" (\" + k + \" samples)\", 'value': v}}),\n title: `Display this residue`,\n label: \"Beavis\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1766,"value":"viewof mapViewOptions = checkbox({\n options: [\n { value: \"q\", label: \"Sqrt color-scale\" },\n { value: \"w\", label: \"Zero-counts are shown as grey (missing = always grey)\"}\n ],\n value: [\"w\",\"q\"],\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":810,"value":"viewof date_range = rangeSlider(samplesByTimeAndResidue, d=>d.date, value=>d3.sum(value.values.map(d=>d.count)), {yTicks:2,\n yScale:d3.scalePow().exponent(1)})","pinned":false,"hidden":false,"mode":"ojs"},{"id":747,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":626,"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":518,"value":"viewof treeViewOptions = checkbox({\n options: [\n { value: \"a\", label: \"Amino-acids\" },\n { value: \"h\", label: \"Only show changes\" },\n { value: \"c\", label: \"Restrict to the same location as in frequency plot\" },\n { value: \"f\", label: \"Censor long (≥0.01) branches (show as dashed)\" }\n ],\n value: [\"h\",\"f\"],\n //submit: true\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1712,"value":"treeLegend = swatches({\n color: d3.scaleOrdinal(['red','lightgrey','black','purple']).domain (['Non-synonymous substitution','No change', 'Synonymous substitution','Episode of selection']),\n swatchSize: 10\n //tickFormat: \"%\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":467,"value":"html`\n \n \n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1098,"value":"md`--- \n### Code and data below this point`","pinned":false,"hidden":false,"mode":"ojs"},{"id":485,"value":"renderedTree = {\n if (site2view.length > 1) {\n let dim = _.map (treeDim.split (\"x\"), (d)=>+d);\n return renderTree (tree, \"#tree_container\", codonStates, render_country == \"World\" || !treeViewCountry ? duplicateCount : copyNumberByCountry (render_country), dim.length == 2 ? dim : null, siteInformationRecord['meme-ebf'])\n } \n return null\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":471,"value":"$37","pinned":false,"hidden":false,"mode":"ojs"},{"id":25,"value":"tree = site2view.length > 1 ? new phylotree.phylotree (selectionData[site2view[0]].tree) : null","pinned":false,"hidden":false,"mode":"ojs"},{"id":663,"value":"copyNumberByCountry = (country) => {\n let countryIndex = metaData.values[2].indexOf (country);\n if (countryIndex >= 0) {\n let cn = {};\n _.each (codonStates, (v,k)=> {\n if (k in selectionData[site2view[0]].duplicate_map) {\n cn [k] = _.countBy (unpackRangedArray(selectionData[site2view[0]].duplicate_map[k]), (d)=>metaData.meta[d][2])[countryIndex] || 0; \n }\n });\n return cn;\n }\n return null;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":32,"value":"recoverCharacterStates = (T,changes)=> {\n let nodeStates = {};\n function recurse_node (node) {\n if (node.data.name in changes) {\n nodeStates[node.data.name] = changes[node.data.name];\n } else {\n nodeStates[node.data.name] = nodeStates[node.parent.data.name];\n }\n _.each (node.children, (c)=>recurse_node(c)); \n }\n\n recurse_node(tree.nodes); \n return nodeStates;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":39,"value":"unpackArray = (array_object)=> {\n if (!_.isArray (array_object)) {\n return _.map (array_object.values, (d)=>{\n return array_object.keys[d];\n });\n }\n return array_object;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":37,"value":"reconstituteTreeChanges = (array)=> {\n let nodeToState = {};\n let states = unpackArray (array[1]);\n _.each (array[0], (d,i)=> {\n nodeToState[\"\"+d] = states[i];\n });\n return nodeToState;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":127,"value":"unpackRangedArray = (array)=> {\n let unpacked = [];\n _.each (array, (d)=> {\n if (_.isString (d)) {\n let bounds = _.map (d.split (\":\"), (r)=>+r);\n for (let i = bounds[0]; i <= bounds[1]; i++) {\n unpacked.push (i); \n }\n } else {\n unpacked.push (d); \n }\n });\n return unpacked;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":69,"value":"translateToAminoAcids = (array) => {\n let transArray = {};\n _.each (array, (codon, node)=> {\n if (!(codon in translation_table)) {\n translation_table [codon] = translate_ambiguous_codon (codon);\n }\n transArray [node] = translation_table[codon];\n });\n return transArray;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":139,"value":"$38","pinned":false,"hidden":false,"mode":"ojs"},{"id":36,"value":"codonStates = site2view.length > 1 ? recoverCharacterStates (tree, reconstituteTreeChanges (selectionData[site2view[0]].selection[site2view[1]].labels)) : null","pinned":false,"hidden":false,"mode":"ojs"},{"id":505,"value":"duplicateCount = {\n \n let copyNumbers = {}\n if (site2view.length > 1) {\n _.each (codonStates, (v,k)=> {\n if (k in selectionData[site2view[0]].duplicate_map) {\n copyNumbers [k] = unpackRangedArray(selectionData[site2view[0]].duplicate_map[k]).length; \n }\n });\n }\n return copyNumbers;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":203,"value":"sitesWithSelectionSignal = _.flatten (_.map (selectionData, (data, gene)=> {\n return _.map (data[\"selection\"], (ignore, site)=> gene + \"/\" + site)\n }))","pinned":false,"hidden":false,"mode":"ojs"},{"id":211,"value":"site2view = render_site.split (\"/\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":260,"value":"render_country = country2view.split (\"/\")[0]","pinned":false,"hidden":false,"mode":"ojs"},{"id":249,"value":"sequenceCountByLocation = _.chain (selectedSiteTemploralProfile).groupBy (d=>d.C).map ((v,k)=>[k,d3.sum (v, (v)=>v.N)]).sortBy(v=>-v[1]).map (v=>v[0] + \"/\" + v[1] + \" sequences\").value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":1817,"value":"refDataSeconds = d3.timeParse (\"%Y%m%d\")(metaData.reference).getTime()","pinned":false,"hidden":false,"mode":"ojs"},{"id":1814,"value":"daysSince2Date = (d)=>new Date (refDataSeconds + 24*3600000*d)","pinned":false,"hidden":false,"mode":"ojs"},{"id":737,"value":"residuesByCountry = {\n let refDate = d3.timeParse (\"%Y%m%d\")(metaData.reference).getTime();\n const DM = selectionData[site2view[0]].duplicate_map;\n const filter = (d)=> {\n let sampled = metaData.values[0][metaData.meta[d][0]];\n if (sampled) {\n sampled = daysSince2Date(sampled);\n return sampled >= date_range.range[0] && sampled <= date_range.range[1];\n }\n return false;\n };\n let byCountry = {};\n _.each (viewOptionsAA ? translateToAminoAcids(codonStates) : codonStates, (state, sequence) => {\n _.each (unpackRangedArray (DM[sequence]), (i)=> {\n if (filter (i)) {\n const country = metaData.meta[i][2];\n if (! (country in byCountry)) {\n byCountry[country] = {'total' : 0};\n }\n byCountry[country].total += 1;\n byCountry[country][state] = 1 + (byCountry[country][state] ? byCountry[country][state] : 0);\n }\n });\n });\n return byCountry;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":816,"value":"samplesByTimeAndResidue = {\n let refDate = d3.timeParse (\"%Y%m%d\")(metaData.reference).getTime();\n const DM = selectionData[site2view[0]].duplicate_map;\n let timing = [];\n _.each (viewOptionsAA ? translateToAminoAcids(codonStates) : codonStates, (state, sequence) => {\n if (state == useResidueForMap) {\n _.each (unpackRangedArray (DM[sequence]), (i)=> {\n const days = metaData.values[0][metaData.meta[i][0]];\n if (days) {\n timing.push (days);\n }\n \n });\n }\n });\n //console.log (_.countBy (countries))\n return _.map (_.countBy (timing), (d,k)=> {return {'date' : new Date (refDate + 24*3600000*k), 'count' : d}});}","pinned":false,"hidden":false,"mode":"ojs"},{"id":786,"value":"dataForMapPlot = {\n return _.map ( residuesByCountry, (data, cid) => {\n return {\n 'id' : countryIntegerCodeToCCN3[cid],\n 'name' : metaData.values[2][cid],\n 'total' : data.total,\n 'variant': data[useResidueForMap] ? data[useResidueForMap] : 0,\n 'rate': (data[useResidueForMap] ? data[useResidueForMap] : 0) / data.total\n }\n } \n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":159,"value":"selectedSiteTemploralProfile = {\n\n if (site2view.length > 1) {\n let unfiltered = tabulateResiduesByTimeLocation (viewOptionsAA ? translateToAminoAcids (codonStates): codonStates, selectionData[site2view[0]].duplicate_map, metaData, viewOptionsByWeek ? 7 : 1);\n if (!viewOptionsAmbigs) {\n if (viewOptionsByWeek) {\n return _.filter (unfiltered, (d)=>d.R.length == 1); \n }\n }\n return unfiltered;\n }\n return [];\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":460,"value":"dataForTemporalPlot = _.filter (selectedSiteTemploralProfile, (d)=> render_country == d.C)","pinned":false,"hidden":false,"mode":"ojs"},{"id":802,"value":"availableResidues = _.mapValues (_.groupBy (dataForTemporalPlot, (d)=>d.R), (v)=>d3.sum (v, (c)=>c.N))","pinned":false,"hidden":false,"mode":"ojs"},{"id":404,"value":"consistentColorScheme = _.map (buildConsistentColorScheme (availableResidues, viewOptionsAA), (d)=>d[1])","pinned":false,"hidden":false,"mode":"ojs"},{"id":532,"value":"buildConsistentColorScheme = (data, aa) => {\n let handleDuplicates = {};\n let rawColors = _.sortBy(_.map (data, (m,k)=>[k,colorizeCharacter (k,null,aa)]), (d)=>d[0]);\n _.each (rawColors, (d)=> {\n if (d[1] in handleDuplicates) {\n handleDuplicates[d[1]][1] += 0.5;\n d[1] = handleDuplicates[d[1]][0].brighter (handleDuplicates[d[1]][1] - 0.5).formatHex();\n } else {\n handleDuplicates[d[1]] = [d3.color(d[1]), 0.5];\n }\n });\n return rawColors;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2168,"value":"rawData = loaderParagraph.value[0]","pinned":false,"hidden":false,"mode":"ojs"},{"id":8,"value":"$39","pinned":false,"hidden":false,"mode":"ojs"},{"id":2264,"value":"recentDateCutoff = new Date(new Date ().getTime() - 14*3600*24*1000)","pinned":false,"hidden":false,"mode":"ojs"},{"id":954,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs"},{"id":903,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"metaData = loaderParagraph.value[1]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1859,"value":"dateRange = _.map (d3.extent (metaData.values[0]), daysSince2Date)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1183,"value":"siteInformationRecord = site2view.length > 1 ? _.extend (selectionData[site2view[0]].selection[site2view[1]], _.pick(selectionData[site2view[0]], ['L', 'sequences', 'total sequences'])) :{}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1261,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs"},{"id":441,"value":"viewOptionsAA = temporalViewOptions.indexOf (\"a\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":444,"value":"viewOptionsByWeek = temporalViewOptions.indexOf (\"w\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":448,"value":"viewOptionsAmbigs = temporalViewOptions.indexOf (\"b\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":453,"value":"viewOptionsSqrt = temporalViewOptions.indexOf (\"q\") >= 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":523,"value":"treeViewAA = treeViewOptions.indexOf (\"a\")>=0","pinned":false,"hidden":false,"mode":"ojs"},{"id":560,"value":"treeViewHide = treeViewOptions.indexOf (\"h\")>=0","pinned":false,"hidden":false,"mode":"ojs"},{"id":657,"value":"treeViewCountry = treeViewOptions.indexOf (\"c\")>=0","pinned":false,"hidden":false,"mode":"ojs"},{"id":1719,"value":"treeViewCensor = treeViewOptions.indexOf (\"f\")>=0","pinned":false,"hidden":false,"mode":"ojs"},{"id":550,"value":"arrayToDict = (array)=> {\n let dict = {};\n _.each (array, (d)=>dict[d[0]] = d[1]);\n return dict;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":282,"value":"aminoAcids = _.flatten ([_.sortBy(_.uniq(_.filter (_.values (translation_table), (d)=>d.length == 1 && d.toLowerCase() != d.toUpperCase()))),\"-\"])","pinned":false,"hidden":false,"mode":"ojs"},{"id":371,"value":"colorizeCharacter = (aa, ambig, doAA)=> {\n if (!doAA) {\n aa = translateToAminoAcids ([aa])[0];\n }\n if (aa in aminoAcidColors) {\n return aminoAcidColors[aa];\n }\n if (aa == \"-\") return \"#000000\";\n return ambig ? ambig (aa) : \"#888888\";\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":366,"value":"aminoAcidColors = {\n return _.fromPairs(_.map ( [\"rgb(240,163,255)\",\"rgb(0,117,220)\",\"rgb(153,63,0)\",\"rgb(76,0,92)\",\"rgb(25,25,25)\",\"rgb(0,92,49)\",\"rgb(43,206,72)\",\"rgb(255,204,153)\",\"rgb(128,128,128)\",\"rgb(148,255,181)\",\"rgb(143,124,0)\",\"rgb(157,204,0)\",\"rgb(194,0,136)\",\"rgb(0,51,128)\",\"rgb(255,164,5)\",\"rgb(255,168,187)\",\"rgb(66,102,0)\",\"rgb(255,0,16)\",\"rgb(94,241,242)\",\"rgb(0,153,143)\",\"rgb(224,255,102)\",\"rgb(116,10,255)\",\"rgb(153,0,0)\",\"rgb(255,255,128)\",\"rgb(255,255,0)\",\"rgb(255,80,5)\"],(d,i)=>[aminoAcids[i],d]));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":753,"value":"world = d3.json(\"https://unpkg.com/world-atlas@1/world/110m.json\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":763,"value":"countryIntegerCodeToCCN3 = {\n let recode = {\"democratic republic of the congo\" : \"republic of the congo\",\n \"crimea\" : \"ukraine\"};\n return _.map (metaData.values[2], (common_name)=> {\n common_name = common_name.toLowerCase();\n if (common_name in recode) common_name = recode[common_name];\n let cc = _.find (country_equiv, (d)=>d.name.common.toLowerCase () == common_name || d.name.official.toLowerCase () == common_name || d.altSpellings.find ((d)=>d.toLowerCase() == common_name));\n if (cc) return cc.ccn3;\n return common_name;\n });\n \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":759,"value":"country_equiv = d3.json (\"https://raw.githubusercontent.com/mledoze/countries/master/dist/countries.json\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1040,"value":"gene_coordinates = _.map (_.sortBy([[21563,'S',25385],\n [25393,'ORF3a',26220],\n [26523,'M',27191],\n [27202,'ORF6',27387],\n [27394,'ORF7a',27759],\n [27894,'ORF8',28259],\n [28274,'N',29533],\n [266, \"leader\", 805],\n [806, \"nsp2\", 2719],\n [2720, \"nsp3\", 8554],\n [8555, \"nsp4\", 10054],\n [10055, \"3C\", 10972],\n [10973, \"nsp6\",11842],\n [11843, \"nsp7\", 12091],\n [12092, \"nsp8\", 12685],\n [12686, \"nsp9\", 13024],\n [13025, \"nsp10\",13442],\n [16237, \"helicase\",18039],\n [18040, \"exonuclease\", 19620],\n [19621, \"endornase\", 20658],\n [20659, \"methyltransferase\", 21552],\n [26244, \"E\",26471],\n [29557, \"ORF10\",29673],\n [13441,\"RdRp\",16235]], (d)=>d[0]), (d,i)=>{\n d.push (i);\n return d;\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1592,"value":"hlaData = d3.json (\"https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/data/ctl/epitopes.json\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1066,"value":"offsetsByGene = {\n return _.chain (gene_coordinates).map((g)=>[g[1],g[0]]).fromPairs().value();\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":56,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1853,"value":"siteHistory = d3.csv (_timeDirectory+\"/temporal-gene-sites.csv\",d3.autoType)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1950,"value":"siteHistoryDates = _.sortBy(_.map (_.uniqBy (siteHistory, (d)=>d.date.getTime()), d=>d.date))","pinned":false,"hidden":false,"mode":"ojs"},{"id":1991,"value":"dataForSelectionHistoryPlot = {\n if (selectedSiteTemploralProfile.length) {\n let rawCounts = _.filter (siteHistory, (d)=>d.coordinate == site2view[0] + \" \" + site2view[1]);\n return rawCounts;\n \n }\n return [];\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":20,"value":"phylotree=require (\"https://dl.dropboxusercontent.com/s/i528j2lqnyzknit/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":187,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":2346,"value":"_baseDirectory = loaderParagraph.value[2]","pinned":false,"hidden":false,"mode":"ojs"},{"id":2357,"value":"_timeDirectory = loaderParagraph.value[4]","pinned":false,"hidden":false,"mode":"ojs"},{"id":2350,"value":"_analysisTitle=loaderParagraph.value[3]||\"\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":194,"value":"import {select,checkbox, autoSelect, text} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":812,"value":"import {rangeSlider} from \"@bumbeishvili/utils\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":60,"value":"import {translation_table,translate_ambiguous_codon} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1696,"value":"import { legend, swatches } from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":2209,"value":"import {loader} from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W3d","stdlib":"1","titling":"auto"}