31:T779,table (by_gene[0], { limit: 5000, enableCSVDownload: true, sort: true, enableFilter: false, columns: [ { key: 'gene', name: 'Gene/ORF' }, { key: 'sequences', name: 'Seqs' }, { key: 'total', name: 'Sites' }, { key: 'variable', name: "Sites w/variants", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'variable-aa', name: "AA variants", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'variable-2x', name: "Shared variants", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'variable-2x-aa', name: "Shared AA variants", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'selected-positive', name: "+ selection", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'selected-negative', name: "- selection", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'in_epitope', name: "HLA epitope", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'in_epitope_positive', name: "HLA epitope, +", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] }, { key: 'in_epitope_negative', name: "HLA epitope, -", render: (val)=>per_kp ? d3.format ("1g")(val[1]) : val[0] } ] });32:Tc87,genome_view = vegalite({ "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "config": { "view": { "stroke": null }, }, "data": { "values": _.filter (by_gene_plot, (r)=>r.gene == gene) }, "vconcat": [{ "height": 150, "width": 1500, "mark": { type: "tick", filled : true, tooltip: true }, "encoding": { "y": { "field": "kind", "type": "nominal", "sort": null, "scale" : { "domain" : ['Nucleotide', 'Nucleotide 2x', 'Aminoacid', 'Aminoacid 2x', 'Intrahost SILENT', 'Intrahost MISSENSE', '+ selection in SARS-CoV-2', '+ selection in beta-CoV', '- selection in SARS-CoV-2', '- selection in beta-CoV', 'nCOV more conserved', 'nCOV less conserved','Unexpected codons'] }, "axis": { "domain": false, "offset": 10, "labelFontSize": "12", "ticks": false, "grid": true, "title": null } }, "size" : { "value" :10, }, "color" : { "field" : "type", "legend" : {"title" : "Site kind", "orient" : "bottom"} }, "x": { "field": "coord", "type": "quantitative", "scale": { /*"domain": { "selection": "brush" }*/ }, "axis": { "title": "Codon site in " + gene, "grid": false, "orient" : "top", "titleFontSize": "14", "labelFontSize": "12", } }, } }, /*{ "height": 40, "width": 750, "layer": [{ "selection": { "brush": { "type": "interval", "encodings": ["x"], "mark": { "fill": "#fdbb84", "fillOpacity": 0.5, "stroke": "#e34a33" } } }, "transform": [{ "calculate": "3", "as": "y" }, { "calculate": "12", "as": "y2" }], "mark": { type: "rule" }, "encoding": { "tooltip": [{"field": "position", "type": "quantitative"}, {"field": "gene", "type": "nominal"}, {"field": "site_in_gene", "type": "quantitative"}, {"field": "score", "type": "quantitative"}, {"field": "type", "type": "nominal"}, {"field": "peptide", "type": "nominal"},], "x": { "field": "position", "type": "quantitative", "axis": null, }, "y": { "field": "y", "type": "quantitative", "axis": null, }, "y2": { "field": "y2", "type": "quantitative", "axis": null, }, "color": { "field": "score", "type": "nominal", "legend": { "title": "Site score", "orient": "bottom" }, "scale": { "scheme": "lightgreyred" } } } } ] },*/ ] })33:Td30,counts_scatter = vegalite({ "title": null, data: {values: by_gene[1]}, "vconcat" : _.map (["variable","variable-2x","variable-aa","variable-2x-aa","selected-positive","selected-negative"], (info)=>{ return { width : 300, height: 300, "transform" : [{"filter": "datum.kind=='" + info + "'"}], "layer" : [ { "mark": {"type": "point", "size" : 150, clip: true, filled : true}, "title" : info, "encoding": { "x": { field: "sites", type: "quantitative", axis: {"title": "Sites", titleFontSize : 14, grid : false}, "scale": {"type": "log"} }, "y": {"field": "value", "type": "quantitative", axis: { "title": "Variants", "titleFontSize" : 14, "grid" : false, }, "scale": { "type": "log", }}, "color" : { "sort": {"field": "gene"}, "field" : "gene" , "type": "nominal", "scale": {"scheme": "set1"}, "legend" : {"title" : "Gene", titleFontSize : 14, labelFontSize: 12, orient : "right"} } } }, { "mark": { "type": "line", "color": "black" }, "transform": [ { "regression": "value", "on": "sites", //"method" : "poly" } ], "encoding": { "x": { "field": "sites", "type": "quantitative" }, "y": { "field": "value", "type": "quantitative" } } }, { "transform": [ { "regression": "value", "on": "sites", //"method" : "poly", "params": true }, {"calculate": "'R²: '+format(datum.rSquared, '.2f')", "as": "R2"} ], "mark": { "type": "text", "color": "firebrick", "x": "width", "align": "right", "y": -5 }, "encoding": { "text": {"type": "nominal", "field": "R2"} } } ] } }) }) 34:Tabb,counts_scatter_hla = vegalite({ "title": null, data: {values: by_gene[2]}, "hconcat" : [ { width : 300, height: 300, "mark": {"type": "point", "size" : 150, clip: true, filled : true}, "title" : null, "encoding": { "x": { field: "positive_in_hla", type: "quantitative", axis: {"title": "Positively Selected Sites in HLA epitopes", titleFontSize : 14, grid : false}, "scale": { "type": "linear", "domain" : [-0.01, 0.15] } }, "y": {"field": "positive_out_hla", "type": "quantitative", axis: { "title": "Positively Selected Sites NOT in HLA epitopes", "titleFontSize" : 14, "grid" : false, }, "scale": { "type": "linear", "domain" : [-0.01, 0.15] }}, "color" : { "sort": {"field": "gene"}, "field" : "gene" , "type": "nominal", "scale": {"scheme": "set1"}, "legend" : {"title" : "Gene", titleFontSize : 14, labelFontSize: 12, orient : "right"} } } }, { width : 300, height: 300, "mark": {"type": "point", "size" : 150, clip: true, filled : true}, "title" : null, "encoding": { "x": { field: "negative_in_hla", type: "quantitative", axis: {"title": "Negatively Selected Sites in HLA epitopes", titleFontSize : 14, grid : false}, "scale": {"type": "linear","domain" : [-0.01, 0.15]} }, "y": {"field": "negative_out_hla", "type": "quantitative", axis: { "title": "Negatively Selected Sites NOT in HLA epitopes", "titleFontSize" : 14, "grid" : false, }, "scale": { "type": "linear", "domain" : [-0.01, 0.15] }}, "color" : { "sort": {"field": "gene"}, "field" : "gene" , "type": "nominal", "scale": {"scheme": "set1"}, "legend" : {"title" : "Gene", titleFontSize : 14, labelFontSize: 12, orient : "right"} } } } ] })35:T51d,aa_variation_plot = vegalite({ "title": null, data: {values: temporal_summary}, transform: [{"calculate" : "datum.prot_num_var_sites_minor/datum.num_sites", "as" : "fraction_2aa"}, {"calculate" : "datum.codon_num_var_sites/datum.num_sites", "as" : "fraction_nuc"}], hconcat : _.map ([["Fraction of sites with shared amino-acid changes", "fraction_2aa"], ["Fraction of sites with any changes", "fraction_nuc"]], (r)=> { return { width : 300, height: 300, "mark": {"type": "line", "interpolate" : "monotone", "strokeWidth" : 3}, "encoding": { "x": {field: "analysis_date", type: "temporal", axis: {"title": "Analysis date", titleFontSize : 14, grid : false}}, "y": {"field": r[1], "type": "quantitative", axis: { "title": r[0], "titleFontSize" : 14, "grid" : false }, "scale": { "type": "linear" }}, "color" : { "sort": {"field": "gene"}, "field" : "gene" , "type": "nominal", "scale": {"scheme": "set1"}, "legend" : {"title" : "Gene", titleFontSize : 14, labelFontSize: 12, orient : "right"} }} }}) })36:T438,bl_plot = vegalite({ "title": null, data: {values: temporal_summary}, hconcat : _.map ([["Total branch length leaves", "tree_len_terminal"], ["Total branch length internal", "tree_len_internal"]], (r)=> { return { width : 300, height: 300, "mark": {"type": "line", "interpolate" : "monotone", "strokeWidth" : 3}, "encoding": { "x": {field: "analysis_date", type: "temporal", axis: {"title": "Analysis date", titleFontSize : 14, grid : false}}, "y": {"field": r[1], "type": "quantitative", axis: { "title": r[0], "titleFontSize" : 14, "grid" : false }, "scale": { "type": "linear", }}, "color" : { "sort": {"field": "gene"}, "field" : "gene" , "type": "nominal", "scale": {"scheme": "set1"}, "legend" : {"title" : "Gene", titleFontSize : 14, labelFontSize: 12, orient : "right"} }} }}) })37:T46e,omega_variation_plot = vegalite({ "title": null, data: {values: temporal_summary}, hconcat : _.map ([["dN/dS Leaves", "mean_dnds_leaf"], ["dN/dS Internal Branches", "mean_dnds_internal"]], (r)=> { return { width : 300, height: 300, "mark": {"type": "line", "interpolate" : "monotone", "strokeWidth" : 3, clip: true}, "encoding": { "x": {field: "analysis_date", type: "temporal", axis: {"title": "Analysis date", titleFontSize : 14, grid : false}}, "y": {"field": r[1], "type": "quantitative", axis: { "title": r[0], "titleFontSize" : 14, "grid" : false, }, "scale": { "type": "linear", "domain" : [0,2], }}, "color" : { "sort": {"field": "gene"}, "field" : "gene" , "type": "nominal", "scale": {"scheme": "set1"}, "legend" : {"title" : "Gene", titleFontSize : 14, labelFontSize: 12, orient : "right"} }} }}) })38:T726,omega_vs_freq = vegalite({ "title": null, data: {values: _.filter (omega_freq, (r)=>r.rv < 20000)}, layer: [{ width : 400, height: 400, "mark": { "type": "errorbar", "extent": "ci", "ticks": true, clip : true }, "encoding": { "x": { field: "variants", type: "ordinal", axis: {"title": "Variant Frequency", titleFontSize : 14, grid : false }, "scale" : {"type": "ordinal", "domain" : ["1","2","3","4","5","6","7-10","11-20","21-3000",">3000"] } }, "size" : {"value" : 3}, "y": {"field": "omega", "type": "quantitative", axis: { "title": "SLAC dN-dS", "titleFontSize" : 14, "grid" : false, }, "scale": { "type": "linear", "domain" : [-2,2] }}, } }, { width : 500, height: 500, "mark": { "type": "point", "filled" : true, clip : true }, "encoding": { "size" : {"value" : 100}, "x": { field: "variants", type: "ordinal", "scale" : {"type": "ordinal", "domain" : ["1","2","3","4","5","6","7-10","11-20","21-3000",">3000"]} }, "y": {aggregate : "mean", "field": "omega", "type": "quantitative", axis: { axis: null, "grid" : false, }, "scale": { "type": "linear", "domain" : [-2,2] }}, } }] })39:Td88,by_gene = { let by_gene = {}; _.each (comparative_data, (site)=> { if (!(site["G"] in by_gene)) { by_gene[site["G"]] = { 'gene' : site["G"], 'sequences' : d3.sum (_.values(site['cdn'])), 'variable' : 0, 'total' : 0, 'variable-aa' : 0, 'variable-2x' : 0, 'variable-2x-aa' : 0, 'selected-positive' : 0, 'selected-negative' : 0, 'in_epitope' : 0, 'in_epitope_positive' : 0, 'in_epitope_negative' : 0 }; } let ns = false; by_gene[site["G"]]['total'] ++; let cdn_variants = _.sortBy (_.filter (site['cdn'], (v,k)=> {return k.indexOf ('-') < 0 && k != 'NNN'})); if (cdn_variants.length > 1) { by_gene[site["G"]]['variable'] ++; if (_.some (cdn_variants, (v,i) => {return v>=2&&i {return k != '-'})); if (cdn_variants.length > 1) { by_gene[site["G"]]['variable-aa'] ++; if (_.some (cdn_variants, (v,i) => {return v>=2&&ig.sequences > 0), (d)=>-d["selected-positive"]), (v)=>{ _.each (['variable-aa', 'variable', 'variable-2x', 'variable-2x-aa', 'selected-positive', 'selected-negative', 'in_epitope', 'in_epitope_positive', 'in_epitope_negative'], (k)=>{v[k] = [v[k],(v[k]/v["total"])*1000/3]}); return v; }); return [ gene_data, _.flatten (_.map (gene_data, (r)=> { return _.map (['variable-aa','variable','variable-2x','variable-2x-aa','selected-positive','selected-negative'], (m)=>{return {"gene" : r['gene'],'sites': r['total'],'kind' : m, 'value' : Math.max (r[m][0],1)};})} )), _.flatten (_.map (gene_data, (r)=> { return {"gene" : r['gene'], 'positive_in_hla' : r['in_epitope_positive'][0] / r['in_epitope'][0], 'negative_in_hla' : r['in_epitope_negative'][0] / r['in_epitope'][0], 'positive_out_hla': (r['selected-positive'][0]-r['in_epitope_positive'][0]) / (r['total']-r['in_epitope'][0]), 'negative_out_hla': (r['selected-negative'][0]-r['in_epitope_negative'][0]) / (r['total']-r['in_epitope'][0]), }; })) ]; }3a:T47b,by_gene_comp = { let by_gene = {}; _.each (comparative_data, (site)=> { if (!(site["G"] in by_gene)) { by_gene[site["G"]] = { 'gene' : site["G"], 'selected-positive' : 0, 'selected-negative' : 0, 'different+' : 0, 'different-' : 0 }; } let dp = false; if ("bFEL" in site) { if (site.bFEL.p <= pv) { if (site.bFEL.a < site.bFEL.b) { by_gene[site["G"]]['selected-positive'] ++; dp = true; } else { by_gene[site["G"]]['selected-negative'] ++; } } } if (("bMEME" in site) && !dp) { if (site.bMEME.p <= pv) { by_gene[site["G"]]['selected-positive'] ++; } } if (("bCFEL" in site)) { if (site.bCFEL.p <= pv) { if (site.bCFEL['b-nCOV'] > site.bCFEL['b']) { by_gene[site["G"]]['different+'] ++; } else { by_gene[site["G"]]['different-'] ++; } } } }); return _.sortBy (by_gene, "gene"); }3b:Tdc4,by_gene_plot = { let variants = []; _.each (comparative_data, (site, key)=> { let plot_object = { 'gene' : site["G"], 'coord' : +site["S"], 'type' : null, 'kind' : null }; function add_point (kind, type) { plot_object['type'] = type || "Variable Site"; plot_object['kind'] = kind; variants.push (_.clone ( plot_object)); }; let cdn_variants = _.sortBy (_.filter (site['cdn'], (v,k)=> {return k.indexOf ('-') < 0 && k != 'NNN'})); if (cdn_variants.length > 1) { add_point ("Nucleotide"); if (_.some (cdn_variants, (v,i) => {return v>=2&&i {return k != '-'})); if (aa_variants.length > 1) { add_point ("Aminoacid"); if (_.some (aa_variants, (v,i) => {return v>=2&&i{ if (c in intra_host) { ihv = _.extend (ihv, intra_host[c]); } }); _.each (ihv, (v,k)=> { add_point ("Intrahost " + k,"Intrahost variants"); }); if (site["evo"]) { let nuc = {'A': 1, 'C': 1, 'G' :1, 'T': 1}; cdn_variants = _.filter (_.map (site['cdn'], (c,k)=>[k,c]), (c)=>_.every (c[0], (n)=>{return (n in nuc);})); if (_.some (cdn_variants, (c)=> { if (c[0] in site["evo"]) { return false; } if (site["G"] == "S") console.log (c, site); return c[1] >= 5; })) { add_point ("Unexpected codons","Unexpected codons"); } } }); return variants; }3c:T50b,omega_freq = { let resolved = {'A' : 1, 'C': 1, 'G' : 1, 'T' : 1}; return _.filter (_.map (_.filter (comparative_data, (d)=> ('SLAC' in d) && (d.SLAC.N + d.SLAC.S > 0)), (d)=> { let passing_filter = _.filter (_.map (d.cdn, (count, codon) => [codon, count]), (cdn) => { return _.every (cdn[0], (letter)=>(letter in resolved)); }); if (passing_filter.length != 2) { return ; } let weight = d3.sum (passing_filter, (f) => f[1]); let all_variants = d3.sum (_.filter (passing_filter, (f)=>f[0] != d.bSC2), (f) => f[1]); if (all_variants == 0) { return; } let rv = all_variants; if (all_variants > 6) { if (all_variants <= 10) { all_variants = "7-10" } else { if (all_variants <= 20) { all_variants = "11-20" } else { if (all_variants <= 3000) { all_variants = "21-3000"; } else { all_variants = ">3000"; } } } } else { all_variants = "" + all_variants; } return {'omega' : d.SLAC.NmS, 'variants' : all_variants, 'rv' : rv, 'p' : d.SLAC.p}; }), (d)=>d); }3d:T677,aggregated_omega_freq = { let resolved = {'A' : 1, 'C': 1, 'G' : 1, 'T' : 1}; let bins = {}; _.each (_.filter (comparative_data, (d)=> ('SLAC' in d) && (d.SLAC.S + d.SLAC.N)), (d)=> { let passing_filter = _.filter (_.map (d.cdn, (count, codon) => [codon, count]), (cdn) => { return _.every (cdn[0], (letter)=>(letter in resolved)); }); let weight = d3.sum (passing_filter, (f) => f[1]); if (_.filter (passing_filter, (f)=>f[0] != d.bSC2).length > 1) { return; } let all_variants = d3.sum (_.filter (passing_filter, (f)=>f[0] != d.bSC2), (f) => f[1]); let rv = all_variants; if (all_variants > 6) { if (all_variants <= 10) { all_variants = "7-10" } else { if (all_variants <= 20) { all_variants = "11-20" } else { if (all_variants <= 3000) { all_variants = "21-3000"; } else { all_variants = ">3000"; } } } } else { all_variants = "" + all_variants; } if (!(all_variants in bins)) { bins[all_variants] = {'N' : 0, 'S' : 0, 'EN' : 0, 'ES' : 0, 'count' : 0, 'vars': []}; } bins[all_variants]['S'] += d.SLAC.S; bins[all_variants]['N'] += d.SLAC.N; bins[all_variants]['ES'] += d.SLAC.ES; bins[all_variants]['EN'] += d.SLAC.EN; bins[all_variants]['vars'].push (passing_filter); bins[all_variants]['count'] ++; }); return bins; }3e:[] 2f:{"title":"Summary of SARS-CoV-2 genomic diversity","cells":[{"id":0,"value":"md`# Summary of SARS-CoV-2 genomic diversity`","pinned":false,"hidden":false,"mode":"ojs"},{"id":784,"value":"md`A quick summary of variation found in SARS-CoV-2 genomic samples from GISAID. Main analysis page is [here](https://observablehq.com/@spond/natural-selection-analysis-of-sars-cov-2-covid-19)`","pinned":false,"hidden":false,"mode":"ojs"},{"id":963,"value":"md`### Summary of sequence diversity/selection in SARS-CoV-2 isolates by gene/ORF`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1345,"value":"viewof per_kp = checkbox({\n options: [{ value: \"off\", label: \"Show counts per kB\" }],\n value: \"toggle\",\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":943,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":966,"value":"md`### Summary of sequence diversity/selection in related beta-CoV by gene/ORF`","pinned":false,"hidden":false,"mode":"ojs"},{"id":978,"value":"table (by_gene_comp,\n {\n limit: 5000,\n enableCSVDownload: true,\n sort: true,\n enableFilter: false,\n columns: [\n \n {\n key: 'gene',\n name: 'Gene/ORF'\n },\n {\n key: 'selected-positive',\n name: \"+ selection\",\n },\n {\n key: 'selected-negative',\n name: \"- selection\",\n },\n {\n key: 'different+',\n name: \"Less conservation in nCoV\",\n },\n {\n key: 'different-',\n name: \"More conservation in nCoV\",\n }\n ]\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":887,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1233,"value":"viewof gene = {\n const dd3 = select({\n title: \"View this gene\",\n options: _.map (_.uniqBy (by_gene[0],\"gene\"), (g)=>g.gene)\n \n });\n dd3.input.style.fontSize = \"30px\";\n dd3.input.style.marginTop = \"8px\";\n return dd3;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":996,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":1487,"value":"md`### Relationship between gene/ORF length and the number of variable sites`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1354,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":1503,"value":"md`### Relationship between gene/ORF sites in HLA epitopes and the number of sites selected`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1499,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":1540,"value":"md`### Temporal trends in per-site variability in different genes`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1230,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":1543,"value":"md`### Temporal trends in cumulative branch lengths`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1326,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":1548,"value":"md`### dN/dS temporal trends`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1264,"value":"$37","pinned":false,"hidden":false,"mode":"ojs"},{"id":1272,"value":"omega_scatter = vegalite({\n \"title\": null,\n data: {values: temporal_summary},\n\n width : 300,\n height: 300,\n\n \"mark\": {\"type\": \"point\", \"strokeWidth\" : 3, clip: true},\n \"encoding\": {\n \"x\": {field: \"mean_dnds_leaf\", type: \"quantitative\", axis: {\"title\": \"dN/dS terminal braches\", titleFontSize : 14, grid : false}},\n\n \"y\": {\"field\": \"mean_dnds_internal\", \"type\": \"quantitative\", axis: {\n \"title\": \"dN/dS internal braches\",\n \"titleFontSize\" : 14,\n \"grid\" : false,\n \n },\n \"scale\": { \n \"type\": \"linear\",\n \"domain\" : [0,2],\n }},\n \"color\" : {\n \"sort\": {\"field\": \"gene\"},\n \"field\" : \"gene\" ,\n \"type\": \"nominal\",\n \"scale\": {\"scheme\": \"set1\"},\n \"legend\" : {\"title\" : \"Gene\", titleFontSize : 14, labelFontSize: 12, orient : \"right\"}\n }}\n\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1551,"value":"md`### Distributions of variant frequencies`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1285,"value":"variant_histograms = vegalite({\n \"title\": \"Amino-acid variants at ≤1.0%\",\n width : 400,\n height: 400,\n data: {values: variant_frequencies},\n transform :[{\"filter\" : \"datum[4]<0.01\"}],\n \"mark\": {\"type\": \"bar\"},\n\n encoding: {\n /*\"facet\" : {\n \"field\" : \"2\" ,\n \"type\": \"ordinal\",\n \"columns\": 3,\n \"title\" : \"Amino-acid\",\n \"sort\": {\"field\": \"2\"}\n },*/\n \n \"x\": {field: \"4\", \n type: \"quantitative\", \n axis: {\"title\": \"Variant frequency\", titleFontSize : 14, grid : false, format: \"2p\"}, \n \"bin\": {\n \"bin\" :true,\n \"maxbins\" : 50\n }\n \n },\n \"y\": {\n axis: {\"title\": \"Count\", titleFontSize : 14, grid : false},\n \"aggregate\": \"count\",\n \"type\": \"quantitative\"\n }\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1322,"value":"variant_histograms_common = vegalite({\n \"title\": \"Amino-acid variants at >1.0%\",\n width : 400,\n height: 400,\n data: {values: variant_frequencies},\n transform :[{\"filter\" : \"datum[4]>0.01\"}],\n \"mark\": {\"type\": \"bar\"},\n\n encoding: {\n /*\"facet\" : {\n \"field\" : \"2\" ,\n \"type\": \"ordinal\",\n \"columns\": 3,\n \"title\" : \"Amino-acid\",\n \"sort\": {\"field\": \"2\"}\n },*/\n \n \"x\": {field: \"4\", \n type: \"quantitative\", \n axis: {\"title\": \"Variant frequency\", titleFontSize : 14, grid : false, format: \"2p\"}, \n \"bin\": {\n \"bin\" :true,\n \"maxbins\" : 50\n }\n \n },\n \"y\": {\n axis: {\"title\": \"Count\", titleFontSize : 14, grid : false},\n \"aggregate\": \"count\",\n \"type\": \"quantitative\"\n }\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1574,"value":"$38","pinned":false,"hidden":false,"mode":"ojs"},{"id":1771,"value":"ag_omega_vs_freq = vegalite({\n \"title\": null,\n data: {values: _.filter(_.map (aggregated_omega_freq, (d,k)=> [k,(d.N/d.S)/(d.EN/d.ES)]), (f)=>f[0] != \"0\")},\n\n layer: [{\n width : 400,\n height: 400,\n \n\n \"mark\": {\n \"type\": \"point\",\n \"filled\" : true,\n clip : true\n },\n \"encoding\": {\n \"size\" : {\"value\" : 100},\n \"x\": {\n field: \"0\", \n \"title\" : \"Variant Frequency\",\n type: \"ordinal\", \n \"scale\" : {\"type\": \"ordinal\", \"domain\" : [\"1\",\"2\",\"3\",\"4\",\"5\",\"6\",\"7-10\",\"11-20\",\"21-3000\",\">3000\"]}\n },\n\n \"y\": {\"field\": \"1\", \"type\": \"quantitative\", axis: {\n \"title\" : \"dN/dS\",\n axis: null,\n \"grid\" : false,\n \n },\n \n \n\n \"scale\": { \n \"type\": \"linear\",\n \n }},\n }\n }]\n\n})","pinned":true,"hidden":false,"mode":"ojs"},{"id":5,"value":"md`---`","pinned":false,"hidden":false,"mode":"ojs"},{"id":930,"value":"pv = 0.1","pinned":false,"hidden":false,"mode":"ojs"},{"id":907,"value":"$39","pinned":false,"hidden":false,"mode":"ojs"},{"id":1252,"value":"variant_frequencies = {\n let variants = [];\n _.each (comparative_data, (site)=> {\n var denominator = d3.sum (_.values (site['aa']));\n _.each (site['aa'], (v,k)=> {\n if (k != site['bSC2-aa']) {\n if (k.indexOf('-')<0) {\n variants.push ([site['G'],site['S'],k,v,v/denominator,v>1 ? \"Repeated\" : \"Singleton\"]);\n }\n }\n })\n });\n return variants;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":971,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs"},{"id":1006,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs"},{"id":1554,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs"},{"id":1729,"value":"_.filter (_.map (aggregated_omega_freq, (d,k)=> [k,(d.N/d.S)/(d.EN/d.ES)]), (f)=>f[0] != \"0\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1712,"value":"$3d","pinned":false,"hidden":false,"mode":"ojs"},{"id":904,"value":"comparative_data = await d3.json (\"https://raw.githubusercontent.com/veg/SARS-CoV-2/segmented/data/comparative-annotation.json\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1155,"value":"temporal_summary = {\n let ts = await d3.csv (\"https://dl.dropbox.com/s/sme0q2hkpk85j98/report.csv\");\n let parsers = [d3.timeParse (\"%Y-%m-%d\"), d3.timeParse (\"%Y%m%d\")];\n let valid_dates = {};\n \n _.each (ts, (r)=> {\n if (!(r['analysis_date'] in valid_dates)) {\n valid_dates [r['analysis_date']] = {}\n }\n if (_.every (r, (f)=>f.length != 0)) {\n valid_dates [r['analysis_date']][r[\"gene\"]] = 1;\n }\n });\n \n ts = _.filter (ts, (t)=>_.size (valid_dates[t['analysis_date']]) == 9);\n _.each (ts, (r)=> {\n r['analysis_date'] =_.find (_.map (parsers, (p)=>p (r['analysis_date'])));\n r['tree_len_internal'] = parseFloat (r['tree_len_internal']);\n });\n return ts;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1089,"value":"gene_coordinates = _.map ([\n [266,'ORF1a',13483],\n [13471, 'ORF1b',21555],\n [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 //[29558,'ORF10',29674]\n], (d,i)=>{\n d.push (i);\n return d;\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1087,"value":"intra_host = {\n let raw_variants = await d3.tsv (\"https://raw.githubusercontent.com/galaxyproject/SARS-CoV-2/master/genomics/4-Variation/variant_list.05.tsv\", d3.autoType);\n /*\n Sample\tCHROM\tPOS\tREF\tALT\tDP\tAF\tSB\tDP4\tIMPACT\tFUNCLASS\tEFFECT\tGENE\tCODON\ttype\n \"*/\n let binned = _.countBy (raw_variants, (v)=>v.Sample);\n let vars = {};\n let data = _.each (_.filter (raw_variants, (v)=>v.POS >= gene_coordinates[0][0] && binned[v.Sample] <= 75 && v.AF >= 0.05 && v.AF <= .90), (v)=> {\n let gene = _.find (gene_coordinates, (d,i)=> i == gene_coordinates.length -1 || gene_coordinates[i][0] <= v.POS && gene_coordinates[i+1][0] > v.POS);\n \n let offset = 0;\n if (gene[1] == \"ORF1b\") {\n offset = 3; \n }\n if (!(v.POS in vars)) {\n vars[v.POS] = {}; \n }\n vars[v.POS][v['EFF[*].FUNCLASS']] = true;\n \n });\n \n \n\n return vars;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":9,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"_=require(\"lodash\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":30,"value":"vegalite = require(\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":764,"value":"import {select, slider, checkbox} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":841,"value":"import {rangeSlider} from \"@mootari/range-slider\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":940,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W3e","stdlib":"1","titling":"auto"}