29:null 2a:["$","title",null,{"children":"Selection history of genes in SARS-CoV-2/COVID-19 genomes enabled by data from | Sergei Pond | Observable"}] 2f:T109e,main_view = vegalite({ "title": null, data: {values: site_tracking}, transform: [{"calculate": "-log(datum.p)/log(10)", "as" : "psize"}, {"calculate": "-log(datum.fel)/log(10)", "as" : "pfsize"}, {"calculate": "datum.maf*100", "as" : "pmaf"}], width : 400, encoding: { "color" : { "sort": {"field": "site"}, "field" : "pmaf" , "title" : "% with mutations", "type": "quantitative", "scale": {"type": "threshold", "domain": [0.01, 0.1, 0.5, 1, 5, 10, 50], "scheme": "reds"}, //"legend" : null }, }, //"title" : r[0], layer: [{ "transform" : [{"filter" : "datum.type"}], "mark": {"type": "circle", "opacity" : 0.5, "stroke": "black", "strokeWidth": 1, size : 40, tooltip : true}, "encoding": { "x": {field: "date", timeUnit: "yearmonthdate", type: "temporal", scale: {nice: true, padding : 0.5}, axis: {"title": "Analysis date", titleFontSize : 14, grid : false, "labelFontSize" : 12}}, tooltip : [ {"field": "site", "type": "ordinal", "title": "Site"}, {"field": "date", "type": "temporal", "title": "Analysis date"}, {"field": "p", "type": "quantitative", "title": "MEME p-value", "format" : ".2g"}, {"field": "fel", "type": "quantitative", "title": "FEL p-value", "format" : ".2g"}, {"field": "kind", "type": "orgina", "title": "FEL selection type"}, {"field": "pmaf", "type": "quantitative", "title": "% with mutations", "format" : ".2g"} ], "y": {"sort": "ascending", "field": yaxis_label, "type": "nominal", axis: { "titleFontSize" : 14, "labelFontSize" : 14, "grid" : false, "title" : null, "labelFont" : "courier" }, }, "size" : {"field" : "psize", "type" : "quantitative", "legend" : { "tickCount" : 5, "title" : "-log10 (p)"} }, } }, { "transform" : [{"filter" : "!datum.type"}], "mark": {"type": "square", "opacity" : 0.5, "stroke": "black", "strokeWidth": 1, size : 40, tooltip : true}, "encoding": { "x": {field: "date", type: "temporal", axis: {"title": "Analysis date", titleFontSize : 14, grid : false, "labelFontSize" : 12}}, tooltip : [ {"field": "site", "type": "ordinal", "title": "Site"}, {"field": "date", "type": "temporal", "title": "Analysis date"}, {"field": "p", "type": "quantitative", "title": "MEME p-value", "format" : ".2g"}, {"field": "fel", "type": "quantitative", "title": "FEL p-value", "format" : ".2g"}, {"field": "kind", "type": "orgina", "title": "FEL selection type"}, {"field": "pmaf", "type": "quantitative", "title": "% with mutations", "format" : ".2g"} ], "y": {"sort": "ascending", "field": yaxis_label, "type": "nominal", axis: { "titleFontSize" : 14, "labelFontSize" : 14, "grid" : false, "title" : null, "labelFont" : "courier" }, }, "size" : {"field" : "pfsize", "type" : "quantitative", "legend" : { "tickCount" : 5, "title" : "-log10 (p)"} }, } }, { "mark": {"type": "rule", "opacity" : 0.25, "color" : "black"}, "encoding": { "x": {"aggregate": "min", field: "date", type: "temporal", axis: {"title": "Analysis date", titleFontSize : 14, grid : false, "labelFontSize" : 12}}, "x2": {"aggregate": "max", field: "date", type: "temporal"}, "y": {"field": yaxis_label, "type": "nominal", axis: { "titleFontSize" : 14, "labelFontSize" : 12, "grid" : false, }, }, } } ] })30:T4f5,site_tracking = { const min_p = +pv; const fmt = d3.format (" >4d"); const ps = columns2Display.indexOf ("p")>=0; const ns = columns2Display.indexOf ("n")>=0; let siteList = new Set (); if (segment.split (",").length > 1) { // a list of sites siteList = parseFilterString (segment); siteList = new Set(_.chain (siteList).map ((s)=>reverseLookup [parseInt(s)]).map ((d)=>_.map (d, (f)=>_.map(_.filter (f, (c)=>c.split("/").length > 1), (c)=>c.split ("/").join (" ").toUpperCase()))).flatten().flatten().value()); } return _.map(_.filter (siteHistory, (d)=> { return (parseInt(d.coordinate.split (" ")[1]) > 0 && (d.gene == segment || siteList.has (d.coordinate.toUpperCase())) && ((ps && (d.p <= min_p || d.fel <= min_p && d.kind == 'positive')) || (ns && ( d.fel <= min_p && d.kind != 'positive')))); }), (d)=> { let coord = parseInt(d.coordinate.split (" ")[1]); d.site = d.gene + "/" + fmt(coord); d.type = d.p <= min_p || d.fel <= min_p && d.kind == "positive"; d.nuc = parseInt (jsonCodonLookup [(d.gene + "/" + coord).toUpperCase()]); if (d.nuc <= offsetsByGene ["S"]) { d.orf = "ORF1ab/" + fmt ((d.nuc-266)/3 + 1); } else { d.orf = d.site; } return d; }); }31:T5d4,generateSiteRowList = (list, c2d, pv)=> { const intFormat = d3.format ("d"); const nullOrFmt = (d, fmt) => _.isUndefined (d) || _.isNull (d) || _.isNaN (d) ? "N/A" : fmt (d); const fracFormat = d3.format (".3f"); const pValueFormat = (v)=> { let pvv = nullOrFmt (v, fracFormat); if (v <= pv) { return "" + pvv + ""; } return pvv; } const floatFormat = d3.format (".1f"); if (list.length == 0) { return [ {"No sites selected" : ""} ] } const columnProcessor = { 'n' : ["Coordinate", (v)=>v], 'segment' : ["Gene", (v)=>v], 'SS' : ["Site", (v)=>intFormat(v)], 'MEME.p' : ["MEME", (v)=>pValueFormat (v)], 'MEME.br' : ["Events", (v)=>nullOrFmt(v,intFormat)], 'FEL.p' : ["FEL", (v)=>pValueFormat (v)], 'FEL.kind' : ["Type", (v)=>v == "Pos." ? "Pos." : (v == "Neg." ? "Neg." : null)], 'trend' : ["TrendZ", (v)=>nullOrFmt(v,floatFormat)], 'hla' : ["Epitopes", (v)=>nullOrFmt(_.size (v),intFormat)], 'maf' : ["MAF", (v)=>nullOrFmt(v,fracFormat)], 'unusual' : ["Unexpected", (v)=>nullOrFmt(v,intFormat)] }; let columns2View = c2d || columns2Display; return _.map (list, (row)=> { return _.fromPairs (_.map (columns2View, (c)=> { return [columnProcessor[c][0], columnProcessor[c][1](_.get (row,c))]; })); }); }32:[] 2d:{"id":"b0f782ead117a88e","slug":"sc2-genes","title":"Selection history of genes in SARS-CoV-2/COVID-19 genomes enabled by data from ","thumbnail":"53cae8802380cd364248645b1829720e7c310735e20c3c23f03e4f8c841ada64","access_level":"public","create_time":"$D2021-01-09T15:35:40.296Z","update_time":"$D2021-04-22T20:29:29.911Z","view_time":null,"first_public_time":"$D2021-01-09T16:26:36.920Z","has_unpublished_edits":null,"fork":{"id":"9749811453d1b25b","slug":"evolutionary-annotation-of-sars-cov-2-covid-19-genomes-enab","title":"Evolutionary annotation of SARS-CoV-2/COVID-19 genomes enabled by data from ","owner":{"id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond"}},"stars":2,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024"},"version":663,"publish_version":663,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null}],"members":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":2,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Selection history of genes in SARS-CoV-2/COVID-19 genomes enabled by data from ","cells":[{"id":0,"value":"md`# Selection history of genes in SARS-CoV-2/COVID-19 genomes enabled by data from $\"gisaid-logo\"$
\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":253,"value":"viewof segment = autoSelect ({\n options: _.sortBy(_.keys(_.countBy (siteHistory, (d)=>d.coordinate.split (\" \")[0]))),\n value: params.get(\"segment\") || params.get (\"sites\") || \"S\",\n title: \"Gene/ORF/peptide\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":436,"value":"viewof pv = text({value: params.get(\"p\") || \"0.01\", description: \"p-value cutoff\", submit: \"Update\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":93,"value":"viewof columns2Display = checkbox({\n options: [\n { value: \"p\", label: \"Positively selected\" },\n { value: \"n\", label: \"Negatively selected\"}\n \n ],\n value: [\"p\"],\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":451,"value":"md`**History of selection detection in ${segment}.**\n\n\n\nEach site that reached significance at p ≤ ${pv}. At least once during our selection analyses is shown on the plot. Lines indicate the range of detection (to make it easier to see the range of detection). Larger cicrles = smaller p-values. The color of the cirlce indicates the frequency of non-reference alleles. **Negatively selected sites** are marked shown with rectangles; positively selected sites with circles.\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":613,"value":"viewof yaxis = radio({\n options: [\n { value: \"g\", label: \"Product/site\" },\n { value: \"o\", label: \"Gene or ORF/site\"},\n { value: \"n\", label: \"Nucleotide\"}, \n ],\n value: \"g\",\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":425,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"md`--- \n### Code and data below this point`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"md`#### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":402,"value":"siteHistory = _.filter (await d3.csv (_baseDir + \"/temporal-gene-sites.csv\",d3.autoType))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":624,"value":"yaxis_label = yaxis == \"g\" ? \"site\" : yaxis == \"n\" ? \"nuc\" : \"orf\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":429,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":528,"value":"params = new URLSearchParams(location.search)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":536,"value":"_baseDir = params.get (\"time\") ? params.get (\"time\") : (params.get (\"dir\") ? params.get (\"dir\") : \"https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/data/\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":576,"value":"reverseLookup = _.groupBy (_.toPairs(jsonCodonLookup), (d)=>d[1])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":629,"value":"jsonCodonLookup","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":382,"value":"md`#### Functions`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":309,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"md`#### Module Requires`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":64,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":397,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":398,"value":"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"md`#### Imports`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"import {select,checkbox, autoSelect, text, radio} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":51,"value":"import {offsetsByGene} from \"@spond/revised-sars-cov-2-analytics-page\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":556,"value":"import {parseFilterString, jsonCodonLookup} from \"@spond/sars_cov_2_sites\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1"}} 2e:"$2d:body"