2b:null 2c:["$","title",null,{"children":"ARGOS NGS QC data exploration | Joe Gergely | Observable"}] 31:T716,html`

${selectedOrganism.length} samples	${countUniqueKeys("lineage")} lineages	${countUniqueKeys("strain")} strains
${d3.mean (_.map (selectedLineage, (c)=>c.ngs_gc_content)).toFixed (2)} mean GC Content Strain	${d3.mean (_.map (selectedOrganism, (c)=>c.avg_read_length)).toFixed (2)} mean read length	${d3.mean (_.map (selectedOrganism, (c)=>c.ngs_gc_content)).toFixed (2)} Mean GC content	${countUniqueKeys("instrument")} Instrument	${countUniqueKeys("genome_assembly_id")} Genome Assembly Ids

`32:T566,contrast_plot = (nfield, cfield,plot_title) => ({ "data": {"values": stratify_data (table_data, nfield, cfield)}, "resolve": {"scale": {"x": "shared"}}, //"title" : plot_title, "hconcat" : [{ "mark": { "type": "rect", }, //height : 200, "encoding": { "y": {"field": "type", "type": "nominal", "axis" : {"title" : cfield, "titleFontSize": 14, "labelFontSize" : 12, "labelFont" : "courier"}}, "x": { "field": "value", "type": "quantitative", "bin": {"maxbins":60}, "scale": {"type" : "linear"}, "axis" : {"title" : nfield, "titleFontSize": 14}, }, "color": { "aggregate": "count", "type": "quantitative", "title" : "Count", "legend" : {"orient" : "bottom"}, "scale" : {"type" : "symlog","scheme": "purples"} } } }, { "mark": { "type": "boxplot", //"extent": "min-max" }, //height : 200, "encoding": { "y": {"field": "type", "type": "nominal", axis: {"title" : cfield, "titleFontSize": 14, "labelFontSize" : 12, "labelFont" : "courier"}}, "x": { "field": "value", "type": "quantitative", "scale": {"zero": false, "type" : "linear"}, "axis" : {"title" : null, "grid" : false, "titleFontSize": 14}, }, "color" : {"value" : "purple"} } }, ] })33:T734,variant_density = (data, field, label)=>{ label = label || field; return vegalite ({ "config": { "style": { "cell": { "stroke": "transparent" } } }, //"resolve": {"scale": {"x": "independent"}}, //"title" : title ? title[i] : null, "data": { "values": _.filter (data, (c)=>_.isNumber (c[field])) }, "layer" : [ { "width": 800, "height": 60, "transform":[{ "density": field, "bandwidth": 0 }], "mark": {type: "area", "opacity" : 0.2, line : true, clip: true}, "encoding": { "x": { "field": "value", "grid" : null, "title": label, "type": "quantitative", "scale" : {"type" : "linear"}, "axis": {"grid": false, "titleFontSize" : 14, "labelFontSize" : 12} }, "y": { "field": "density", "type": "quantitative", "title" : "Density (AU)", "axis": {"grid": false, "titleFontSize" : 14} }, "color" : {"value" : "grey"}, } }, { "mark": {type: "tick", "opacity" : 0.5, clip: true, tooltip : {"content" : "data"}, size : 15, thickness: 2}, "transform":[{ "calculate": "-0", "as": "placement" }], "encoding": { "x": { "field": field, "grid" : null, //"title": "AV frequency", "type": "quantitative", "axis": {"grid": false} }, "y" : { "type": "quantitative", "field" : "placement" }, "color" : {"value" : "firebrick"}, } } ] } ); }34:Td4d,html` `35:[] 2f:{"id":"b05f3f12e7de98c4","slug":null,"title":"ARGOS NGS QC data exploration","thumbnail":"97f6275d5d4d533453d8594f7fe0decdfb7cc9c4a5ce216dd61ccc4e3d9856f3","access_level":"public","create_time":"$D2022-08-24T17:07:04.556Z","update_time":"$D2022-11-11T02:32:02.981Z","view_time":null,"first_public_time":"$D2022-12-14T18:53:06.135Z","has_unpublished_edits":null,"fork":{"id":"33112ca3d3a2cd80","slug":null,"title":"ARGOS NGS QC Summary Data","owner":{"id":"adea462ffc6621bd","login":"jgergely","name":"Joe 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(\" + x.count + \")\", value: listOfOrganisms.find(t => t.tag === \"Salmonella_enterica\")})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1394,"value":"viewof dataset2 = Inputs.select(listOfLineages, {label: \"Lineages\", format: x => x.label + \" (\" + x.count + \")\", value: listOfLineages.find(t => t.tag === \"strain_LT2\")})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":926,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1111,"value":"viewof numerical_field = Inputs.select(numerical_fields, {label: \"Numerical field\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1117,"value":"variant_density (table_data, numerical_field)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1138,"value":"viewof numerical_field_x = Inputs.select(numerical_fields, {label: \"Numerical field\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1140,"value":"viewof categorical_field_x = Inputs.select(categorical_fields, {label: \"Categorical field\", \"value\" : \"instrument\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1160,"value":"vegalite(contrast_plot (numerical_field_x,categorical_field_x))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1191,"value":"viewof numerical_x = Inputs.select(numerical_fields, {label: \"x\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1194,"value":"viewof numerical_y = Inputs.select(numerical_fields, {label: \"y\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1209,"value":"vegalite (compareEstimates (table_data, numerical_x, numerical_y))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":986,"value":"viewof searchHT = Inputs.search(selectedOrganism)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1237,"value":"embed = 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data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"viewof table_data = Inputs.table(searchHT, {\n \"height\" : 500\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1202,"value":"html`

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":878,"value":"qc_data = await d3.tsv (\"https://raw.githubusercontent.com/Jgergely11/test2/main/.github/workflows/ngsQC_HL.tsv\",d3.autoType)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":908,"value":"listOfOrganisms = _.chain (qc_data).countBy ((d)=>d.organism_name).map ((d,k)=>({'label' : k.split ('_').join (' '), 'tag' : k, 'count' : d})).value()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":937,"value":"selectedOrganism = _.filter (qc_data, (d)=>d.organism_name == dataset.tag)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1398,"value":"selectedLineage = _.filter (qc_data, (d)=>d.lineage == dataset2.tag)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1392,"value":"listOfLineages = _.chain (qc_data).countBy ((d)=>d.lineage).map ((d,k)=>({'label' : k.split ('_').join (' '), 'tag' : k, 'count' : d})).value()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1086,"value":"numerical_fields = _.filter (_.keys (selectedOrganism[0]), (d)=> {\n const number_count = _.countBy (selectedOrganism, (c)=>_.isNumber (c[d]) ? 1 : 0);\n return (number_count[1] || 0) > (number_count[0] || 0);\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1129,"value":"categorical_fields = _.filter (_.keys (selectedOrganism[0]), (d)=> {\n const number_count = _.countBy (selectedOrganism, (c)=>_.isNumber (c[d]) ? 1 : 0);\n const cat_count = _.size(_.countBy (selectedOrganism, (c)=>c[d]));\n return (number_count[1] || 0) < (number_count[0] || 0) && cat_count <= 10 && cat_count >= 2;\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":504,"value":"data_sources = [\n {'url' : 'https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_EMPIRICAL_UNMASKED_SELECTOME_BUSTEDS_and_BUSTEDS-MH.csv', 'label' : \"Selectome\"},\n {'url': \"https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_13Datasets_BUSTEDS_and_BUSTEDS-MH.csv\", \"label\" : \"13 datasets\"},\n {'url' : \"https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_SIMULATIONS-SHULTZ-SACKTON_BUSTEDS_and_BUSTEDS-MH.csv\", \"label\" : \"Null simulations\"}\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"stratify_data = (data, nfield, cfield) => {\n return _.filter (_.map (data, (c)=> {\n return {'value' : c[nfield], 'type' : c[cfield]}\n }), (d)=>_.isNumber (d.value));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":1152,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":626,"value":"extract_omega_distributions = (d)=> {\n let result = [];\n\n _.each ([\"BUSTEDS\",\"BUSTEDS-MH\"], (model)=> {\n _.each ([[\"w1\",\"p1\"],[\"w2\",\"p2\"],[\"w3\",\"p3\"]], (rate,i)=> {\n let record = {};\n record.gene = d.gene;\n record.type = model;\n record.value = d[model + \"|\" + rate[0]];\n record.weight = d[model + \"|\" + rate[1]];\n record.index = i;\n result.push (record);\n });\n });\n return result;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":265,"value":"binByGene = (data, p, aggregator, filter) => {\n p = p || 0.05;\n aggregator = aggregator || ((d)=>0);\n filter = filter || ((d)=>true);\n const data_2 = _.chain (data).groupBy ((d)=>d.Gene).mapValues ((d)=>_.groupBy (d, (c)=>c.Method)).mapValues (d=>_.mapValues (d, (c)=>c[0])).value();\n //return data_2;\n let result = [];\n _.each (data_2, (d, g)=> {\n let rec = {};\n rec.gene = g;\n if ((\"BUSTEDS\" in d) && (\"BUSTEDS-MH\" in d)) {\n if (filter (d)) {\n rec.ps = (d[\"BUSTEDS\"][\"LRT p-value\"] <= p ? 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SH+	${formatP(m21)}	${formatP(m22)}	${formatP(m21+m22)}
Total	${formatP(m11+m21)}	${formatP(m12+m22)}	${N}

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