31:Tb92,vegalite ({ "data": { "values": _.filter (for_par_cor, (d)=>d.class != '--' && d.class != '-+' && d["BUSTEDS-MH|cAIC"] > d["BUSTEDS|cAIC"]) }, "width": 600, "height": 600, "transform": [ {"window": [{"op": "count", "as": "index"}]}, {"fold": ["DH_Rate", "TH_Rate", "MH|omega3","SH|omega3"]}, { "joinaggregate": [ {"op": "min", "field": "value", "as": "min"}, {"op": "max", "field": "value", "as": "max"} ], "groupby": ["key"] }, { "calculate": "(datum.value - datum.min) / (datum.max-datum.min)", "as": "norm_val" }, { "calculate": "(datum.min + datum.max) / 2", "as": "mid" } ], "layer": [{ "mark": {"type": "rule", "color": "#ccc"}, "encoding": { "detail": {"aggregate": "count"}, "x": {"field": "key", "scale" : {"domain" : ["SH|omega3", "MH|omega3", "DH_Rate", "TH_Rate"]}} } }, { "mark": "line", "encoding": { "color": {"type": "nominal", "field": "class", "legend" : {"symbolOpacity" : 1, "orient" : "bottom", "titleFontSize" : 16, "labelFontSize" : 16}}, "detail": {"type": "nominal", "field": "index"}, "opacity": {"value": 0.3}, "x": {"type": "nominal", "field": "key"}, "y": {"type": "quantitative", "field": "norm_val", "axis": null}, /*"tooltip": [{ "type": "quantitative", "field": "Beak Length (mm)" }, { "type": "quantitative", "field": "Beak Depth (mm)" }, { "type": "quantitative", "field": "Flipper Length (mm)" }, { "type": "quantitative", "field": "Body Mass (g)" }]*/ } }, { "encoding": { "x": {"type": "nominal", "field": "key"}, "y": {"value": 0} }, "layer": [{ "mark": {"type": "text", "style": "label"}, "encoding": { "text": {"aggregate": "max", "field": "max"} } }, { "mark": {"type": "tick", "style": "tick", "size": 8, "color": "#ccc"} }] }, { "encoding": { "x": {"type": "nominal", "field": "key"}, "y": {"value": 150} }, "layer": [{ "mark": {"type": "text", "style": "label"}, "encoding": { "text": {"aggregate": "min", "field": "mid"} } }, { "mark": {"type": "tick", "style": "tick", "size": 8, "color": "#ccc"} }] }, { "encoding": { "x": {"type": "nominal", "field": "key"}, "y": {"value": 300} }, "layer": [{ "mark": {"type": "text", "style": "label"}, "encoding": { "text": {"aggregate": "min", "field": "min"} } }, { "mark": {"type": "tick", "style": "tick", "size": 8, "color": "#ccc"} }] }], "config": { "axisX": {"domain": false, "labelAngle": 0, "tickColor": "#ccc", "title": null}, "view": {"stroke": null}, "style": { "label": {"baseline": "middle", "align": "right", "dx": -5}, "tick": {"orient": "horizontal"} } } })32:T9ba,vegalite ( { "width": 200, "height": 70, "layer" : [/*{ "data": { "values": extract_omega_distributions (omega[2]) }, "mark": { "type": "circle", "opacity": 0.8, "stroke": "black", "strokeWidth": 1 }, "encoding": { "x": { "field": "value", "type": "quantitative", "axis": {"grid": false, "title" : false, "titleFontSize" : 14, "tickCount" : 5}, "scale" : {"type" : "symlog"} }, "y": { "field" : "y", "type": "quantitative", "axis" : null }, "color" : {"field" : "type", "legend" : {"title" : null, "orient" : "top"}}, "size": { "field": "weight", "type": "quantitative", "title": "Proportion", "legend": false,//{"clipHeight": 50, "orient": "top"}, "scale": {"rangeMax": 400} }, }},*/ { "data" : {"values" : _.chain (extract_omega_distributions (omega[2])).groupBy (d=>d.index).map (d=>{ let wedge = []; let result = {}; result.y = d[0].type == "BUSTEDS" ? 1 : 0; let pair = [d[0].value - Math.sqrt(d[0].weight)*0.25, d[1].value - Math.sqrt(d[1].weight)*0.25]; result.x = d3.min (pair); result.x2 = d3.max (pair); wedge.push (_.clone (result)); result.y = d[1].type == "BUSTEDS" ? 1 : 0; pair = [d[0].value + Math.sqrt(d[0].weight)*0.25, d[1].value + Math.sqrt(d[1].weight)*0.25]; result.x = d3.min (pair); result.x2 = d3.max (pair); wedge.push (_.clone (result)) return wedge; }).value()[0]}, "mark": {"type": "area", "opacity" : 0.5, "color":"black"}, "encoding" : { "y": {"field": "y", "type": "quantitative"}, //"y2": {"datum": {"expr": "'BUSTEDS-MH'"},"type": "nominal"}, "x": { "field": "x", "type" : "quantitative", //"axis" : {"grid" : false, "title" : "IC50"}, }, "x2": { "field": "x2", "type" : "quantitative", //"axis" : null, } } }, /*{ "mark": { "type": "rule", "color": "red", "strokeWidth": "2", }, "encoding": { "x": { "datum": {"expr": "1"}, "type": "quantitative", } } }*/ ], "config": { "style": { "cell": { "stroke": "transparent" } } } } )33:T428,data_sources = [ {'url' : 'https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_EMPIRICAL_UNMASKED_SELECTOME_BUSTEDS_and_BUSTEDS-MH.csv', 'label' : "Selectome"}, {'url': "https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_14-datasets_results.csv", "label" : "14 datasets"}, {'url' : "https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_SIMULATIONS-SHULTZ-SACKTON_BUSTEDS_and_BUSTEDS-MH.csv", "label" : "Null simulations"}, {'url': "https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_EMPIRICAL_SHULTZ_results.csv", "label": "Shultz"}, {'url': "https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_EMPIRICAL_ENARD_results.csv", "label": "Enard"}, {'url': "https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_Empirical_mtDNAVertebrate_results.csv", "label": "mtDNA_Vertebrate"}, {'url': "https://raw.githubusercontent.com/aglucaci/BUSTEDS-MH/main/tables/Table_Empirical_mtDNAInvertebrate_results.csv", "label": "mtDNA_Invertebrate"}]34:T5c6,contrast_plot = (agg,filter,plot_title, axis_label) => ({ "data": {"values": binByGene (data, 0.05, agg, filter)}, "title" : plot_title, "hconcat" : [{ "mark": { "type": "boxplot", "extent": "min-max" }, //height : 200, "encoding": { "y": {"field": "ps", "type": "nominal", "scale" : {"domain" : ['--','++','-+','+-']}, "axis" : {"title" : "Classification", "titleFontSize": 16, "labelFontSize" : 16, "labelFont" : "courier"}}, "x": { "field": "delta", "type": "quantitative", "scale": {"zero": false, "type" : "sqrt"}, "axis" : {"title" : axis_label, "titleFontSize": 14}, }, "color" : {"value" : "purple"} } }, { "mark": { "type": "rect", //"extent": "min-max" }, //height : 200, "encoding": { "y": {"field": "ps", "type": "nominal", "scale" : {"domain" : ['--','++','-+','+-']}, "axis" : {"title" : "", "labels" : false, "titleFontSize": 16, "labelFontSize" : 16, "labelFont" : "courier"}}, "x": { "field": "delta", "type": "quantitative", "bin": {"maxbins":60}, "scale": {"type" : "linear"}, "axis" : {"title" : axis_label, "titleFontSize": 14}, }, "color": { "aggregate": "count", "type": "quantitative", "title" : "Count", "legend" : {"orient" : "bottom"}, "scale" : {"type" : "symlog","scheme": "purples"} } } }] })35:T778,compareEstimates = (data, field, title_x, title_y, field_2) => ( { "data": {"values": data}, "hconcat" : [{ "width" : 400, "height" : 400, "mark": "rect", "transform": [ {"filter" : "datum['BUSTEDS|cAIC'] > datum['BUSTEDS-MH|cAIC']"} ], "title" : {"text" :"Multi-hit preferred by cAIC", "fontSize" : 20}, "encoding": { "x": {"field": "BUSTEDS|" + field, "type": "quantitative", "scale" : {"type" : "linear"}, "axis" : {"title" : title_x, "titleFontSize" : 18, "tickCount" : 10}, "bin": {"maxbins":50}}, "y": {"field": "BUSTEDS-MH|" + (field_2||field), "type": "quantitative", "scale" : {"type" : "linear"},"axis" : {"tickCount" : 10, "title" : title_y, "titleFontSize" : 18}, "bin": {"maxbins":50}}, "size" : {"value" : 5}, "color": { "aggregate": "count", "type": "quantitative", "title" : "Count", "legend" : {"orient" : "bottom"}, "scale" : {"type" : "symlog","scheme": "purples"} } } }, { "title" : {"text" :"Single-hit preferred by cAIC", "fontSize" : 20}, "width" : 400, "height" : 400, "mark": "rect", "transform": [ {"filter" : "datum['BUSTEDS|cAIC'] <= datum['BUSTEDS-MH|cAIC']"} ], "encoding": { "x": {"field": "BUSTEDS|" + field, "type": "quantitative", "scale" : {"type" : "linear"}, "axis" : {"title" : title_x, "titleFontSize" : 18, "tickCount" : 10}, "bin": {"maxbins":50}}, "y": {"field": "BUSTEDS-MH|" + (field_2||field), "type": "quantitative", "scale" : {"type" : "linear"},"axis" : {"tickCount" : 10, "title" : "", "titleFontSize" : 18}, "bin": {"maxbins":50}}, "size" : {"value" : 5}, "color": { "aggregate": "count", "type": "quantitative", "title" : "Count", "legend" : {"orient" : "bottom"}, "scale" : {"type" : "symlog","scheme": "purples"} } } }] } )36:[] 2f:{"title":"BUSTED[S] vs BUSTED[S]-MH","cells":[{"id":4,"value":"# BUSTED[S] vs BUSTED[S]-MH\n","pinned":false,"hidden":false,"mode":"md"},{"id":507,"value":"viewof dataset = Inputs.select(data_sources, {label: \"Dataset\", format: x => x.label, value: data_sources.find(t => t.label === \"Selectome\")})","pinned":false,"hidden":false,"mode":"ojs"},{"id":6,"value":"viewof search = Inputs.search(data)","pinned":false,"hidden":false,"mode":"ojs"},{"id":7,"value":"Inputs.table(search, {\n format: {\n Year: d3.format(\"d\") // format as \"1960\" rather than \"1,960\"\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":219,"value":"md`**Table 1**. Method performance comparison (all data, p = 0.05)`","pinned":false,"hidden":false,"mode":"ojs"},{"id":153,"value":"twoByTwo (...getCounts (pv))","pinned":false,"hidden":false,"mode":"ojs"},{"id":223,"value":"md`**Table 2**. Method performance comparison (all data, p = 0.001)`","pinned":false,"hidden":false,"mode":"ojs"},{"id":226,"value":"twoByTwo (...getCounts (pv, 0.001))","pinned":false,"hidden":false,"mode":"ojs"},{"id":229,"value":"md`**Table 3**. Method performance comparison (MH preferred, p = 0.05)`","pinned":false,"hidden":false,"mode":"ojs"},{"id":233,"value":"twoByTwo (...getCounts (_.filter (pv, (datum)=>datum['BUSTEDS|cAIC'] > datum['BUSTEDS-MH|cAIC'])))","pinned":false,"hidden":false,"mode":"ojs"},{"id":239,"value":"md`**Table 4**. Method performance comparison (SH preferred, p = 0.05)`","pinned":false,"hidden":false,"mode":"ojs"},{"id":242,"value":"twoByTwo (...getCounts (_.filter (pv, (datum)=>datum['BUSTEDS|cAIC'] < datum['BUSTEDS-MH|cAIC'])))","pinned":false,"hidden":false,"mode":"ojs"},{"id":296,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.min (2,d[\"BUSTEDS-MH\"].DH_Rate);}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\", \"Double hit rate\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":399,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.min (2,d[\"BUSTEDS-MH\"].DH_Rate);}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC > d[\"BUSTEDS\"].cAIC,\"SH preferred by AIC\", \"Double hit rate\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":374,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.min (2,d[\"BUSTEDS-MH\"].TH_Rate);}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\",\"Triple hit rate\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":576,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.min (2, d[\"BUSTEDS-MH\"].TH_Rate);}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC >= d[\"BUSTEDS\"].cAIC,\"SH preferred by AIC\",\"Triple hit rate\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":461,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.max (-2, Math.min (2,d[\"BUSTEDS-MH\"].w1 * d[\"BUSTEDS-MH\"].p1 +d[\"BUSTEDS-MH\"].w2 * d[\"BUSTEDS-MH\"].p2 + d[\"BUSTEDS-MH\"].w3 * d[\"BUSTEDS-MH\"].p3 - (d[\"BUSTEDS\"].w1 * d[\"BUSTEDS\"].p1 +d[\"BUSTEDS\"].w2 * d[\"BUSTEDS\"].p2 + d[\"BUSTEDS\"].w3 * d[\"BUSTEDS\"].p3) ));}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\",\"E [MH-ω - SH-ω]\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":519,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.max (-2, Math.min (2,d[\"BUSTEDS-MH\"].w1 * d[\"BUSTEDS-MH\"].p1 +d[\"BUSTEDS-MH\"].w2 * d[\"BUSTEDS-MH\"].p2 + d[\"BUSTEDS-MH\"].w3 * d[\"BUSTEDS-MH\"].p3 - (d[\"BUSTEDS\"].w1 * d[\"BUSTEDS\"].p1 +d[\"BUSTEDS\"].w2 * d[\"BUSTEDS\"].p2 + d[\"BUSTEDS\"].w3 * d[\"BUSTEDS\"].p3) ));}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC >= d[\"BUSTEDS\"].cAIC,\"SH preferred by AIC\",\"E [MH-ω - SH-ω]\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":563,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.sqrt(d[\"BUSTEDS\"].Sequences * d[\"BUSTEDS\"].Codons);}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\",\"Sqrt (Sample Size)\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":480,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.max (-2, Math.min (2,d[\"BUSTEDS-MH\"].w1 - d[\"BUSTEDS\"].w1));}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\",\"MH-ω1 - SH-ω1\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":487,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.max (-2, Math.min (2,d[\"BUSTEDS-MH\"].w2 - d[\"BUSTEDS\"].w2));}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\",\"MH-ω2 - SH-ω2\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":491,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.max (-2, Math.min (2,d[\"BUSTEDS-MH\"].w3 - d[\"BUSTEDS\"].w3));}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC < d[\"BUSTEDS\"].cAIC,\"MH preferred by AIC\",\"MH-ω3 - SH-ω3\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":516,"value":"vegalite (contrast_plot (\n (d, res)=> {res.delta = Math.max (-2, Math.min (2,d[\"BUSTEDS-MH\"].w3 - d[\"BUSTEDS\"].w3));}, \n (d)=>d[\"BUSTEDS-MH\"].cAIC >= d[\"BUSTEDS\"].cAIC,\"SH preferred by AIC\",\"MH-ω3 - SH-ω3\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":71,"value":"vegalite (compareEstimates (pv, \"LRT p-value\", \"SH p\", \"MH p\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":430,"value":"vegalite (compareEstimates (srv, \"CV(alpha)\", \"SH CV(alpha)\", \"MH CV(alpha)\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":776,"value":"vegalite (compareEstimates (_.filter (pv, (d)=>d[\"BUSTEDS|LRT p-value\"] < 0.05 && d[\"BUSTEDS-MH|LRT p-value\"] >= 0.05), \"selected\", \"SH selected\", \"MH selected\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":530,"value":"vegalite (compareEstimates (_.filter (pv, (d)=>d[\"BUSTEDS|LRT p-value\"] < 0.05 && d[\"BUSTEDS-MH|LRT p-value\"] >= 0.05), \"delta\", \"log (p|MH) - log (p|SH)\", \"DH Rate\",\"DH_Rate\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":898,"value":"vegalite (compareEstimates (_.filter (pv2, (d)=>d[\"BUSTEDS|LRT p-value\"] < 0.05 && d[\"BUSTEDS-MH|LRT p-value\"] >= 0.05), \"psi\", \"log (p|MH) - log (p|SH)\", \"TH Rate\",\"TH_Rate\"))","pinned":false,"hidden":false,"mode":"ojs"},{"id":579,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":868,"value":"## Experimental Viz","pinned":true,"hidden":false,"mode":"md"},{"id":635,"value":"vegalite (plot_omega (_.filter (extract_omega_distributions (omega[2]), (d)=>d.type == \"BUSTEDS-MH\"), false))\n ","pinned":false,"hidden":false,"mode":"ojs"},{"id":856,"value":"vegalite (plot_omega (_.filter (extract_omega_distributions (omega[2]), (d)=>d.type == \"BUSTEDS\"), false))","pinned":false,"hidden":false,"mode":"ojs"},{"id":802,"value":"_.chain (extract_omega_distributions (omega[2])).groupBy (d=>d.index).map (d=>{\n let wedge = [];\n let result = {};\n result.y = d[0].type == \"BUSTEDS\" ? 1 : 0;\n let pair = [d[0].value - Math.sqrt(d[0].weight)*0.25, d[1].value - Math.sqrt(d[1].weight)*0.25];\n result.x = d3.min (pair); result.x2 = d3.max (pair);\n wedge.push (_.clone (result));\n result.y = d[1].type == \"BUSTEDS\" ? 1 : 0;\n pair = [d[0].value + Math.sqrt(d[0].weight)*0.25, d[1].value + Math.sqrt(d[1].weight)*0.25];\n result.x = d3.min (pair); result.x2 = d3.max (pair);\n wedge.push (_.clone (result))\n return wedge;\n }).value()[0]","pinned":false,"hidden":false,"mode":"ojs"},{"id":853,"value":"extract_omega_distributions (omega[2])","pinned":false,"hidden":false,"mode":"ojs"},{"id":810,"value":"extract_omega_distributions (omega[2])","pinned":false,"hidden":false,"mode":"ojs"},{"id":699,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":882,"value":"## Evidence Ratio analysis","pinned":false,"hidden":false,"mode":"md"},{"id":879,"value":"Plot.plot({\n y: {\n grid: true\n },\n color: {\n legend: true\n },\n marks: [\n Plot.rectY(search, Plot.binX({y: \"count\"}, {x: \"NUM_ER_SITES\", fill: \"Method\"})),\n Plot.ruleY([0])\n ]\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":871,"value":"## Imports / Declares","pinned":false,"hidden":false,"mode":"md"},{"id":630,"value":"extract_omega_distributions (omega[0])","pinned":false,"hidden":false,"mode":"ojs"},{"id":727,"value":"_.chain (extract_omega_distributions (omega[0])).groupBy (d=>d.index).map (d=>{\n let result = {};\n result[d[0].type] = d[0].value;\n result[d[1].type] = d[1].value;\n return result;\n}).value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":68,"value":"pv = contrastByGene (data, [\"LRT p-value\",\"cAIC\",\"DH_Rate\",\"p3\",\"w3\"], (d)=> {\n d[\"BUSTEDS-MH|DH_Rate\"] = Math.min (1, d[\"BUSTEDS-MH|DH_Rate\"]);\n d[\"BUSTEDS|delta\"] = Math.log (Math.max (1e-10,d[\"BUSTEDS-MH|LRT p-value\"])) - Math.log (Math.max (1e-10,d[\"BUSTEDS|LRT p-value\"]));\n d[\"BUSTEDS-MH|selected\"] = Math.log (Math.max (1e-10,d[\"BUSTEDS-MH|p3\"]*d[\"BUSTEDS-MH|w3\"]));\n d[\"BUSTEDS|selected\"] = Math.log (Math.max (1e-10,d[\"BUSTEDS|p3\"]*d[\"BUSTEDS|w3\"]));\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":907,"value":"pv2 = contrastByGene (data, [\"LRT p-value\",\"cAIC\",\"TH_Rate\",\"p3\",\"w3\"], (d)=> {\n d[\"BUSTEDS-MH|TH_Rate\"] = Math.min (1, d[\"BUSTEDS-MH|TH_Rate\"]);\n d[\"BUSTEDS|psi\"] = Math.log (Math.max (1e-10,d[\"BUSTEDS-MH|LRT p-value\"])) - Math.log (Math.max (1e-10,d[\"BUSTEDS|LRT p-value\"]));\n d[\"BUSTEDS-MH|selected\"] = Math.log (Math.max (1e-10,d[\"BUSTEDS-MH|p3\"]*d[\"BUSTEDS-MH|w3\"]));\n d[\"BUSTEDS|selected\"] = Math.log (Math.max (1e-10,d[\"BUSTEDS|p3\"]*d[\"BUSTEDS|w3\"]));\n})","pinned":true,"hidden":false,"mode":"ojs"},{"id":585,"value":"for_par_cor = contrastByGene (data, [\"LRT p-value\",\"cAIC\",\"DH_Rate\",\"TH_Rate\",\"w3\"], (d)=> {\n d[\"class\"] = (d[\"BUSTEDS|LRT p-value\"] <= 0.05 ? \"+\" : \"-\") + (d[\"BUSTEDS-MH|LRT p-value\"] <= 0.05 ? \"+\" : \"-\");\n d[\"DH_Rate\"] = Math.min (0.5, d[\"BUSTEDS-MH|DH_Rate\"]);\n d[\"TH_Rate\"] = Math.min (0.5, d[\"BUSTEDS-MH|TH_Rate\"]);\n d[\"MH|omega3\"] = Math.log (d[\"BUSTEDS-MH|w3\"]);\n d[\"SH|omega3\"] = Math.log (d[\"BUSTEDS|w3\"]);\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":425,"value":"srv = contrastByGene (data, [\"cAIC\", \"CV(alpha)\"])","pinned":false,"hidden":false,"mode":"ojs"},{"id":436,"value":"omega = contrastByGene (data, [\"cAIC\", \"w1\",\"w2\",\"w3\",\"p1\",\"p2\",\"p3\"], (d)=> {\n d[\"BUSTEDS|mean\"] = Math.min (2, d[\"BUSTEDS|w1\"] * d[\"BUSTEDS|p1\"] + d[\"BUSTEDS|w2\"] * d[\"BUSTEDS|p2\"] + d[\"BUSTEDS|w3\"] * d[\"BUSTEDS|p3\"]) ;\n d[\"BUSTEDS-MH|mean\"] = Math.min( d[\"BUSTEDS-MH|w1\"] * d[\"BUSTEDS-MH|p1\"] + d[\"BUSTEDS-MH|w2\"] * d[\"BUSTEDS-MH|p2\"] + d[\"BUSTEDS-MH|w3\"] * d[\"BUSTEDS|p3\"],2 );\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":875,"value":"### Data tables, Github repo","pinned":false,"hidden":false,"mode":"md"},{"id":504,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":25,"value":"data = await d3.csv (dataset.url,d3.autoType)","pinned":false,"hidden":false,"mode":"ojs"},{"id":31,"value":"contrastByGene = (data, field, pp) => {\n let result = {};\n _.each (data, (r)=> {\n const gene = r.Gene;\n if (! (gene in result)) {\n result[gene] = {};\n }\n _.each (field, (f) => {\n result[gene][r.Method + \"|\" + f] = r[f];\n });\n if (pp) {\n pp (result[gene]);\n }\n });\n return _.chain (result).toPairs().map (d=>_.extend ({'gene' : d[0]}, d[1])).value();\n}","pinned":false,"hidden":false,"mode":"ojs"},{"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"},{"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 ? \"+\" : \"-\") + (d[\"BUSTEDS-MH\"][\"LRT p-value\"] <= p ? \"+\" : \"-\");\n aggregator (d, rec);\n result.push (rec);\n }\n }\n });\n return result;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":380,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":148,"value":"twoByTwo = (m11,m12,m21,m22) => {\n const N = m11 + m12 + m21 + m22;\n const fmtP = d3.format (\".3p\");\n const formatP = (d)=>\"\" + d + \" (\" + fmtP (d/N) + \")\";\n return html`\n \n \n \n \n \n

	MH-	MH+	Total
SH-	${formatP(m11)}	${formatP(m12)}	${formatP(m11+m21)}
SH+	${formatP(m21)}	${formatP(m22)}	${formatP(m21+m22)}
Total	${formatP(m11+m21)}	${formatP(m12+m22)}	${N}

\n Cohen's κ = ${cohen_kappa (m11, m12, m21, m22)}\n `;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":247,"value":"cohen_kappa = (m11, m12, m21, m22) => {\n const N = m11 + m12 + m21 + m22; \n const p_0 = (m11 + m22) / N;\n const p_e = ((m11 + m12) * (m11 + m21) + (m21 + m22) * (m12 + m22)) / N / N;\n return (p_0 - p_e) / (1 - p_e);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":197,"value":"getCounts = (d,p)=> {\n p = p || 0.05;\n return [_.filter (d, (c)=>c[\"BUSTEDS|LRT p-value\"] >p && c[\"BUSTEDS-MH|LRT p-value\"] >p).length,\n _.filter (d, (c)=>c[\"BUSTEDS|LRT p-value\"] >p && c[\"BUSTEDS-MH|LRT p-value\"] <=p).length,\n _.filter (d, (c)=>c[\"BUSTEDS|LRT p-value\"] <=p && c[\"BUSTEDS-MH|LRT p-value\"] > p).length,\n _.filter (d, (c)=>c[\"BUSTEDS|LRT p-value\"] <=p && c[\"BUSTEDS-MH|LRT p-value\"] <= p).length];\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":407,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":693,"value":"plot_omega = (d, label)=> (\n {\n \"data\": {\n \"values\": d\n },\n \"width\": 200,\n //\"height\": 400,\n \"layer\" : [{\n \"mark\": {\n \"type\": \"circle\",\n \"opacity\": 0.8,\n \"stroke\": \"black\",\n \"strokeWidth\": 1\n },\n \"encoding\": {\n \"x\": {\n \"field\": \"value\",\n \"type\": \"quantitative\",\n \"axis\": {\"grid\": false, \"title\" : label ? label : false, \"titleFontSize\" : 14, \"tickCount\" : 5},\n \"scale\" : {\"type\" : \"symlog\"}\n },\n \"color\" : {\"value\" : \"darkgrey\"},\n \"size\": {\n \"field\": \"weight\",\n \"type\": \"quantitative\",\n \"title\": \"Proportion\",\n \"legend\": false,//{\"clipHeight\": 50, \"orient\": \"top\"},\n \"scale\": {\"rangeMax\": 400}\n },\n }},{\n \"mark\": {\n \"type\": \"rule\",\n \"color\": \"red\",\n \"strokeWidth\": \"2\",\n },\n \"encoding\": {\n \"x\": {\n \"datum\": {\"expr\": \"1\"},\n \"type\": \"quantitative\",\n }\n }\n }\n \n \n ],\n \"config\": {\n \"style\": {\n \"cell\": {\n \"stroke\": \"transparent\"\n }\n }\n }\n}\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":65,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W36","stdlib":"1","titling":"auto"}