29:null 2a:["$","title",null,{"children":"BUSTED-E results with HMMCleaner AND BMGE using schulz-sackton data | Avery Selberg | Observable"}] 2f:T434,detection_plot ? md`View detailed results: BUSTED: ${detection_plot.ID}${suffix['BUSTED p-val'][1]} BUSTED-E: ${detection_plot.ID}${suffix['BUSTED-E p-val'][1]} HMM + BUSTED: ${detection_plot.ID}${suffix['BUSTED_HMM p-val'][1]} BMGE + BUSTED: ${detection_plot.ID}${suffix['BUSTED_BMGE p-val'][1]}` : md`Select a bubble to view more details for BUSTED, BUSTED-E, HMM + BUSTED, BMGE + BUSTED`30:T5a6,viewof detection_plot = { let xvar = compare1 + ' p-val' let yvar = compare2 + ' p-val' return Plot.plot({ round: true, height: 330, width : 450, marginTop: 30, marginBottom: 40, marginLeft: 50, paddingBottom : 10, x: {type: "log", "tickFormat" : "2f", "domain" : [1e-8,0.5], "clamp" : true, 'label' : xvar }, y: {type: "log", "tickFormat" : "2f", "domain" : [1e-8,0.5], "clamp" : true, 'label' : yvar }, marks: [ Plot.dot(table_data, {"x": xvar, "y" : yvar, "opacity" : 0.5, "fill" : "darkgrey", channels : {Gene: 'ID', BUSTEDE_filtered : 'BUSTED-E % sites filtered', HMM_filtered : 'HMM % sites filtered', BMGE_filtered : 'BMGE % sites filtered'}, tip: true}), Plot.dot(table_data, Plot.pointer({x: xvar, y: yvar, fill: "dodgerblue"})), Plot.text ([ {"x" : 0.0000001, "y": 0.0000001, "t" : _.filter (table_data, (d)=>d[xvar] <= pvcut && d[yvar] <= pvcut).length}, {"x" : 0.0000001, "y": 0.1, "t" : _.filter (table_data, (d)=>d[xvar] <= pvcut && d[yvar] > pvcut).length}, {"y" : 0.0000001, "x": 0.15, "t" : _.filter (table_data, (d)=>d[xvar] > pvcut && d[yvar] <= pvcut).length}, {"y" : 0.1, "x": 0.15, "t" : _.filter (table_data, (d)=>d[xvar] > pvcut && d[yvar] > pvcut).length} ], {"x" : "x", "y" : "y", "text" : "t", "fontSize" : 14, "fill" : "firebrick"}), Plot.ruleY([pvcut]), Plot.ruleX([pvcut]), Plot.ruleY([0]) ] }) }31:T650,upset_data = { let data = []; // Function to add element with scenario to all_psg array function addToAllPsg(id, scenario) { let foundIndex = data.findIndex(obj => obj.name === id); if (foundIndex !== -1) { data[foundIndex].sets.push(scenario); } else { data.push({ name: id, sets: [scenario] }); } } let busted_e_psg = _.map(_.filter (table_data, (d)=>d['BUSTED-E p-val'] <= pvcut), d=> d.ID) let HMM_psg = _.map(_.filter (table_data, (d)=>d['HMM_BUSTED p-val'] <= pvcut), d=> d.ID) let BMGE_psg = _.map(_.filter (table_data, (d)=>d['BMGE_BUSTED p-val'] <= pvcut), d=> d.ID) let unfiltered_psg = _.map(_.filter (table_data, (d)=>d['BUSTED p-val'] <= pvcut), d=> d.ID) let HMM_bustede_psg = _.map(_.filter (table_data, (d)=>d['HMM_BUSTED-E p-val'] <=pvcut), d=>d.ID) let BMGE_bustede_psg = _.map(_.filter (table_data, (d)=>d['BMGE_BUSTED-E p-val'] <=pvcut), d=>d.ID) //let all_genes = _.map(table_data, d=> d.ID) //let all_selected = _.union(busted_e_psg, BMGE_psg) //let no_selection = _.difference(_.map(table_data, d=> d.ID), all_selected) //all_genes.forEach(id => addToAllPsg(id, "All genes")); HMM_psg.forEach(id => addToAllPsg(id, "HMMCleaner")); BMGE_psg.forEach(id => addToAllPsg(id, "BMGE")); busted_e_psg.forEach(id => addToAllPsg(id, "BUSTED-E")); unfiltered_psg.forEach(id => addToAllPsg(id, "Unfiltered")); //HMM_bustede_psg.forEach(id => addToAllPsg(id, "HMM BUSTED-E")); //BMGE_bustede_psg.forEach(id => addToAllPsg(id, "BMGE BUSTED-E")); //no_selection.forEach(id => addToAllPsg(id, "No selection")); return data }32:T621,viewof filter_plot_id = { let xvar = x_model + ' % sites filtered' let yvar = y_model + ' % sites filtered' return Plot.plot({ round: true, height: 400, width : 600, marginTop: 40, marginBottom: 40, marginLeft: 50, paddingBottom : 10, x: {type: "log", "tickFormat" : "2f", "clamp" : true, 'label' : xvar}, y: {type: "log", "tickFormat" : "2f", "clamp" : true, 'label' : yvar}, marks: [ Plot.dot(table_data, {"x": xvar, "y" : yvar, "opacity" : 0.5, "fill" : "darkgrey", channels : {Gene: 'ID'}, tip: true}), Plot.dot(table_data, Plot.pointer({x: xvar, y: yvar, fill: "dodgerblue"})), Plot.line([{'x' : 1e-5, 'y': 1e-5},{'x' : 0.05, 'y': 0.05}], {x: "x", y: "y", "stroke" : "black", strokeWidth: 0.7}), Plot.text ([ {"x" : 0.000015, "y": 0.01, "t" : _.filter (table_data, (d)=> d[xvar] === 0 && d[yvar] != 0).length}, {"x" : 0.003, "y": 0.04, "t" : _.filter (table_data, (d)=>d[xvar] < d[yvar]).length}, {"x" : 0.03, "y": 0.005, "t" : _.filter (table_data, (d)=>d[yvar] < d[xvar]).length}, {"x" : 0.01, "y": 0.00002, "t" : _.filter (table_data, (d)=> d[yvar] === 0 && d[xvar] != 0).length}, {"x" : 0.00002, "y": 0.00002, "t" : _.filter (table_data, (d)=> d[yvar] === 0 && d[xvar] === 0).length}, {"x" : 0.1, "y": 0.1, "t" : _.filter (table_data, (d)=> d[xvar] != 0 && d[yvar] != 0).length}, ], {"x" : "x", "y" : "y", "text" : "t", "fontSize" : 14, "fill" : "firebrick"}), Plot.ruleY([0]), Plot.ruleX([0]) ] }) }33:Tc13,plot_data_busted = _.flatten(_.map (results, (d, key)=> { return [ { 'ID' : key, 'omegaE' : d["BUSTED-E"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['omega'], 'log_10_omegaE' : Math.log10(d["BUSTED-E"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['omega']), 'weightE' : d["BUSTED-E"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['proportion'], 'omega3' : d["BUSTED-E"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['omega'], 'log_10_omega3' : Math.log10(d["BUSTED-E"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['omega']), 'weight3' : d["BUSTED-E"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['proportion'], 'model' : 'BUSTED-E', 'p-value' : d["BUSTED-E"]['test results']['p-value'], 'LRT' : d["BUSTED-E"]['test results']['LRT'], 'error_pval' : d['BUSTED-E']['test for error']['p-value'] }, { 'ID' : key, 'omegaE' : d["BUSTED_E_HMM"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['omega'], 'log_10_omegaE' : Math.log10(d["BUSTED_E_HMM"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['omega']), 'weightE' : d["BUSTED_E_HMM"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['proportion'], 'omega3' : d["BUSTED_E_HMM"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['omega'], 'log_10_omega3' : Math.log10(d["BUSTED_E_HMM"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['omega']), 'weight3' : d["BUSTED_E_HMM"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['proportion'], 'model' : 'BUSTED_E_HMM', 'p-value' : d["BUSTED_E_HMM"]['test results']['p-value'], 'LRT' : d["BUSTED_E_HMM"]['test results']['LRT'], 'error_pval' : d['BUSTED_E_HMM']['test for error']['p-value']}, { 'ID' : key, 'omegaE' : d["BUSTED_E_BMGE"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['omega'], 'log_10_omegaE' : Math.log10(d["BUSTED_E_BMGE"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['omega']), 'weightE' : d["BUSTED_E_BMGE"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][0]['proportion'], 'omega3' : d["BUSTED_E_BMGE"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['omega'], 'log_10_omega3' : Math.log10(d["BUSTED_E_BMGE"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['omega']), 'weight3' : d["BUSTED_E_BMGE"]["fits"]["Unconstrained model"]["Rate Distributions"]["Test"][3]['proportion'], 'model' : 'BUSTED_E_BMGE', 'p-value' : d["BUSTED_E_BMGE"]['test results']['p-value'], 'LRT' : d["BUSTED_E_BMGE"]['test results']['LRT'], 'error_pval' : d['BUSTED_E_BMGE']['test for error']['p-value']} ] })) 34:Taed,table_data = _.flatten(_.map (results, (d, key)=> { const methods = ['BUSTED', 'BUSTED-E', 'HMM_BUSTED', 'BUSTED_E_HMM', 'BMGE_BUSTED', 'BUSTED_E_BMGE']; //const methods = ['BUSTED', 'BUSTED-E', 'HMM_BUSTED', 'BMGE_BUSTED',]; let significant_methods = _.filter(methods, method => { return d[method] && d[method]['test results']['p-value'] < 0.05; }).join(',') significant_methods = significant_methods.replace('BUSTED_E_HMM', 'HMM_BUSTED-E') significant_methods = significant_methods.replace('BUSTED_E_BMGE', 'BMGE_BUSTED-E') return [ { "ID" : key, "BUSTED-E_ωE" : results[key]['BUSTED-E']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['omega'], "BUSTED-E_pE" : results[key]['BUSTED-E']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['proportion'], 'BUSTED p-val': results[key]['BUSTED']['test results']['p-value'], 'BUSTED-E p-val': results[key]['BUSTED-E']['test results']['p-value'], "HMM_BUSTED-E_ωE" : results[key]['BUSTED_E_HMM']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['omega'], "HMM_BUSTED-E_pE" : results[key]['BUSTED_E_HMM']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['proportion'], 'HMM_BUSTED p-val': results[key]['HMM_BUSTED']['test results']['p-value'], 'BMGE_BUSTED p-val': results[key]['BMGE_BUSTED']['test results']['p-value'], 'HMM_BUSTED-E p-val': results[key]['BUSTED_E_HMM']['test results']['p-value'], "BMGE_BUSTED-E_ωE" : results[key]['BUSTED_E_BMGE']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['omega'], "BMGE_BUSTED-E_pE" : results[key]['BUSTED_E_BMGE']['fits']['Unconstrained model']['Rate Distributions']['Test'][0]['proportion'], 'BMGE_BUSTED-E p-val': results[key]['BUSTED_E_BMGE']['test results']['p-value'], // % sites filtered 'BUSTED-E % sites filtered' : results[key]['BUSTED-E_FASTA']['indel change'], 'HMM % sites filtered' : results[key]['HMM_FASTA']['indel change'], 'BMGE % sites filtered': results[key]['BMGE_FASTA']['indel change'], // runtime 'BUSTED runtime' : results[key]['BUSTED']['runtime'], 'BUSTED-E runtime' : results[key]['BUSTED-E']['runtime'], 'BMGE runtime' : results[key]['bmge runtime'], 'HMM runtime' : NaN, // sequences //'BUSTED sequences' : results[key]['BUSTED']['input']['number of sequences'], //'HMM_BUSTED sequences' : results[key]['HMM_BUSTED']['input']['number of sequences'], //'BMGE_BUSTED sequences' : results[key]['BMGE_BUSTED']['input']['number of sequences'], 'length' : results[key]['BUSTED']['input']['number of sites'], 'significant' : significant_methods } ] })) 35:[] 2d:{"id":"68588b18a1c00eb7","slug":"busted-e-hmmcleaner-bmge","title":"BUSTED-E results with HMMCleaner AND BMGE using schulz-sackton data","thumbnail":"b8b66c11d55b680f6dcef20616fed067aaf2e09e7ee957c269c83e4480f5bdcf","access_level":"public","create_time":"$D2024-08-05T20:19:53.010Z","update_time":"$D2024-09-30T15:13:38.416Z","view_time":null,"first_public_time":"$D2024-08-07T19:17:23.143Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":"starter_2024"},"version":2392,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null}],"members":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null,"role":"editor"},{"type":"team","id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"BUSTED-E results with HMMCleaner AND BMGE using schulz-sackton data","cells":[{"id":0,"value":"# BUSTED-E results with HMMCleaner AND BMGE using schulz-sackton data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":65,"value":"viewof search = Inputs.search(table_data)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":68,"value":"table1 = Inputs.table(search, {\n rows : 15\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":500,"value":"Table 1. Results from BUSTED-E analysis before and after alignment filtering methods were applied\n\na. omegaE value from raw schulz-sackton data\n\nb. omegaE weight from raw schulz-sackton data\n\nc. p-value from BUSTED-E test for positive selection using raw schulz-sackton data\n\nd. omegaE value from HMMCleaner filtered data\n\ne. omegaE weight from HMMCleaner filtered data\n\nf. p-value from BUSTED-E test for positive selection using HMMCleaner filtered data\n\ng. omegaE value from BMGE filtered data\n\nh. omegaE weight from BMGE filtered data\n\ni. p-value from BUSTED-E test for positive selection using BMGE filtered data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":282,"value":"## BUSTED-E analysis - before and after BMGE filtering","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":749,"value":"pvcut = 0.05","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":744,"value":"viewof compare1 = Inputs.select ([\"BUSTED\", \"BUSTED-E\", \"HMM_BUSTED\",\"BMGE_BUSTED\",\"BUSTED-E_HMM\", \"BMGE_BUSTED-E\"], {\"label\" : \"x\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":741,"value":"viewof compare2 = Inputs.select ([\"BUSTED\", \"BUSTED-E\", \"HMM_BUSTED\",\"BMGE_BUSTED\",\"BUSTED-E_HMM\", \"BMGE_BUSTED-E\"], {\"label\" : \"y\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":924,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2329,"value":"no_bustede = {\n let nobustede = _.map(\n _.filter(table_data, (d) => d['BUSTED-E p-val'] >= pvcut && d['HMM_BUSTED p-val'] < pvcut && d['BMGE_BUSTED p-val'] < pvcut && d['length'] > 200),\n (d, key) => ({\n 'ID': d.ID,\n 'BUSTED-E sites filtered' : d['BUSTED-E % sites filtered'], \n 'HMM sites filtered': d['HMM % sites filtered'],\n 'BUSTED p-value': d['BUSTED p-val'],\n 'BUSTED-E p-value' : d['BUSTED-E p-val'],\n 'length' : d.length\n })\n);\n\nreturn nobustede.sort((a, b) => b['BUSTED-E sites filtered'] - a['BUSTED-E sites filtered']);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1654,"value":"neg_result = \n_.map(\n _.filter(table_data, (d) => d['BUSTED-E p-val'] <= pvcut && d['HMM_BUSTED p-val'] > pvcut),\n (d, key) => ({\n 'ID': d.ID,\n 'BUSTED-E sites filtered' : d['BUSTED-E % sites filtered'], \n 'HMM sites filtered': d['HMM % sites filtered'],\n 'BUSTED p-value': d['BUSTED p-val'],\n 'length' : d.length\n })\n);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1666,"value":"percent_both_no_filtering = _.filter(neg_result, d=> d['BUSTED-E sites filtered'] - d['HMM sites filtered']=== 0)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1674,"value":"percent_bustede_more_filtering = _.filter(neg_result, d=> d['BUSTED-E sites filtered'] > d['HMM sites filtered'])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1676,"value":"percent_bustede_less_filtering = _.filter(neg_result, d=> d['BUSTED-E sites filtered'] < d['HMM sites filtered'])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1705,"value":"percent_no_BUSTED = _.filter(neg_result, d=> d['BUSTED p-value'] > 0.05).length/neg_result.length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":747,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1286,"value":"viewof appState = upsetApp({ set: upset_data })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1293,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":967,"value":"viewof x_model = Inputs.select ([\"BUSTED-E\", \"HMM\",\"BMGE\",], {\"label\" : \"x\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":970,"value":"viewof y_model = Inputs.select ([\"BUSTED-E\", \"HMM\",\"BMGE\",], {\"label\" : \"y\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1415,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2341,"value":"BUSTED_E_any_filtering = _.filter(table_data, (d)=>d['BUSTED-E % sites filtered'] != 0).length/table_data.length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2351,"value":"BMGE_any_filtering = _.filter(table_data, (d)=>d['BMGE % sites filtered'] != 0).length/table_data.length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2354,"value":"HMM_any_filtering = _.filter(table_data, (d)=>d['HMM % sites filtered'] != 0).length/table_data.length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":442,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":97,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1737,"value":"counters = {\n let counter = new Map()\n \n table_data.forEach(el => {\n \n let methods = el.significant.split(\",\")\n methods.forEach(method => {\n if (!counter.has(method)){\n counter.set(method, 0)\n }\n counter.set(method, counter.get(method) + 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50);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1827,"value":"chart = {\n let height = 600\n let width = 1000\n \n const svg = d3.create(\"svg\")\n .attr(\"viewBox\", [0, 0, width, height]);\n \n svg.append(\"g\")\n .attr(\"id\", \"venn\")\n \n svg.select(\"#venn\").datum(sets).call(diagram);\n\nsvg.selectAll(\"#venn .venn-circle path\")\n .style(\"fill-opacity\", 0.18)\n .style(\"stroke-width\", 3)\n .style(\"stroke-opacity\", .9)\n .style(\"stroke\", function(d,i) { return colours[i]})\n .style(\"fill\", function(d,i) { return colours[i]})\n .style(\"mix-blend-mode\", 'multiply');\nsvg.selectAll(\"#venn .venn-circle text\")\n .style(\"fill\", function(d,i) { return colours[i]})\n .style(\"font-size\", \"20px\")\n .style(\"font-weight\", \"100\");\n return svg.node();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2102,"value":"colours = ['#b2df8a', '#33a02c', '#1f78b4', '#a6cee3', '#fb9a99', '#e31a1c'];","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2085,"value":"my_colors = {\n\n\n// Set up the SVG canvas dimensions\nconst width = 600;\nconst height = 100;\nconst rectWidth = width / colours.length;\nconst svg = d3.create(\"svg\")\n .attr(\"width\", width)\n .attr(\"height\", height);\n\n// Append a rectangle for each color in the array\ncolours.forEach((color, i) => {\n svg.append(\"rect\")\n .attr(\"x\", i * rectWidth)\n .attr(\"y\", 0)\n .attr(\"width\", rectWidth)\n .attr(\"height\", height)\n .attr(\"fill\", color);\n});\n\nreturn svg.node()\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":147,"value":"plot_data_score = _.flatten(_.map (results, (d, key)=> {\n return [\n { 'ID' : Number(key),\n 'res' : 'BUSTED-E',\n 'indel change' : d['BUSTED-E_FASTA']['indel change']\n },\n {'res' : 'BMGE',\n 'indel change' : d['BMGE_FASTA']['indel change']\n\n },\n { 'ID' : Number(key),\n 'res' : 'HMMCleaner',\n 'indel change' : d['HMM_FASTA']['indel change']\n\n }, \n \n ]\n })) ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2104,"value":"function shuffleArray(array) {\n for (let i = array.length - 1; i > 0; i--) {\n const j = Math.floor(Math.random() * (i + 1)); // Pick a random index\n [array[i], array[j]] = [array[j], array[i]]; // Swap elements\n }\n return array;\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":10,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":29,"value":"results = Object.fromEntries(\n Object.entries(full_results).filter(([key, value]) =>\n 'BUSTED' in value &&\n 'BUSTED-E' in value &&\n 'HMM_BUSTED' in value &&\n 'BUSTED_E_HMM' in value &&\n 'BMGE_BUSTED' in value &&\n 'BUSTED_E_BMGE' in value //&&\n //'ORIGINAL_FASTA' in value &&\n //'HMM_FASTA' in value &&\n //'BMGE_FASTA' in value //&&\n //'BUSTEDE_BMGE_BLAST' in value\n )\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"full_results = await d3.json (url + 'bmge_hmm_compare.json')\n// 'sackton_combined.json') \n//'shultz-sackton.json')\n//'compare_bmge_time.json')\n//'compare_sackton.json')\n//'indel_change.json')\n//(url + 'percent_increase.json')\n //(url + 'nospace_blast.json')\n ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":827,"value":"url = \"https://data.hyphy.org/web/busted-e/alignment_filter/\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":841,"value":"suffix = {\n let obj = {}\n obj[\"BUSTED p-val\"] = ['https://data.hyphy.org/web/selection-data/30620335/results/', '.BUSTED.json.gz']\n obj[\"BUSTED-E p-val\"] = ['https://data.hyphy.org/web/selection-data/30620335/results/', '.BUSTED-E.json.gz']\n obj[\"BUSTED_HMM p-val\"] = ['https://data.hyphy.org/web/busted-e/alignment_filter/jsons/', '_hmm.BUSTED.json.gz']\n obj[\"BUSTED_BMGE p-val\"] = ['https://data.hyphy.org/web/busted-e/alignment_filter/jsons/', '.bmge.BUSTED.json.gz']\n obj[\"BUSTED-E_HMM p-val\"] = ['https://data.hyphy.org/web/busted-e/alignment_filter/jsons/', '_hmm.BUSTED-E.json.gz']\n obj[\"BUSTED-E_BMGE p-val\"] = ['https://data.hyphy.org/web/busted-e/alignment_filter/jsons/', '.bmge.BUSTED-E.json.gz']\n return obj\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":172,"value":"average = arr => arr.length > 0 ? arr.reduce((sum, value) => sum + value, 0) / arr.length : null;","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1288,"value":"import {upsetApp} from \"@trebor/upset-demonstrator\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1754,"value":"venn = require(\"venn.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2373,"value":"_.filter(Object.fromEntries(\n Object.entries(full_results).filter(([key, value]) =>\n 'BUSTED_E_BMGE' in value)), d=> d.BUSTED_E_BMGE['test results']['p-value'] < 0.05).length/(Object.keys(Object.fromEntries(\n Object.entries(full_results).filter(([key, value]) =>\n 'BUSTED_E_BMGE' in value))).length)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2149,"value":"busted_e_res = 'https://data.hyphy.org/web/busted-e/alignment_filter/jsons/12890.bmge.BUSTED.json.gz'","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2268,"value":"import {contributing_sites}\nwith {busted_e_res as results_file}\nfrom \"@averyselberg/busted-contributing-sites\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2316,"value":"contributing_sites","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W35","stdlib":"1","titling":"auto"}} 2e:"$2d:body"