31:T4ba,meme_table = { let unfilt_content = results_json[gene_id]['MEME_UNFILTERED']['MLE']['content'][0] let filt_content = results_json[gene_id]['MEME_FILTERED']['MLE']['content'][0] let table = [] for (let i = 0; i < unfilt_content.length; i++){ if (unfilt_content[i][6] < pval || filt_content [i][6] < pval){ let compare_p = "" if (unfilt_content[i][6] < pval && filt_content [i][6] < pval){ compare_p = '++' } else if (unfilt_content[i][6] < pval && filt_content [i][6] > pval){ compare_p = '+-' } else if (unfilt_content[i][6] < pval && filt_content [i][6] > pval){ compare_p = '+-' } else if (unfilt_content[i][6] > pval && filt_content [i][6] < pval){ compare_p = "-+" } const obj = { 'Site' : i, 'Unfiltered alpha' : unfilt_content[i][0], 'Unfiltered beta+' : unfilt_content[i][3], 'Filtered alpha' : filt_content[i][0], 'Filtered beta+' : filt_content[i][3], 'Unfiltered p-value' : unfilt_content[i][6], 'Filtered p-value' : filt_content[i][6], 'Compare p-value' : compare_p } table.push(obj) } } return table //return headers }32:Tc00,table_data = { let for_table = [] for (const key in mod_results_json ) { let has_site_LRT_unfilt = _.find (_.get(mod_results_json[key]['MEME_UNFILTERED'], ["MLE","headers"]), (d)=>d[0] == "Variation p") let has_site_LRT_filt = _.find (_.get(mod_results_json[key]['MEME_FILTERED'], ["MLE","headers"]), (d)=>d[0] == "Variation p") let absrel_filt_true = _.filter(_.map(mod_results_json[key]['aBSREL_FILTERED']['branch attributes'], d=> d['Corrected P-value'] <= pval), value => value === true).length let absrel_filt_false = _.filter(_.map(mod_results_json[key]['aBSREL_FILTERED']['branch attributes'], d=> d['Corrected P-value'] <= pval), value => value === false).length let absrel_unfil_true = _.filter(_.map(mod_results_json[key]['aBSREL_UNFILTERED']['branch attributes'], d=> d['Corrected P-value'] <= pval), value => value === true).length let absrel_unfil_false = _.filter(_.map(mod_results_json[key]['aBSREL_UNFILTERED']['branch attributes'], d=> d['Corrected P-value'] <= pval), value => value === false).length let fil_sites_with_variation = has_site_LRT_filt ? _.chain (mod_results_json[key]['MEME_FILTERED']["MLE"]["content"]).mapValues ((d)=>_.filter (d, (r)=>r[11] <= pval).length).values().sum().value() : "N/A" let unfil_sites_with_variation = has_site_LRT_unfilt ? _.chain (mod_results_json[key]['MEME_UNFILTERED']["MLE"]["content"]).mapValues ((d)=>_.filter (d, (r)=>r[11] <= pval).length).values().sum().value() : "N/A" const obj = { "ID" : key, "BUSTED-E Filtered sites" : _.reduce(mod_results_json[key]['FILTER']['filter'], (count, filter) => count + _.keys(filter).length, 0), "Filtered MEME selected sites" : _.chain (mod_results_json[key]['MEME_FILTERED']['MLE']["content"]).mapValues ((d)=>_.filter (d, (r)=>r[6] <= pval).length).values().sum().value(), "Unfiltered MEME selected sites" : _.chain (mod_results_json[key]['MEME_UNFILTERED']['MLE']["content"]).mapValues ((d)=>_.filter (d, (r)=>r[6] <= pval).length).values().sum().value(), "MEME-filtered variable sites" : fil_sites_with_variation, "MEME-unfiltered variable sites" : unfil_sites_with_variation, "aBSREL-fil selected branches" : absrel_filt_true, 'abSREL-fil total branches' : absrel_filt_false+absrel_filt_true, "aBSREL-unfil selected branches" : absrel_unfil_true, "aBSREL- unfil total branches" : absrel_unfil_true+absrel_unfil_false, "cmc/M2_rel-filtered" : mod_results_json[key]['CMC_FILTERED']['test results']['Clade C model|M2_rel']['p-value'], //"cmc filtered omega" : largest_omega_fil, "cmc/M2_rel-unfiltered" : mod_results_json[key]['CMC_UNFILTERED']['test results']['Clade C model|M2_rel']['p-value'], //"cmc unfiltered omega" : largest_omega_unfil, "B-S-filtered" : mod_results_json[key]['B-S_FILTERED']['test results']['Model A|Model A neutral']['p-value'], "B-S-unfiltered" : mod_results_json[key]['B-S_UNFILTERED']['test results']['Model A|Model A neutral']['p-value'], } for_table.push(obj) } return for_table }33:T4e0,absrel_filt_table = { let table = [] for (let i in absrel_fill_class){ let add_branches = 0 let add_under_sel = 0 let total_branches = 0 let total_bl = 0 let class_bl = 0 //return absrel_fill_class[i] for (let j in mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes']){ //return mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'][j] total_branches += 1 total_bl += mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'][j]['Full adaptive model'] if (mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'][j]['Rate classes'] === absrel_fill_class[i]){ add_branches += 1 class_bl += mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'][j]['Full adaptive model'] if (mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'][j]['Corrected P-value'] <= pval){ add_under_sel += 1 } } } const obj = { "Omega rate class" : absrel_fill_class[i], "# branches" : add_branches, "% branches" : add_branches/total_branches, "% tree length" : class_bl/total_bl, "# branches under selection" : add_under_sel, } table.push(obj) } return table }34:T4ed,absrel_unfilt_table = { let table = [] for (let i in absrel_unfill_class){ let add_branches = 0 let add_under_sel = 0 let total_branches = 0 let total_bl = 0 let class_bl = 0 //return absrel_fill_class[i] for (let j in mod_results_json[gene_id]['aBSREL_UNFILTERED']['branch attributes']){ //return mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'][j] total_branches += 1 total_bl += mod_results_json[gene_id]['aBSREL_UNFILTERED']['branch attributes'][j]['Full adaptive model'] if (mod_results_json[gene_id]['aBSREL_UNFILTERED']['branch attributes'][j]['Rate classes'] === absrel_unfill_class[i]){ add_branches += 1 class_bl += mod_results_json[gene_id]['aBSREL_UNFILTERED']['branch attributes'][j]['Full adaptive model'] if (mod_results_json[gene_id]['aBSREL_UNFILTERED']['branch attributes'][j]['Corrected P-value'] <= pval){ add_under_sel += 1 } } } const obj = { "Omega rate class" : absrel_fill_class[i], "# branches" : add_branches, "% branches" : add_branches/total_branches, "% tree length" : class_bl/total_bl, "# branches under selection" : add_under_sel, } table.push(obj) } return table }35:[] 2f:{"title":"Using BUSTED-E filtering script on pollock data to run other HyPhy methods","cells":[{"id":3,"value":"# Using BUSTED-E filtering script on pollock data to run other HyPhy methods","pinned":false,"hidden":false,"mode":"md"},{"id":16,"value":"viewof search = Inputs.search(table_data)","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"table1 = Inputs.table(search, {\n rows : 15\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":53,"value":"viewof gene_id = Inputs.select(OnlySearchResults, {label: \"Show this gene:\", sort: true})","pinned":false,"hidden":false,"mode":"ojs"},{"id":402,"value":"viewof pval = Inputs.range([0, 1], {label: \"P-value threshold\", step: .01, value: 0.05})","pinned":false,"hidden":false,"mode":"ojs"},{"id":464,"value":"## BUSTED-E filtering data from ${gene_id}","pinned":false,"hidden":false,"mode":"md"},{"id":491,"value":"total_count = _.reduce(results_json[gene_id]['FILTER']['filter'], (count, filter) => count + _.keys(filter).length, 0);","pinned":false,"hidden":false,"mode":"ojs"},{"id":497,"value":"unique_sites = {\n let list = []\n let filter_list = results_json[gene_id]['FILTER']['filter']\n for (let key in filter_list){\n for (let i =0; i< Object.keys(filter_list[key]).length; i++){\n list.push(filter_list[key][i])\n }\n }\n return [...new Set(list)]\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":69,"value":"## Using MEME to analyze ${gene_id}","pinned":false,"hidden":false,"mode":"md"},{"id":59,"value":"For the gene **${gene_id}**, **${matchingEntry['Filtered MEME sites']}** sites were identified as under positive selection when a BUSTED-E filtered fasta was used, while **${matchingEntry['Unfiltered MEME sites']}** sites were identified using unfiltered fasta. Additionally, **${matchingEntry['MEME-filtered variable sites']}** sites were identified with variable omega across branches using a BUSTED-E filtered fasta and **${matchingEntry['MEME-unfiltered variable sites']}** using an unfiltered fasta. ","pinned":false,"hidden":false,"mode":"md"},{"id":418,"value":"meme_plot = { \n return Plot.plot({\n color: {legend: true},\n marks: [ Plot.link(meme_table, {\n x1: 0,\n y1: 0,\n x2: max_beta,\n y2: max_beta,\n strokeWidth: 0.05\n }),\n \n Plot.dot(meme_table, {x: \"Unfiltered beta+\", y: \"Filtered beta+\", stroke: \"Compare p-value\", fill: \"Compare p-value\"})\n ]\n})\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":457,"value":"Figure 1. Comparison between MEME beta values using filtered and unfiltered data. ++ indicates the site is under positive selection in both filtered and unfiltered data. -+ indicates the site was under positive selection in only filtered data, not unfiltered data. +- indicates the site was under positive selection in unfiltered data but not filtered data. ","pinned":false,"hidden":false,"mode":"md"},{"id":368,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":441,"value":"max_beta = Math.max(..._.map(meme_table, d=> d[\"Unfiltered beta+\"]).concat(_.map(meme_table, d=> d[\"Unfiltered beta+\"])))","pinned":false,"hidden":false,"mode":"ojs"},{"id":74,"value":"## Using aBSREL to analyze ${gene_id}","pinned":false,"hidden":false,"mode":"md"},{"id":140,"value":"##### aBSREL tree data when filtered fasta was used to analyze ${gene_id}:","pinned":false,"hidden":false,"mode":"md"},{"id":134,"value":"Inputs.table(absrel_filt_table)","pinned":false,"hidden":false,"mode":"ojs"},{"id":142,"value":"#### aBSREL tree data when unfiltered fasta was used to analyze ${gene_id}:","pinned":false,"hidden":false,"mode":"md"},{"id":137,"value":"Inputs.table(absrel_unfilt_table)","pinned":false,"hidden":false,"mode":"ojs"},{"id":150,"value":"## Using HyPhy's CMC PAML emulator to analyze ${gene_id}","pinned":false,"hidden":false,"mode":"md"},{"id":181,"value":"The filtered data p-vale is **${mod_results_json[gene_id]['CMC_FILTERED']['test results']['Clade C model|M2_rel']['p-value'].toFixed(3)}** while the unfiltered data has a p-value of **${mod_results_json[gene_id]['CMC_UNFILTERED']['test results']['Clade C model|M2_rel']['p-value'].toFixed(3)}**. ","pinned":false,"hidden":false,"mode":"md"},{"id":203,"value":"##### Clade model C data when filtered fasta was used to analyze ${gene_id}:","pinned":false,"hidden":false,"mode":"md"},{"id":210,"value":"Inputs.table(cmc_fil_table)","pinned":false,"hidden":false,"mode":"ojs"},{"id":208,"value":"##### Clade model C data when unfiltered fasta was used to analyze ${gene_id}:","pinned":false,"hidden":false,"mode":"md"},{"id":214,"value":"Inputs.table(cmc_unfil_table)","pinned":false,"hidden":false,"mode":"ojs"},{"id":169,"value":"## Using HyPhy's branch-site PAML emulator to analyze ${gene_id}","pinned":false,"hidden":false,"mode":"md"},{"id":243,"value":"The filtered data p-vale is **${mod_results_json[gene_id]['B-S_FILTERED']['test results']['Model A|M1a']['p-value'].toFixed(3)}** while the unfiltered data has a p-value of **${mod_results_json[gene_id]['B-S_UNFILTERED']['test results']['Model A|M1a']['p-value'].toFixed(3)}**. ","pinned":false,"hidden":false,"mode":"md"},{"id":248,"value":"##### Branch-site model data when filtered fasta was used to analyze ${gene_id}:","pinned":false,"hidden":false,"mode":"md"},{"id":237,"value":"Inputs.table(bs_fil_table)","pinned":false,"hidden":false,"mode":"ojs"},{"id":253,"value":"##### Branch-site model data when unfiltered fasta was used to analyze ${gene_id}:","pinned":false,"hidden":false,"mode":"md"},{"id":240,"value":"Inputs.table(bs_unfil_table)","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":56,"value":"OnlySearchResults = {\n var data = []\n for(var i = 0;i< search.length;i++){\n data.push(search[i][\"ID\"])\n }\n return data\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":63,"value":"matchingEntry = Object.values(table_data).find(entry => entry.ID === gene_id)","pinned":false,"hidden":false,"mode":"ojs"},{"id":29,"value":"mod_results_json = {\nlet json = results_json\n if (\"og9298\" in json) {\n // Remove the key from the new object\n delete json.og9298;\n}\nreturn json\n\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":84,"value":"absrel_fill_class = _.uniq(_.map(mod_results_json[gene_id]['aBSREL_FILTERED']['branch attributes'], d=> d['Rate classes']))","pinned":false,"hidden":false,"mode":"ojs"},{"id":96,"value":"absrel_unfill_class = _.uniq(_.map(mod_results_json[gene_id]['aBSREL_UNFILTERED']['branch attributes'], d=> d['Rate classes']))","pinned":false,"hidden":false,"mode":"ojs"},{"id":81,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":128,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":173,"value":"cmc_fil_table = {\n let cmc_fil = mod_results_json[gene_id]['CMC_FILTERED']['fits']['Clade model C']\n cmc_fil['Test'] = 'CMC alternative model'\n delete cmc_fil['Log Likelihood']\n let m2a_fil = mod_results_json[gene_id]['CMC_FILTERED']['fits']['M2_rel model']\n delete m2a_fil['Log Likelihood']\n m2a_fil['Test'] = 'CMC null model'\n let table = []\n table.push(cmc_fil)\n table.push(m2a_fil)\n return table\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":315,"value":"largest_omega_fil = {\nlet omega_list = [];\n\nfor (const key in cmc_fil_table[0]) {\n if (key.includes('omega')) {\n omega_list.push(cmc_fil_table[0][key]);\n }\n}\n return Math.max(...omega_list)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":200,"value":"cmc_unfil_table = {\n let cmc_unfil = mod_results_json[gene_id]['CMC_UNFILTERED']['fits']['Clade model C']\n cmc_unfil['Test'] = 'CMC alternative model'\n delete cmc_unfil['Log Likelihood']\n let m2a_unfil = mod_results_json[gene_id]['CMC_UNFILTERED']['fits']['M2_rel model']\n delete m2a_unfil['Log Likelihood']\n m2a_unfil['Test'] = 'CMC null model'\n let table = []\n table.push(cmc_unfil)\n table.push(m2a_unfil)\n return table\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":330,"value":"largest_omega_unfil = {\nlet omega_list = [];\n\nfor (const key in cmc_unfil_table[0]) {\n if (key.includes('omega')) {\n omega_list.push(cmc_unfil_table[0][key]);\n }\n}\n return Math.max(...omega_list)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":232,"value":"bs_unfil_table = {\n let bs_unfil = mod_results_json[gene_id]['B-S_UNFILTERED']['fits']['Branch-site model A ']\n bs_unfil['Test'] = 'B-S model A alternative'\n delete bs_unfil['Log Likelihood']\n let m1a_unfil = mod_results_json[gene_id]['B-S_UNFILTERED']['fits']['M1a model']\n delete m1a_unfil['Log Likelihood']\n m1a_unfil['Test'] = 'M1a model null'\n let table = []\n table.push(bs_unfil)\n table.push(m1a_unfil)\n return table\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":222,"value":"bs_fil_table = {\n let bs_fil = mod_results_json[gene_id]['B-S_FILTERED']['fits']['Branch-site model A ']\n bs_fil['Test'] = 'B-S model A alternative'\n delete bs_fil['Log Likelihood']\n let m1a_fil = mod_results_json[gene_id]['B-S_FILTERED']['fits']['M1a model']\n delete m1a_fil['Log Likelihood']\n m1a_fil['Test'] = 'M1a model null'\n let table = []\n table.push(bs_fil)\n table.push(m1a_fil)\n return table\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":7,"value":"results_json = await d3.json (\"https://data.hyphy.org/web/busted-e/filt_msa_pollock.json\");","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W35","stdlib":"1","titling":"auto"}