31:T7c6, ** Table 1. ** Column definitions are as follows: 1. **ID** the candidate gene/alignment under study 2. **Sequences** the number of sequences in the alignment 3. **Sites** the number of codons in the alignment 4. **Num_FG** the number of foreground (i.e. Test) species and ancestral nodes in the alignment 5. **LRT** Likelihood Ratio Test for BUSTED-E (alternative model) vs BUSTED (null) 6. **error P-value** P-value for BUSTED-E vs BUSTED LRT 7. **filter?** interpretation of BUSTED-E vs BUSTED LRT; is filtered or unfiltered data recommended? 8. **FDR_E_sig?** interpretation of BUSTED-E vs BUSTED LRT using FDR adjusted q-values 9. **ω1** the first omega value (usually negative selection) reported for BUSTED-PH in the FOREGROUND 10. **ω2** the second omega value (usually neutral or negative selection) reported for BUSTED-PH in the FOREGROUND 11. **ω3** the third omega value (usually positive or neutral selection) reported for BUSTED-PH in the FOREGROUND 12. **FG_pval** the BUSTED-PH LRT p-value for the test for positive selection in the foreground (test) species 13. **BG_pval** the BUSTED-PH LRT p-value for the test for positive selection in the background species 14. **DF_pval** the BUSTED-PH LRT p-value for the test for the difference between the two selective regimes 15. **FDR_FG_sig?** interpretation of BUSTED-PH foreground LRT using FDR adjusted q-values 16. **FDR_BG_sig?** interpretation of BUSTED-PH background LRT using FDR adjusted q-values 17. **FDR_DF_sig?** interpretation of BUSTED-PH difference LRT using FDR adjusted q-values 18. **Class** the significance of BUSTED-PH p values (FG_pval, BG_pval, and DF_pval respectively) where 1 indicates significance and 0 indicates non-significance at a threshold of 0.05 (table 2) 19. **FDR_class** the significance of BUSTED-PH FDR adjusted q-values (FG_pval, BG_pval, and DF_pval respectively) where 1 indicates significance and 0 indicates non-significance at a threshold of 0.05 (table 2). 32:T8ed,displayed_tree = { let tree = tree_object[0]; var t = tree.render("#tree_container", { //height:1024, width:800, 'show-scale' : true, 'left-right-spacing': 'fit-to-size', //'top-bottom-spacing': 'fit-to-size', //'internal-names' : true, 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { return 3; } return 1; }; let nodeStates = null; t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = true; t.font_size = 10; t.spacing_x (10); t.phylotree.branch_length_accessor = n=> { //console.log (summary_json[segment_id]); let bl = tree_object[2][n.data.name]; /*if (bl > 0.25) { n.data.censored_bl = true; return 0.25; } else { n.data.censored_bl = false; }*/ return bl; } t.node_label ((n)=>{ return n.data.name.split ("_").slice (0,3).join (" "); //return ""; }); function sort_nodes (asc) { tree.traverse_and_compute (function (n) { var d = 1; if (n.children && n.children.length) { d += d3.max (n.children, function (d) { return d["count_depth"];}); } n["count_depth"] = d; }); tree.resort_children (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); t.style_nodes ((e,n) => { e.selectAll ("title").data ([n.data.name]).join ("title").text ((d)=>d); if (n.data.name in tree_object[1]) { let binfo = tree_object[1][n.data.name]; e.selectAll ("circle").style ('fill', species_colors (binfo)); e.selectAll ("text").style ('fill', species_colors (binfo)); } //} }); t.style_edges ((e,d) => { if (d.target.data.name in tree_object[1]) { let binfo = tree_object[1][d.target.data.name]; console.log (e); e.style ('stroke', species_colors (binfo)); e.style ('stroke-width', 2); } }); t.placenodes(); t.update(); return t; }33:T524,interpretation = { let inter = "" if (chosen_json['tests']['FG']['p-value'] > 0.05){ inter = "There is no evidence of this gene experiencing positive selection associated with the foreground (test) branches." } else { if (chosen_json['tests']['BG']['p-value'] > 0.05) { if (chosen_json['tests']['DIFF']['p-value'] > 0.05) { inter = "There is evidence of this gene experiencing positive selection associated with the foreground (test) branches, but there is no statistically significant difference between the test and background branches in terms of selective pressure." } else { inter = "There is strong evidence of this gene experiencing positive selection associated with the foreground (test) branches." } } else { inter = "For this gene, selection is acting on the foreground (test) branches, but selection is also acting on background branches. " if (chosen_json['tests']['DIFF']['p-value'] > 0.05) { inter = inter + "There is no statistically significant difference between the test and background branches in terms of selective pressure." } else { inter = inter + "There is a statistically significant difference between the test and background branches in terms of selective pressure." } } } return inter }34:T882,table_data = { let for_table = [] let cclass = "" let busted_sce = fdr_or_no for (const key in results_json) { if (busted_sce === 'BUSTED-PH_' + scenario){ cclass = "C" + (results_json[key][busted_sce]['tests']['FG']['p-value'] < 0.05 ? 1 : 0) + (results_json[key][busted_sce]['tests']['BG']['p-value'] >= 0.05 ? 0 : 1) + (results_json[key][busted_sce]['tests']['DIFF']['p-value'] < 0.05 ? 1: 0) } else { cclass = "C" + (results_json[key][busted_sce]['fdr significance']['FG'] ? 1 : 0) + (results_json[key][busted_sce]['fdr significance']['BG'] ? 0 : 1) + (results_json[key][busted_sce]['fdr significance']['DIFF'] ? 1: 0) } const obj = { "ID" : key, 'LRT' : results_json[key]['BUSTED_E']['test for error']['LRT'], 'error P-value' : results_json[key]['BUSTED_E']['test for error']['p-value'], 'filter?' : results_json[key][busted_sce]['filtered?'], "Sequences" : results_json[key][busted_sce]['sequences'], "Sites" : results_json[key][busted_sce]['sites'], "Num_FG" : Object.values(results_json[key][busted_sce]['tested'][0]).filter(val => val === "test").length, "FG_pval" : results_json[key][busted_sce]['tests']['FG']['p-value'], "BG_pval" : results_json[key][busted_sce]['tests']['BG']['p-value'], "DF_pval" : results_json[key][busted_sce]['tests']['DIFF']['p-value'], "ω1" : results_json[key][busted_sce]['distributions']['unconstrained']['Rate Distributions']['Test'][0]['omega'], "p1" : results_json[key][busted_sce]['distributions']['unconstrained']['Rate Distributions']['Test'][0]['proportion'], "ω2" : results_json[key][busted_sce]['distributions']['unconstrained']['Rate Distributions']['Test'][1]['omega'], "p2" : results_json[key][busted_sce]['distributions']['unconstrained']['Rate Distributions']['Test'][1]['proportion'], "ω3" : results_json[key][busted_sce]['distributions']['unconstrained']['Rate Distributions']['Test'][2]['omega'], "p3" : results_json[key][busted_sce]['distributions']['unconstrained']['Rate Distributions']['Test'][2]['proportion'], "Class" : cclass } for_table.push(obj) } return for_table }35:T5a6,sc1_cfdr101_111 = ["E1755_NT_Cleaned_Aligned", "E1776_NT_Cleaned_Aligned", "E1800_NT_Cleaned_Aligned", "E1838_NT_Cleaned_Aligned", "E1837_NT_Cleaned_Aligned", "E1869_NT_Cleaned_Aligned", "E1851_NT_Cleaned_Aligned", "E1905_NT_Cleaned_Aligned", "E1915_NT_Cleaned_Aligned", "E1935_NT_Cleaned_Aligned", "E1939_NT_Cleaned_Aligned", "E1945_NT_Cleaned_Aligned", "E1954_NT_Cleaned_Aligned", "E2001_NT_Cleaned_Aligned", "E2022_NT_Cleaned_Aligned", "E2076_NT_Cleaned_Aligned", "E2106_NT_Cleaned_Aligned", "E2088_NT_Cleaned_Aligned", "E2096_NT_Cleaned_Aligned", "E2098_NT_Cleaned_Aligned", "E2115_NT_Cleaned_Aligned", "E2121_NT_Cleaned_Aligned", "E2143_NT_Cleaned_Aligned", "E2147_NT_Cleaned_Aligned", "E2152_NT_Cleaned_Aligned", "E2201_NT_Cleaned_Aligned", "E2243_NT_Cleaned_Aligned", "E2245_NT_Cleaned_Aligned", "E2257_NT_Cleaned_Aligned", "E2279_NT_Cleaned_Aligned", "E2282_NT_Cleaned_Aligned", "E2307_NT_Cleaned_Aligned", "E2308_NT_Cleaned_Aligned", "E2339_NT_Cleaned_Aligned", "E2355_NT_Cleaned_Aligned", "E2369_NT_Cleaned_Aligned", "E2398_NT_Cleaned_Aligned", "E2426_NT_Cleaned_Aligned", "E2475_NT_Cleaned_Aligned", "E2454_NT_Cleaned_Aligned", "E2491_NT_Cleaned_Aligned", "E2497_NT_Cleaned_Aligned", "E2515_NT_Cleaned_Aligned", "E2561_NT_Cleaned_Aligned", "E2588_NT_Cleaned_Aligned", "E2601_NT_Cleaned_Aligned", "E2583_NT_Cleaned_Aligned", "E2589_NT_Cleaned_Aligned", "E2622_NT_Cleaned_Aligned", "E2623_NT_Cleaned_Aligned", "E2644_NT_Cleaned_Aligned"]36:T846,sc4_cfdr101_111 = ["E1755_NT_Cleaned_Aligned", "E1760_NT_Cleaned_Aligned", "E1776_NT_Cleaned_Aligned", "E1820_NT_Cleaned_Aligned", "E1837_NT_Cleaned_Aligned", "E1843_NT_Cleaned_Aligned", "E1869_NT_Cleaned_Aligned", "E1849_NT_Cleaned_Aligned", "E1851_NT_Cleaned_Aligned", "E1879_NT_Cleaned_Aligned", "E1905_NT_Cleaned_Aligned", "E1925_NT_Cleaned_Aligned", "E1939_NT_Cleaned_Aligned", "E1945_NT_Cleaned_Aligned", "E1954_NT_Cleaned_Aligned", "E1957_NT_Cleaned_Aligned", "E1953_NT_Cleaned_Aligned", "E1958_NT_Cleaned_Aligned", "E1964_NT_Cleaned_Aligned", "E2008_NT_Cleaned_Aligned", "E2025_NT_Cleaned_Aligned", "E2043_NT_Cleaned_Aligned", "E2038_NT_Cleaned_Aligned", "E2052_NT_Cleaned_Aligned", "E2076_NT_Cleaned_Aligned", "E2061_NT_Cleaned_Aligned", "E2067_NT_Cleaned_Aligned", "E2088_NT_Cleaned_Aligned", "E2096_NT_Cleaned_Aligned", "E2101_NT_Cleaned_Aligned", "E2116_NT_Cleaned_Aligned", "E2121_NT_Cleaned_Aligned", "E2143_NT_Cleaned_Aligned", "E2147_NT_Cleaned_Aligned", "E2152_NT_Cleaned_Aligned", "E2167_NT_Cleaned_Aligned", "E2163_NT_Cleaned_Aligned", "E2181_NT_Cleaned_Aligned", "E2217_NT_Cleaned_Aligned", "E2201_NT_Cleaned_Aligned", "E2228_NT_Cleaned_Aligned", "E2234_NT_Cleaned_Aligned", "E2225_NT_Cleaned_Aligned", "E2268_NT_Cleaned_Aligned", "E2271_NT_Cleaned_Aligned", "E2262_NT_Cleaned_Aligned", "E2279_NT_Cleaned_Aligned", "E2282_NT_Cleaned_Aligned", "E2294_NT_Cleaned_Aligned", "E2290_NT_Cleaned_Aligned", "E2325_NT_Cleaned_Aligned", "E2326_NT_Cleaned_Aligned", "E2346_NT_Cleaned_Aligned", "E2364_NT_Cleaned_Aligned", "E2392_NT_Cleaned_Aligned", "E2395_NT_Cleaned_Aligned", "E2408_NT_Cleaned_Aligned", "E2417_NT_Cleaned_Aligned", "E2455_NT_Cleaned_Aligned", "E2467_NT_Cleaned_Aligned", "E2510_NT_Cleaned_Aligned", "E2497_NT_Cleaned_Aligned", "E2506_NT_Cleaned_Aligned", "E2511_NT_Cleaned_Aligned", "E2521_NT_Cleaned_Aligned", "E2540_NT_Cleaned_Aligned", "E2561_NT_Cleaned_Aligned", "E2556_NT_Cleaned_Aligned", "E2560_NT_Cleaned_Aligned", "E2584_NT_Cleaned_Aligned", "E2583_NT_Cleaned_Aligned", "E2591_NT_Cleaned_Aligned", "E2623_NT_Cleaned_Aligned", "E2644_NT_Cleaned_Aligned", "E2648_NT_Cleaned_Aligned"]37:T87b,sc1_c101_111 = ["E1755_NT_Cleaned_Aligned", "E1756_NT_Cleaned_Aligned", "E1800_NT_Cleaned_Aligned", "E1838_NT_Cleaned_Aligned", "E1837_NT_Cleaned_Aligned", "E1843_NT_Cleaned_Aligned", "E1851_NT_Cleaned_Aligned", "E1879_NT_Cleaned_Aligned", "E1915_NT_Cleaned_Aligned", "E1935_NT_Cleaned_Aligned", "E1945_NT_Cleaned_Aligned", "E1954_NT_Cleaned_Aligned", "E1958_NT_Cleaned_Aligned", "E1964_NT_Cleaned_Aligned", "E1985_NT_Cleaned_Aligned", "E2001_NT_Cleaned_Aligned", "E2008_NT_Cleaned_Aligned", "E2022_NT_Cleaned_Aligned", "E2057_NT_Cleaned_Aligned", "E2076_NT_Cleaned_Aligned", "E2110_NT_Cleaned_Aligned", "E2088_NT_Cleaned_Aligned", "E2096_NT_Cleaned_Aligned", "E2098_NT_Cleaned_Aligned", "E2115_NT_Cleaned_Aligned", "E2121_NT_Cleaned_Aligned", "E2143_NT_Cleaned_Aligned", "E2147_NT_Cleaned_Aligned", "E2148_NT_Cleaned_Aligned", "E2152_NT_Cleaned_Aligned", "E2167_NT_Cleaned_Aligned", "E2163_NT_Cleaned_Aligned", "E2206_NT_Cleaned_Aligned", "E2217_NT_Cleaned_Aligned", "E2196_NT_Cleaned_Aligned", "E2201_NT_Cleaned_Aligned", "E2225_NT_Cleaned_Aligned", "E2243_NT_Cleaned_Aligned", "E2245_NT_Cleaned_Aligned", "E2251_NT_Cleaned_Aligned", "E2257_NT_Cleaned_Aligned", "E2265_NT_Cleaned_Aligned", "E2271_NT_Cleaned_Aligned", "E2276_NT_Cleaned_Aligned", "E2279_NT_Cleaned_Aligned", "E2282_NT_Cleaned_Aligned", "E2288_NT_Cleaned_Aligned", "E2290_NT_Cleaned_Aligned", "E2307_NT_Cleaned_Aligned", "E2308_NT_Cleaned_Aligned", "E2339_NT_Cleaned_Aligned", "E2355_NT_Cleaned_Aligned", "E2369_NT_Cleaned_Aligned", "E2398_NT_Cleaned_Aligned", "E2424_NT_Cleaned_Aligned", "E2426_NT_Cleaned_Aligned", "E2475_NT_Cleaned_Aligned", "E2454_NT_Cleaned_Aligned", "E2470_NT_Cleaned_Aligned", "E2476_NT_Cleaned_Aligned", "E2478_NT_Cleaned_Aligned", "E2491_NT_Cleaned_Aligned", "E2497_NT_Cleaned_Aligned", "E2515_NT_Cleaned_Aligned", "E2561_NT_Cleaned_Aligned", "E2563_NT_Cleaned_Aligned", "E2573_NT_Cleaned_Aligned", "E2560_NT_Cleaned_Aligned", "E2588_NT_Cleaned_Aligned", "E2601_NT_Cleaned_Aligned", "E2583_NT_Cleaned_Aligned", "E2589_NT_Cleaned_Aligned", "E2591_NT_Cleaned_Aligned", "E2622_NT_Cleaned_Aligned", "E2623_NT_Cleaned_Aligned", "E2644_NT_Cleaned_Aligned", "E2648_NT_Cleaned_Aligned"]38:T9e7,sc4_c101_111 = ["E1755_NT_Cleaned_Aligned", "E1760_NT_Cleaned_Aligned", "E1830_NT_Cleaned_Aligned", "E1820_NT_Cleaned_Aligned", "E1837_NT_Cleaned_Aligned", "E1843_NT_Cleaned_Aligned", "E1849_NT_Cleaned_Aligned", "E1851_NT_Cleaned_Aligned", "E1879_NT_Cleaned_Aligned", "E1905_NT_Cleaned_Aligned", "E1925_NT_Cleaned_Aligned", "E1918_NT_Cleaned_Aligned", "E1945_NT_Cleaned_Aligned", "E1954_NT_Cleaned_Aligned", "E1957_NT_Cleaned_Aligned", "E1953_NT_Cleaned_Aligned", "E1952_NT_Cleaned_Aligned", "E1958_NT_Cleaned_Aligned", "E1964_NT_Cleaned_Aligned", "E1992_NT_Cleaned_Aligned", "E2010_NT_Cleaned_Aligned", "E2008_NT_Cleaned_Aligned", "E2025_NT_Cleaned_Aligned", "E2038_NT_Cleaned_Aligned", "E2052_NT_Cleaned_Aligned", "E2076_NT_Cleaned_Aligned", "E2051_NT_Cleaned_Aligned", "E2061_NT_Cleaned_Aligned", "E2067_NT_Cleaned_Aligned", "E2088_NT_Cleaned_Aligned", "E2090_NT_Cleaned_Aligned", "E2096_NT_Cleaned_Aligned", "E2101_NT_Cleaned_Aligned", "E2116_NT_Cleaned_Aligned", "E2121_NT_Cleaned_Aligned", "E2143_NT_Cleaned_Aligned", "E2147_NT_Cleaned_Aligned", "E2148_NT_Cleaned_Aligned", "E2152_NT_Cleaned_Aligned", "E2167_NT_Cleaned_Aligned", "E2153_NT_Cleaned_Aligned", "E2163_NT_Cleaned_Aligned", "E2181_NT_Cleaned_Aligned", "E2217_NT_Cleaned_Aligned", "E2198_NT_Cleaned_Aligned", "E2201_NT_Cleaned_Aligned", "E2228_NT_Cleaned_Aligned", "E2234_NT_Cleaned_Aligned", "E2225_NT_Cleaned_Aligned", "E2268_NT_Cleaned_Aligned", "E2271_NT_Cleaned_Aligned", "E2269_NT_Cleaned_Aligned", "E2279_NT_Cleaned_Aligned", "E2282_NT_Cleaned_Aligned", "E2294_NT_Cleaned_Aligned", "E2288_NT_Cleaned_Aligned", "E2290_NT_Cleaned_Aligned", "E2325_NT_Cleaned_Aligned", "E2335_NT_Cleaned_Aligned", "E2326_NT_Cleaned_Aligned", "E2364_NT_Cleaned_Aligned", "E2357_NT_Cleaned_Aligned", "E2361_NT_Cleaned_Aligned", "E2382_NT_Cleaned_Aligned", "E2392_NT_Cleaned_Aligned", "E2395_NT_Cleaned_Aligned", "E2398_NT_Cleaned_Aligned", "E2408_NT_Cleaned_Aligned", "E2447_NT_Cleaned_Aligned", "E2419_NT_Cleaned_Aligned", "E2417_NT_Cleaned_Aligned", "E2455_NT_Cleaned_Aligned", "E2467_NT_Cleaned_Aligned", "E2510_NT_Cleaned_Aligned", "E2478_NT_Cleaned_Aligned", "E2497_NT_Cleaned_Aligned", "E2506_NT_Cleaned_Aligned", "E2511_NT_Cleaned_Aligned", "E2521_NT_Cleaned_Aligned", "E2540_NT_Cleaned_Aligned", "E2561_NT_Cleaned_Aligned", "E2556_NT_Cleaned_Aligned", "E2560_NT_Cleaned_Aligned", "E2584_NT_Cleaned_Aligned", "E2583_NT_Cleaned_Aligned", "E2591_NT_Cleaned_Aligned", "E2623_NT_Cleaned_Aligned", "E2644_NT_Cleaned_Aligned", "E2648_NT_Cleaned_Aligned", "E2656_NT_Cleaned_Aligned"]39:[] 2f:{"title":"Ray finned fish with correction for multiple testing- final copy","cells":[{"id":0,"value":"# Ray finned fish with correction for multiple testing- final copy","pinned":false,"hidden":false,"mode":"md"},{"id":448,"value":"viewof scenario = Inputs.select(new Map([[\"Scenario 1\", \"1\"], [\"Scenario 2\", \"2\"], [\"Scenario 3\", \"3\"], [\"Scenario 4\", \"4\"]]), {value: \"1\", label: \"Choose a scenario\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":999,"value":"viewof fdr_or_no = Inputs.select(new Map([[\"No FDR at all\", 'BUSTED-PH_' + scenario], [\"FDR on every test\", 'BUSTED-PH_' + scenario +'_fdr']]), {value: 'BUSTED-PH_' + scenario +'_fdr', label: \"Choose testing correction\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":290,"value":"viewof search = Inputs.search(table_data)","pinned":false,"hidden":false,"mode":"ojs"},{"id":294,"value":"table1 = Inputs.table(search, {\n rows : 15\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1130,"value":"_.filter(table_data, d=> d['filter?'] === 'filtered')","pinned":true,"hidden":false,"mode":"ojs"},{"id":298,"value":"$31","pinned":false,"hidden":false,"mode":"md"},{"id":787,"value":"----","pinned":false,"hidden":false,"mode":"md"},{"id":303,"value":"Class | Interpretation \n-------- | -------- \nC000 | No selection on FG, no selection on BG, no difference between FG and BG selective regimes \nC100 | Selection on FG, no selection on BG, no difference between FG and BG selective regimes\nC010 | No selection on FG, selection on BG, no difference between FG and BG selective regimes\nC001 | No selection on FG, no selection on BG, statistically significant difference between FG and BG selective regimes\nC101 | Selection on FG, no selection on BG, statistically significant difference between FG and BG selective regimes\nC110 | Selection on FG, selection on BG, no difference between FG and BG selective regimes\nC011 | No selection on FG, selection on BG, statistically significant difference between FG and BG selective regimes\nC111 | Selection on FG, selection on BG, statistically significant difference between FG and BG selective regimes","pinned":false,"hidden":false,"mode":"md"},{"id":305,"value":"**Table 2.** Interpretation of class values from table 1. ","pinned":false,"hidden":false,"mode":"md"},{"id":398,"value":"## Error filtering:\n\n","pinned":false,"hidden":false,"mode":"md"},{"id":412,"value":"We have ${table_data.length} total genes, ${filtered_count} underwent BUSTED-E error filtering, ${unfiltered_count} did not. ","pinned":false,"hidden":false,"mode":"md"},{"id":308,"value":"## Exploring individual genes","pinned":false,"hidden":false,"mode":"md"},{"id":223,"value":"viewof gene_id = Inputs.select(only_search_results, {label: \"Show this gene:\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":357,"value":"With a BUSTED-E vs BUSTED p-value of ${matchingEntry['error P-value']} we recommend using the **${matchingEntry['filter?']} results**. These results are displayed below. ","pinned":false,"hidden":false,"mode":"md"},{"id":51,"value":"trendLegend = swatches({\n color: species_colors\n //tickFormat: \"%\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":48,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":178,"value":"\n** Figure 1. **\nGene tree for ${gene_id} generated by BUSTED-PH. Colors indicate foreground, background, and nuisance branches (if using).\n","pinned":false,"hidden":false,"mode":"md"},{"id":101,"value":"## Interpretation of test for positive selection","pinned":false,"hidden":false,"mode":"md"},{"id":104,"value":"1. The p-value for the test for positive selection in the *test* (foreground) branches is: ** ${chosen_json['tests']['FG']['p-value'].toFixed(3)} **\n\n2. The p-value for the test for positive selection in the *background* branches is: ** ${chosen_json['tests']['BG']['p-value'].toFixed(3)} **\n\n3. The p-value for the test for the *difference between* the test (foreground) and background branch sets is: ** ${chosen_json['tests']['DIFF']['p-value'].toFixed(3)} **","pinned":false,"hidden":false,"mode":"md"},{"id":116,"value":"** ${interpretation} **","pinned":false,"hidden":false,"mode":"md"},{"id":121,"value":"## Omega values and their proportions","pinned":false,"hidden":false,"mode":"md"},{"id":126,"value":"omega_plot.legend(\"color\", {\n label: \"Omega values →\",\n tickSize: 3,\n ticks: 10,\n //tickLabelRotate: 45,\n //tickFormat: r.tickFormat,\n //round: r.round,\n width: 600,\n height: 45\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":129,"value":"omega_plot = Plot.plot({\n color: {\n type: \"sqrt\",\n //pivot: 4,\n scheme: \"brbg\",\n reverse: true,\n //legend: true\n }, \n y: {\n domain: ['FG', 'BG', 'ALL']\n },\n marks: [\n Plot.barX(stacked_omegas, {y: \"dist\",x: \"proportion\", fill: 'omega', title: (d) =>\n `${d.dist} omega bin #${d.omega_bin}\\n Omega value: ${d.omega},\\nProportion: ${d.proportion}` }),\n Plot.ruleX([0])\n ]\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":170,"value":"\n** Figure 2. **\nOmega distribution for ${gene_id}. Sites were categorized into three omega values for each of the three distributions. The three distributions include: foreground branches, background branches, and all branches (in both FG and BG). Prop indicates proportion of sites that fall into the omega category. The largest omega value category for each of the three distributions are: ${omega_vals[2].toFixed(3)} for the FG, ${omega_vals[5].toFixed(3)} for the BG, and ${omega_vals[8].toFixed(3)} for all branches. \n","pinned":false,"hidden":false,"mode":"md"},{"id":44,"value":"### Parsing Data","pinned":false,"hidden":false,"mode":"md"},{"id":239,"value":"chosen_json = results_json[gene_id]['BUSTED-PH_' + scenario]","pinned":false,"hidden":false,"mode":"ojs"},{"id":371,"value":"results_json = Object.fromEntries(\n Object.entries(full_json).filter(([key, value]) =>\n 'BUSTED' in value &&\n fdr_or_no in value &&\n 'BUSTED_E' in value \n )\n)\n ","pinned":false,"hidden":false,"mode":"ojs"},{"id":32,"value":"full_json = await d3.json (\"https://data.hyphy.org/web/busted-e/endothermy/fish_053124.json\" );","pinned":false,"hidden":false,"mode":"ojs"},{"id":53,"value":"species_colors = d3.scaleOrdinal(d3.schemeCategory10).domain ([...species]);","pinned":false,"hidden":false,"mode":"ojs"},{"id":56,"value":"species = _.uniq(_.map(chosen_json['tested'][0])).sort()","pinned":false,"hidden":false,"mode":"ojs"},{"id":1139,"value":"chosen_json['tested']","pinned":true,"hidden":false,"mode":"ojs"},{"id":68,"value":"tree_object = [new phylotree.phylotree(chosen_json['tree'] || \"()\"), chosen_json['tested'][0] || [], chosen_json['lengths']]","pinned":false,"hidden":false,"mode":"ojs"},{"id":97,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":108,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":132,"value":"stacked_omegas = {\n\n let test = chosen_json['distributions']['unconstrained']['Rate Distributions']['Test']\n //return test\n let count = 1\n for (const key in test) {\n test[key]['dist'] = 'FG';\n test[key]['omega_bin'] = count;\n count++\n}\n\n//return test\n let bg = chosen_json['distributions']['unconstrained']['Rate Distributions']['Background']\n count = 1\n for (const key in bg) {\n bg[key]['dist'] = 'BG';\n bg[key]['omega_bin'] = count;\n count++\n}\n let shared = chosen_json['distributions']['shared']['Rate Distributions']['Test']\n count = 1\n for (const key in shared) {\n shared[key]['dist'] = 'ALL';\n shared[key]['omega_bin'] = count;\n count++\n}\n \nconst stacked = [\n ...Object.values(test),\n ...Object.values(bg),\n ...Object.values(shared)\n]; \n return stacked\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":173,"value":"omega_vals =_.map(stacked_omegas, d => d.omega)","pinned":false,"hidden":false,"mode":"ojs"},{"id":353,"value":"matchingEntry = Object.values(table_data).find(entry => entry.ID === gene_id)","pinned":false,"hidden":false,"mode":"ojs"},{"id":431,"value":"only_search_results = {\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":270,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":340,"value":"chisqrprob = function chisqrprob ($n,$x) {\n if (($n <= 0) || ((Math.abs($n) - (Math.abs(Math.floor($n)))) != 0)) {\n throw(\"Invalid n: $n\\n\"); /* degree of freedom */\n }\n return _subchisqrprob($n-0, $x-0);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":342,"value":"function _subchisqrprob ($n,$x) {\n var $p;\n\n if ($x <= 0) {\n $p = 1;\n } else if ($n > 100) {\n $p = _subuprob((Math.pow(($x / $n), 1/3)\n - (1 - 2/9/$n)) / Math.sqrt(2/9/$n));\n } else if ($x > 400) {\n $p = 0;\n } else { \n var $a;\n var $i;\n var $i1;\n if (($n % 2) != 0) {\n $p = 2 * _subuprob(Math.sqrt($x));\n $a = Math.sqrt(2/Math.PI) * Math.exp(-$x/2) / Math.sqrt($x);\n $i1 = 1;\n } else {\n $p = $a = Math.exp(-$x/2);\n $i1 = 2;\n }\n\n for ($i = $i1; $i <= ($n-2); $i += 2) {\n $a *= $x / $i;\n $p += $a;\n }\n }\n return $p;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":346,"value":"function _subuprob ($x) {\n var $p = 0; /* if ($absx > 100) */\n var $absx = Math.abs($x);\n\n if ($absx < 1.9) {\n $p = Math.pow((1 +\n $absx * (.049867347\n + $absx * (.0211410061\n + $absx * (.0032776263\n + $absx * (.0000380036\n + $absx * (.0000488906\n + $absx * .000005383)))))), -16)/2;\n } else if ($absx <= 100) {\n for (var $i = 18; $i >= 1; $i--) {\n $p = $i / ($absx + $p);\n }\n $p = Math.exp(-.5 * $absx * $absx) \n / Math.sqrt(2 * Math.PI) / ($absx + $p);\n }\n\n if ($x<0)\n $p = 1 - $p;\n return $p;\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":401,"value":" filtered_count = table_data.filter(obj => obj['filter?'] === 'filtered').length","pinned":false,"hidden":false,"mode":"ojs"},{"id":409,"value":" unfiltered_count = table_data.filter(obj => obj['filter?'] === 'unfiltered').length","pinned":false,"hidden":false,"mode":"ojs"},{"id":478,"value":"alpha_value = 0.05","pinned":false,"hidden":false,"mode":"ojs"},{"id":38,"value":"### Imports","pinned":false,"hidden":false,"mode":"md"},{"id":726,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":7,"value":"import {file} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":20,"value":"import {localFileInput} from \"@mbostock/localfile\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":23,"value":"params = new URLSearchParams(location.search)","pinned":false,"hidden":false,"mode":"ojs"},{"id":62,"value":"import { Legend, swatches } from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":91,"value":"phylotree=require (\"https://dl.dropboxusercontent.com/s/i528j2lqnyzknit/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":153,"value":"import {Plot} from \"@mkfreeman/plot-tooltip\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":323,"value":"import { py, pyodide } from '@gnestor/pyodide'","pinned":false,"hidden":false,"mode":"ojs"},{"id":845,"value":"import {upsetApp} from \"@trebor/upset-demonstrator\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1063,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":1067,"value":"#### Figures for paper","pinned":false,"hidden":false,"mode":"md"},{"id":1072,"value":"fdr version:","pinned":false,"hidden":false,"mode":"md"},{"id":769,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":763,"value":"sc2_cfdr101_111 = [\"E1800_NT_Cleaned_Aligned\", \"E1838_NT_Cleaned_Aligned\", \"E1915_NT_Cleaned_Aligned\", \"E2001_NT_Cleaned_Aligned\", \"E2022_NT_Cleaned_Aligned\", \"E2098_NT_Cleaned_Aligned\", \"E2140_NT_Cleaned_Aligned\", \"E2206_NT_Cleaned_Aligned\", \"E2307_NT_Cleaned_Aligned\", \"E2308_NT_Cleaned_Aligned\", \"E2426_NT_Cleaned_Aligned\", \"E2475_NT_Cleaned_Aligned\", \"E2454_NT_Cleaned_Aligned\", \"E2491_NT_Cleaned_Aligned\", \"E2515_NT_Cleaned_Aligned\", \"E2588_NT_Cleaned_Aligned\", \"E2601_NT_Cleaned_Aligned\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":754,"value":"sc3_cfdr101_111 = [\"E1915_NT_Cleaned_Aligned\", \"E2243_NT_Cleaned_Aligned\", \"E2293_NT_Cleaned_Aligned\", \"E2339_NT_Cleaned_Aligned\", \"E2355_NT_Cleaned_Aligned\", \"E2432_NT_Cleaned_Aligned\", \"E2588_NT_Cleaned_Aligned\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":746,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":789,"value":"all_cfdr101_111 = {\nlet all_psg = [];\n\nfunction addToAllPsg(id, scenario) {\n let foundIndex = all_psg.findIndex(obj => obj.name === id);\n if (foundIndex !== -1) {\n all_psg[foundIndex].sets.push(scenario);\n } else {\n all_psg.push({ name: id, sets: [scenario] }); \n }\n}\n\nsc1_cfdr101_111.forEach(id => addToAllPsg(id, \"Scenario 1\"));\nsc2_cfdr101_111.forEach(id => addToAllPsg(id, \"Scenario 2\"));\nsc3_cfdr101_111.forEach(id => addToAllPsg(id, \"Scenario 3\"));\nsc4_cfdr101_111.forEach(id => addToAllPsg(id, \"Scenario 4\"));\n//_.each(all_psg, function(item) {item.Count = item.Scenario.length;});\nlet temp = all_psg[9];\nall_psg[9] = all_psg[1]\nall_psg[1] = temp\nreturn all_psg\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":850,"value":"viewof appState = upsetApp({ set: all_cfdr101_111 })","pinned":false,"hidden":false,"mode":"ojs"},{"id":1075,"value":"---\n\nno fdr version","pinned":false,"hidden":false,"mode":"md"},{"id":779,"value":"all_psg_nofdr = {\nlet all_fdr_psg = [];\n\n// Function to add element with scenario to all_psg array\nfunction addToAllPsg(id, scenario) {\n let foundIndex = all_fdr_psg.findIndex(obj => obj.name === id);\n if (foundIndex !== -1) {\n all_fdr_psg[foundIndex].sets.push(scenario);\n } else {\n all_fdr_psg.push({ name: id, sets: [scenario] });\n }\n}\n\nsc1_c101_111.forEach(id => addToAllPsg(id, \"Scenario 1\"));\nsc2_c101_111.forEach(id => addToAllPsg(id, \"Scenario 2\"));\nsc3_c101_111.forEach(id => addToAllPsg(id, \"Scenario 3\"));\nsc4_c101_111.forEach(id => addToAllPsg(id, \"Scenario 4\"));\n\nreturn all_fdr_psg\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":766,"value":"$37","pinned":false,"hidden":false,"mode":"ojs"},{"id":760,"value":"sc2_c101_111 = [\"E1756_NT_Cleaned_Aligned\", \"E1800_NT_Cleaned_Aligned\", \"E1838_NT_Cleaned_Aligned\", \"E1915_NT_Cleaned_Aligned\", \"E1923_NT_Cleaned_Aligned\", \"E2001_NT_Cleaned_Aligned\", \"E2022_NT_Cleaned_Aligned\", \"E2098_NT_Cleaned_Aligned\", \"E2115_NT_Cleaned_Aligned\", \"E2140_NT_Cleaned_Aligned\", \"E2135_NT_Cleaned_Aligned\", \"E2206_NT_Cleaned_Aligned\", \"E2205_NT_Cleaned_Aligned\", \"E2213_NT_Cleaned_Aligned\", \"E2245_NT_Cleaned_Aligned\", \"E2307_NT_Cleaned_Aligned\", \"E2355_NT_Cleaned_Aligned\", \"E2426_NT_Cleaned_Aligned\", \"E2463_NT_Cleaned_Aligned\", \"E2475_NT_Cleaned_Aligned\", \"E2454_NT_Cleaned_Aligned\", \"E2476_NT_Cleaned_Aligned\", \"E2510_NT_Cleaned_Aligned\", \"E2491_NT_Cleaned_Aligned\", \"E2530_NT_Cleaned_Aligned\", \"E2515_NT_Cleaned_Aligned\", \"E2563_NT_Cleaned_Aligned\", \"E2588_NT_Cleaned_Aligned\", \"E2601_NT_Cleaned_Aligned\", \"E2633_NT_Cleaned_Aligned\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":757,"value":"sc3_c101_111 = [\"E1915_NT_Cleaned_Aligned\", \"E2022_NT_Cleaned_Aligned\", \"E2115_NT_Cleaned_Aligned\", \"E2148_NT_Cleaned_Aligned\", \"E2197_NT_Cleaned_Aligned\", \"E2243_NT_Cleaned_Aligned\", \"E2257_NT_Cleaned_Aligned\", \"E2293_NT_Cleaned_Aligned\", \"E2308_NT_Cleaned_Aligned\", \"E2339_NT_Cleaned_Aligned\", \"E2355_NT_Cleaned_Aligned\", \"E2398_NT_Cleaned_Aligned\", \"E2432_NT_Cleaned_Aligned\", \"E2424_NT_Cleaned_Aligned\", \"E2588_NT_Cleaned_Aligned\", \"E2589_NT_Cleaned_Aligned\", \"E2605_NT_Cleaned_Aligned\", \"E2629_NT_Cleaned_Aligned\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":749,"value":"$38","pinned":false,"hidden":false,"mode":"ojs"},{"id":875,"value":"viewof upset_plot = upsetApp({ set: all_psg_nofdr })","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W39","stdlib":"1","titling":"auto"}