32:Ta53,joint_site_list = { const use_leaves = options.indexOf ("is") < 0; const use_EBF = options.indexOf ("pv") >= 0; const filter_gaps = options.indexOf ("gaps") >= 0; let rows = []; let classify_site = (s)=> { let site_class = {}; if (s && s.bMEME) { if (s.bMEME.p <= pv) { site_class ['E'] = s.bMEME.br; } else { if (use_EBF && s.lMEME.p <= pv) { site_class ['E'] = s.lMEME.br; } } if (use_EBF) { if (('E' in site_class == false) && s.bMEME.br > 0) { site_class ['E'] = s.bMEME.br; } } if (s.bFEL.p <= pv) { if (s.bFEL.a < s.bFEL.b) { site_class ['P'] = 1; } else { site_class ['N'] = 1; } } if (s.bCFEL.p.overall <= pv) { site_class ['X'] = 1; } if (s.FADE) { let fd = _.filter (_.toPairs(s.FADE), (p)=>p[1] >= 100); if (fd.length) { site_class['D'] = fd; } } } return site_class; } let site_freqs = (s)=> { let site_f = []; if (s && s.aa) { site_f = _.toPairs(_.find (_.toPairs (s.aa), (d)=>d[0] != 'Reference')[1]); } return site_f; } let ref_freqs = (s)=> { let site_f = []; if (s && s.aa) { site_f = _.toPairs(_.find (_.toPairs (s.aa), (d)=>d[0] == 'Reference')[1]); } return site_f; } _.each (joint_MEME, (d)=> { let c = d; let this_row = {}; if (d in reverseLookup == false) { c++; } if (c in reverseLookup == false) return; this_row.n = d; this_row.coord = reverseLookup[c][0][0]; let include = false; _.each (analysis_info, (info,k)=> { this_row[k] = classify_site (info[d]); include = include || _.size (this_row[k]); const sf = site_freqs (info[d]); const rf = ref_freqs (info[d]); if (filter_gaps) { let G = 0; let NG = 0; _.each (sf, (d)=>{if (d[0] == '-') {G+=d[1];} else {NG+=d[1]}}); //_.each (rf, (d)=>{if (d[0] == '-') {G+=d[1];} else {NG+=d[1]}}); if (G / (NG+G) >= 0.10) { include = false; return; } } this_row[k+"F"] = freq_string(sf); if (k == "V1") { this_row ["REF_F"] = freq_string(rf); } }); if (include) rows.push (this_row); }); return rows; }33:T624,polymorphic = { let polymorphic = {}; _.each (summary_info, (segments, clade) => { polymorphic[clade] = {}; _.each (segments, (segment, name)=> { let T = new phylotree.phylotree (segment.tree); let parents = {}; T.traverse_and_compute ((n) => { parents[n.data.name] = n.parent ? n.parent.data.name : null; }); _.each (segment.subs, (subs,site)=> { if (_.size (subs) > 2) { let tag = _.some (subs, (state, node) => { let label = segment.tree_tags[node]; if (label) { label = label[0]; if (label.length > 0 && label != "Reference") { let aa = translation_table[state]; if (aa != '-' && aa != 'X') { let p = parents[node]; while (p && !subs[p]) { p = parents[p]; } if (translation_table[subs[p]] != aa) { return true; } } } } return false; }); if (tag) polymorphic[clade][site] = 1; } }); }); }); return _.mapValues (polymorphic, (d)=>_.map (_.keys (d), (d)=>+d)); }34:[] 30:{"title":"Combined view of sites under selection in N501Y clades","cells":[{"id":0,"value":"md`# Combined view of sites under selection in N501Y clades`","pinned":false,"hidden":false,"mode":"ojs"},{"id":396,"value":"viewof data_from = select ({\n options : [\"February 2021\", \"April 2021\"],\n title: \"Use analysis from: \"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":456,"value":"viewof options = checkbox({\n title: \"Filtering options\",\n options: [\n { value: \"is\", label: \"Selection signal for internal branches only\" },\n { value: \"pv\", label: \"Use MEME EBF-flagged branches as evidence of selection\" },\n { value: \"gaps\", label: \"Filter sites with excessive gaps\"}\n ],\n value: [\"pv\", \"gaps\"],\n submit: false\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":402,"value":"viewof pv = text ({\n value : 0.05,\n title: \"p-value for MEME\",\n submit: true\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":409,"value":"md`Found ${joint_site_list.length} sites`","pinned":false,"hidden":false,"mode":"ojs"},{"id":136,"value":"table(\n joint_site_list,\n {\n maxHeight:4500,\n limit: 500,\n enableFilter: false,\n enableCSVDownload: false,\n columns: [{ \n key: 'n',\n name: 'Nucleotide',\n }, \n { \n key: 'coord',\n name: 'Site',\n },\n { \n key: 'V1',\n name: 'V1 selection',\n render: (val)=>site_string(val)\n },\n { \n key: 'V2',\n name: 'V2 selection',\n render: (val)=>site_string(val)\n },\n { \n key: 'V3',\n name: 'V3 selection',\n render: (val)=>site_string(val)\n },\n { \n key: 'REF_F',\n name: 'Reference composition',\n //render: (val)=>freq_string(val)\n },\n { \n key: 'V1F',\n name: 'V1 composition',\n //render: (val)=>freq_string(val)\n },\n { \n key: 'V2F',\n name: 'V2 composition',\n //render: (val)=>freq_string(val)\n },\n { \n key: 'V3F',\n name: 'V3 composition',\n //render: (val)=>freq_string(val)\n },\n ]\n }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":157,"value":"md`Selection legend\n 1. : episodic selection with this many specific branches\n 2. : pervasive positive\n 3. : pervasive negative\n 4. : different from reference\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":33,"value":"md`### Computed`","pinned":false,"hidden":false,"mode":"ojs"},{"id":145,"value":"freq_string = (f)=> {\n return _.chain (f).sortBy ((d)=>-d[1]).map ((d)=>d[0] + \"_{\" + d[1] + \"}\").value().join(\"\")\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":174,"value":"site_string = (d)=> {\n let res = [];\n if ('E' in d) {\n res.push ('');\n }\n if ('P' in d) {\n res.push ('');\n }\n if ('N' in d) {\n res.push ('');\n }\n if ('X' in d) {\n res.push ('');\n }\n return res.join ('');\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":104,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":36,"value":"joint_MEME = {\n let site_list = {};\n _.each (analysis_info, (data, clade)=> {\n let all_with_tests = _.chain (data).toPairs().filter ((d)=>\"bMEME\" in d[1]).groupBy ((d)=>site2gene(d[0])).value();\n site_list [clade] = _.map (_.toPairs (all_with_tests), (d)=> {\n return [d[0], qvalues(_.map (d[1], (s)=>[s[0],s[1].bMEME.p]))];\n });\n });\n //return _.map (site_list, (d)=>_.flatten(_.map (d, (v)=>v[1])));\n let tagged_sites = new Set();\n _.each (site_list, (d)=>{\n _.each (d, (g)=> {\n _.each (g[1], (s)=> tagged_sites.add (+s[0]));\n });\n });\n return _.sortBy ([...tagged_sites]);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":68,"value":"qvalues = (pvalues,cut)=> {\n cut = cut || qv;\n return _.chain (pvalues).sortBy ((d)=>d[1]).map ((d,i)=>[d[0], d[1], d[1] * pvalues.length/(i+1)]).filter ((d)=>(d[1] <= cut)).value();\n};","pinned":false,"hidden":false,"mode":"ojs"},{"id":53,"value":"site2gene = (site)=> {\n if (site in reverseLookup || (+site + 1) in reverseLookup) {\n let lkup = reverseLookup[site] || reverseLookup[+site + 1];\n if (lkup.length > 2) {\n return lkup[1][0].split (\"/\")[0];\n }\n return lkup[0][0].split (\"/\")[0];\n }\n return \"\";\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":20,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs"},{"id":30,"value":"qv = 0.05","pinned":false,"hidden":false,"mode":"ojs"},{"id":23,"value":"analysis_info = {\n let base_url = \"https://data.hyphy.org/web/SARS-CoV-2/clades/\";\n let info;\n if (data_from == \"April 2021\") {\n info = [{label: \"V1\", value: 'B.1.1.7-202104'},\n { label: \"V2\", value: 'B.1.351-202104'},\n { label: \"V3\", value: 'P.1-202104'}];\n } else {\n info = [{label: \"V1\", value: 'B117-Feb2020'},\n { label: \"V2\", value: 'B1351-Feb2020'},\n { label: \"V3\", value: 'P1-Feb2020'}];\n }\n \n let annotations = {}; \n for (let i = 0; i < info.length; i++) {\n annotations[info[i].label] = await d3.json (base_url + info[i].value + \"-annotation.json\");\n } \n return annotations;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":322,"value":"selected_sites = {\n let ss = {};\n _.each (['V1','V2','V3'], (d)=> {\n ss[d] = _.map (_.filter (joint_site_list, (r)=> r[d] && (r[d].E || r[d].P)), (r)=>r.n);\n });\n return ss;\n} ","pinned":false,"hidden":false,"mode":"ojs"},{"id":289,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":286,"value":"summary_info = {\n let base_url = \"https://data.hyphy.org/web/SARS-CoV-2/clades/\";\n let info;\n if (data_from == \"April 2021\") {\n info = [{label: \"V1\", value: 'B.1.1.7-202104'},\n { label: \"V2\", value: 'B.1.351-202104'},\n { label: \"V3\", value: 'P.1-202104'}];\n } else {\n info = [{label: \"V1\", value: 'B117-Feb2020'},\n { label: \"V2\", value: 'B1351-Feb2020'},\n { label: \"V3\", value: 'P1-Feb2020'}];\n } \n let annotations = {};\n \n for (let i = 0; i < info.length; i++) {\n annotations[info[i].label] = await d3.json (base_url + info[i].value + \"-summary.json\");\n }\n \n return annotations;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":251,"value":"tested = _.mapValues (analysis_info, (annotation_json)=>_.chain (annotation_json).toPairs ().filter ((d)=>d[1].bMEME).map ((d)=>+d[0]).value())","pinned":false,"hidden":false,"mode":"ojs"},{"id":368,"value":"intersect = (s1,s2)=> {\n let o = {};\n _.each (s1, (n)=>o[n]=1);\n _.each (s2, (n)=>(n in o) ? o[n] ++ : o[n]);\n let r = [];\n for (let i in o) {\n if (o[i] > 1) {\n r.push (+i); \n }\n }\n return r;\n }","pinned":false,"hidden":false,"mode":"ojs"},{"id":258,"value":"permuteOverlap = (all1, all2, selected1, selected2, n)=> {\n \n let base = intersect (all1,all2);\n let s1 = intersect (base,selected1);\n let s2 = intersect (base,selected2);\n let overlap = intersect (s1,s2);\n let sampled = [];\n let N = n || 10000;\n _.each (_.range (N), (r)=> {\n let d1 = _.sampleSize (base, s1.length);\n let d2 = _.sampleSize (base, s2.length);\n sampled.push (intersect (d1,d2).length);\n });\n return {\n 'shared' : base.length,\n 's1' : s1.length,\n 's2' : s2.length,\n 'overlap' : overlap.length,\n 'overlapped' : overlap,\n 'samples' : N,\n 'max' : d3.max (sampled),\n 'p' : ((_.filter (sampled, (s)=>s >= overlap.length)).length + 1) / (N+1)\n }\n};","pinned":false,"hidden":false,"mode":"ojs"},{"id":418,"value":"annotation = _.mapValues (await d3.json (/*'https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/data/comparative-annotation.json'*/\"https://dl.dropboxusercontent.com/s/wz40kx05e2no8tt/annotation.json\"), (d)=>{\n if (d.evo) {\n d.evo = _.chain (d.evo).toPairs().map ((d)=>[translation_table[d[0]], d[1]]).groupBy ((d)=>d[0]).mapValues((v)=>d3.sum (v, (c)=>c[1])).value();\n }\n return d;\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":263,"value":"permuteOverlap (polymorphic.V2, polymorphic.V3, selected_sites.V2, selected_sites.V3, 1000)","pinned":false,"hidden":false,"mode":"ojs"},{"id":50,"value":"reverseLookup","pinned":false,"hidden":false,"mode":"ojs"},{"id":344,"value":"joint_MEME_list = buildSiteList (joint_site_list)","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"md`### Libraries`","pinned":false,"hidden":false,"mode":"ojs"},{"id":294,"value":"phylotree=require (\"https://dl.dropbox.com/s/i528j2lqnyzknit/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":421,"value":"import {signatures, buildSiteList} from \"@spond/clade-convergence\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":171,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":309,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":14,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":47,"value":"import {reverseLookup} from \"@spond/sc2-genes\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":17,"value":"import {select,checkbox, autoSelect, text} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":8,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":11,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W34","stdlib":"1","titling":"auto"}