34:["$","title",null,{"children":"Summary of gene/segment level selection inference | Sergei Pond | Observable"}] 3c:[] 38:{"id":"f1050c36b68be0bc","slug":"summary-of-gene-segment-level-selection-inference","title":"Summary of gene/segment level selection inference","thumbnail":"d977f475a7a6b6eca22272b7d42d49d206f616673159c7150d9a90daf5f23fd5","access_level":"public","create_time":"$D2021-02-09T15:00:58.700Z","update_time":"$D2021-02-09T22:30:53.048Z","view_time":null,"first_public_time":"$D2021-02-09T15:20:01.058Z","has_unpublished_edits":null,"fork":{"id":"f423b9161a2d2b7b","slug":"combined-view-of-sites-which-may-be-experiencing-convergen","title":"Combined view of sites which may be experiencing convergence in N501Y clades","owner":{"id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond"}},"stars":0,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024","bio":"","followed_by_you":false,"follows_you":false},"version":444,"publish_version":444,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"bio":"","followed_by_you":false,"follows_you":false}],"members":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Summary of gene/segment level selection inference","cells":[{"id":0,"value":"md`# Summary of gene/segment level selection inference`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":136,"value":"table(\n selection_summary_tale,\n {\n maxHeight:1500,\n limit: 500,\n enableFilter: false,\n enableCSVDownload: true,\n columns: [{ \n key: 'segment',\n name: 'Gene/ORF',\n }, \n { \n key: 'V1',\n name: 'V1',\n render: (val)=>segment_string (val)\n },\n { \n key: 'V2',\n name: 'V2',\n render: (val)=>segment_string (val)\n },\n { \n key: 'V3',\n name: 'V3',\n render: (val)=>segment_string (val)\n },\n ]\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"md`Selection legend\n 1. : BUSTED selection\n 2. : RELAX intensification relative to reference\n 3. : RELAX relaxation relative to reference\n 4. - : analyses not performed due to lack of phylogetic resolution\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":33,"value":"md`### Computed`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":416,"value":"selection_summary_tale = {\n return _.map ( selection_summary, (info, segment) => {\n let row = {'segment' : segment};\n _.each (['V1','V2','V3'], (clade)=> {\n if (clade in info) {\n row[clade] = info[clade]; \n }\n });\n return row;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":411,"value":"selection_summary = {\n let by_segment = {};\n _.each (analysis_info, (segments, clade)=> {\n _.each (segments, (info, segment) => {\n if (segment in by_segment == false) {\n by_segment[segment] = {};\n }\n by_segment[segment][clade] = {};\n if (info.busted) {\n by_segment[segment][clade].busted = info.busted['p'];\n }\n if (info.relax) {\n by_segment[segment][clade].relax = info.relax['p'];\n by_segment[segment][clade].relaxK = info.relax['K'];\n\n }\n });\n });\n return by_segment;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":145,"value":"segment_string = (f)=> {\n if (f) {\n let tags = [];\n if (\"busted\" in f && f.busted <= 0.05) {\n tags.push ('');\n }\n if (\"relax\" in f && f.relax <= 0.05) {\n if (f.relaxK < 1) {\n tags.push ('');\n } else {\n tags.push ('');\n }\n }\n return tags.join (\"\");\n }\n return \"-\";\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":20,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":"pv = 0.05","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"analysis_info = {\n let base_url = \"https://data.hyphy.org/web/SARS-CoV-2/clades/\";\n let info = [{label: \"V1\", value: 'B117-Feb2020'},\n { label: \"V2\", value: 'B1351-Feb2020'},\n { label: \"V3\", value: 'P1-Feb2020'}];\n let annotations = {};\n \n for (let i = 0; i < info.length; i++) {\n annotations[info[i].label] = await d3.json (base_url + info[i].value + \"-summary.json\");\n }\n \n return annotations;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":340,"value":"signatures= _.map ( [[\"S/18\",1,1,0],[\"S/20\",1,1,1],[\"S/26\",1,0,1],[\"S/80\",1,1,0],[\"S/138\",1,1,0],[\"S/190\",1,0,1],[\"S/215\",0,0,1],[\"S/417\",0,1,0],[\"S/484\",0,1,1],[\"S/570\",0,0,1],[\"S/501\",1,1,1],[\"S/655\",1,1,0],[\"S/681\",0,1,0],[\"S/701\",1,1,0],[\"S/716\",1,1,0],[\"S/982\",0,1,0],[\"S/1027\",1,1,0],[\"S/1118\",0,0,1],[\"S/1176\",1,0,0],[\"S/1176\",0,0,1],[\"S/1219\",1,1,0],[\"ORF1a/265\",1,1,0],[\"ORF1a/1001\",1,0,0],[\"ORF1a/1188\",0,0,1],[\"ORF1a/1655\",0,1,0],[\"ORF1a/1708\",1,0,0],[\"ORF1a/1795\",0,0,1],[\"ORF1a/2230\",1,0,0],[\"ORF1a/3353\",1,1,0],[\"ORF1b/1263\",0,0,1],[\"ORF3a/57\",0,1,0],[\"ORF3a/171\",1,1,0],[\"ORF3a/253\",0,0,1],[\"E/71\",0,1,0],[\"ORF8/92\",0,0,1],[\"N/3\",1,0,0],[\"N/80\",0,0,1],[\"N/205\",1,1,0]], (s)=>{return {'site':+jsonCodonLookup[s[0].toUpperCase()],'V1': s[1], 'V2' : s[2], 'V3' : s[3]}})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"md`### Libraries`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":171,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":239,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"import {reverseLookup} from \"@spond/sc2-genes\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"import {select,checkbox, autoSelect, text} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":343,"value":"import {jsonCodonLookup} from \"@spond/sars_cov_2_sites\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":8,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W3c","stdlib":"1"}} 33:null