2e:null 2f:["$","title",null,{"children":"Omicron mutations in sequences up to Oct 2021 enabled by data from | Sergei Pond | Observable"}] 34:T404,vegalite ({ "vconcat" : [{ "data": {"values": flat_mutations}, "width" : 800, "height" : 150, "mark": "bar", "title": {"text" : "All mutations", "fontSize": 20}, "encoding": { "x": { "bin": {"maxbins": 200}, "field": "F", "axis" : {"grid" : false, "title" : "Mutation Frequency", titleFontSize : 16, labelFontSize: 12} }, "y": {"aggregate": "count", "scale" : {"type" : "symlog"}, "axis" : {"grid" : false, "title" : "Count", titleFontSize : 16, labelFontSize: 12}} } },{ "data": {"values": table_data}, "title": {"text" : "Selected mutations", "fontSize": 20}, "width" : 800, "height" : 150, "mark": "bar", "encoding": { "x": { "bin": {"maxbins": 200}, "field": "Freq", "axis" : {"grid" : false, "title" : "Mutation Frequency", titleFontSize : 16, labelFontSize: 12} }, "y": {"aggregate": "count", "scale" : {"type" : "symlog"}, "axis" : {"grid" : false, "title" : "Count", titleFontSize : 16, labelFontSize: 12}} } } ]})35:T5dc,table_data = { let rows = []; _.each (sites2track, (d,s)=>{ let record = {}; record ["Coord"] = +s; record ["Codon"] = d[0]; record ["AA"] = d[1]; let info = combined_data[s]; if (!info) info = combined_data[(+s)+1]; if (info) { record["Gene/site"] =info["L"]; let this_gene = info["L"].split ("/")[0]; let this_codon = _.find (info["V"], (v)=>v[0] == d[0]); let this_aa = _.filter (info["V"], (v)=>v[1] == d[1]); let total = d3.sum (info["V"], (v)=>v[2]); if (this_codon) { record["Count"] = this_codon[2]; record["Freq"] = this_codon[3]; record["GeneRank"] = "" + ranks_by_gene[this_gene][this_codon[2]] + "/" + ranks_by_gene[this_gene]["N"]; } else { record["Count"] = null; record["Freq"] = 1e-6; record["GeneRank"] = null; } record ["AACount"] = d3.sum (this_aa, (v)=>v[2]); record ["AAFreq"] = record ["AACount"]/total; let this_haplo = _.find (info["H"], (v)=>v[0] == d[0]); if (this_haplo) { record["Haplotypes"] = this_haplo[1]; record["HaplotypeRank"] = this_haplo[2]; } else { record["Haplotypes"] = null; record["HaplotypeRank"] = null; } } rows.push (record); }); return rows; }36:Tc29,html` `37:[{"id":"e28bf6c41c2ce5011db7438a82d5d2e644001c5ebee598e5d239b07044f16b9902e6009272bcc2534b7c31894b8129e501afac83d73d02e76b4148cdf25390a4","href":"https://static.observableusercontent.com/files/e28bf6c41c2ce5011db7438a82d5d2e644001c5ebee598e5d239b07044f16b9902e6009272bcc2534b7c31894b8129e501afac83d73d02e76b4148cdf25390a4","name":"combined@1.json","type":"application/json","lastModified":1638366142299.958,"size":8254949}] 32:{"id":"848f10db5703e8c9","slug":"omicron-mutations-tables","title":"Omicron mutations in sequences up to Oct 2021 enabled by data from ","thumbnail":"30d891ec2efcb948d2e01742662a49269a0dcf322397e79d453408af0a7ad329","access_level":"public","create_time":"$D2021-12-01T13:42:22.299Z","update_time":"$D2021-12-02T15:27:08.949Z","view_time":null,"first_public_time":"$D2021-12-01T14:46:30.735Z","has_unpublished_edits":null,"fork":{"id":"128cabf863a48ab0","slug":"sc2-prioritization","title":"Evolutionary prioritization of codons and mutations in SARS-CoV-2 genomes enabled by data from ","owner":{"id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond"}},"stars":2,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024"},"version":2500,"publish_version":2500,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null}],"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":2,"collection":null,"type":"notebook","body":{"title":"Omicron mutations in sequences up to Oct 2021 enabled by data from ","cells":[{"id":0,"value":"md`# Omicron mutations in sequences up to Oct 2021 enabled by data from $\"gisaid-logo\"$
`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2322,"value":"viewof mutations = textarea({\n title: \"Input a mutational signature to analyze\", \n value: \"2830/AGG, 6514/ATA, 8392/ACT, 10027/ATC, 10447/CAC, 11536/GTT, 14406/CTT, 21760/GTT, 21844/ATT, 21985/GAC, 22195/ATA, 22576/GAT, 22672/CTC, 22678/CCA, 22684/TTC, 22810/AAT, 22879/AAG, 22897/AGT, 22990/AAC, 22993/AAA, 23011/GCA, 23038/CGA, 23047/AGT, 23053/CGA, 23062/TAT, 23074/CAC, 23200/AAA, 23401/GGT, 23524/TAT, 23596/AAG, 23602/CAT, 23851/AAA, 23947/TAT, 24127/AAA, 24421/CAT, 24466/AAA, 24502/TTT, 26528/GGT, 26576/GAA, 26708/ACT, 28309/CTC, 28879/AAA, 28882/CGA\", \n spellcheck: false,\n width: \"100%\",\n rows: 5,\n submit: \"Compute\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2284,"value":"genome_view = vegalite(genome_view_spec (genome_display (table_data, [])))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1877,"value":"table1_label = md`**Table 1.** Occurences of specified mutations at the codon level`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2172,"value":"viewof table1 = Inputs.table (table_data, {\n rows : 10,\n format: {\n 'Freq' : (x)=>x.toFixed (4),\n 'AAFreq' : (x)=>x.toFixed (4),\n 'AA' : (x)=>html`${x}`,\n 'Gene/site' : (x)=>html`${x}`,\n 'Predicted' : (x)=>x[0]\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2423,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"md`### Libraries and data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"d3 = require(\"d3@6\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1194,"value":"import {select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"_ = require (\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2335,"value":"sites2track = {\n let s = mutations.split (/,\\s*/);\n let m = {};\n _.each (s, (d)=>{\n let dd = d.split (\"/\");\n m [dd[0]] = [dd[1],translation_table [dd[1]]];\n });\n return m;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2342,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2475,"value":"ranks_by_gene = {\n let by_gene = _.groupBy (combined_data, (d)=>d.L.split (\"/\")[0]);\n return _.mapValues (by_gene, (d)=> {\n let counts = _.sortBy (_.flatten (_.map (d, (v)=>_.map (_.filter (v.V, (c)=>c[0] != v.C), (c)=>c[2]))), (d)=>-d);\n let count_array = {}; \n count_array.N = counts.length;\n _.each (counts, (d,i)=> {\n if (! (d in count_array)) {\n count_array[d] = i+1;\n }\n });\n return count_array;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2406,"value":"flat_mutations = _.flatten(_.map (combined_data, (d,k)=> {\n let v = _.groupBy (d.V, (v)=>v[0]);\n return _.map (d.H, (h)=>({'F' : v[h[0]][0][3], 'C' : k}));\n}));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2107,"value":"combined_data = await (FileAttachment(\"combined@1.json\").json())","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2268,"value":"genome_display = (pset, nset)=> {\n let site_info = [];\n _.each ([[pset,'Pos'],[nset,'Neg']], (d,i)=> {\n _.each (d[0], (s)=> {\n site_info.push ({\n 'coord' : s.Coord,\n 'label' : s[\"Gene/site\"][0],\n 'Score' : s[i?\"CScore\":\"AScore\"],\n 'type' : d[1]\n });\n });\n });\n return site_info; \n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1402,"value":"pad_array = (arr)=>_.map (arr, (d)=>\"Site \" + d.toUpperCase())","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2394,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2316,"value":"import {genome_view_spec} from \"@spond/selection-profile\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2324,"value":"import {checkbox, radio, textarea,select,autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1630,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1633,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W37","stdlib":"1","titling":"auto"}} 33:"$32:body"