44:["$","title",null,{"children":"Dating OGV HIV strains | Sergei Pond | Observable"}] 4c:T754,table( (()=>{ subject; region; return _.map (_.filter(summary_table, (record) => (record.Subject == subject && record.Region == region)), (record) => { var r = {"Region" : record.Region, "Sequence": record.Sequence.split('_').splice (1).join ('_'), "Combined" : record.Combined, "Patristic" : [record.Partistic,record.Partistic_support, record.Partistic_confidence] , "Clade" : [record.Clade,record.Clade_support, record.Clade_confidence], "Placement" : [record.Placement,record.Placement_support], "Regression" : [record.Regression,record.Root_to_tip_r2] }; return r; }); })(),{ enableFilter: true, enableCSVDownload: true, columns : [ 'Region', { key : 'Sequence', render : val => `${render_dna(val)} ${val.length < 20 ? val : val.substr (0,20) + "..."}` }, { key : 'Combined', render : val => `${float_format(val)}` }, { key : 'Patristic', render : val => `${render_icon(val[2])}${int_format(val[0])}${supp_format(val[1])} ` }, { key : 'Clade', render : val => `${render_icon(val[2])}${int_format(val[0])}${supp_format(val[1])}` }, { key : 'Placement', render : val => `${int_format(val[0])}${supp_format(val[1])}` }, { key: "Regression", render : val => `${render_icon(val[1])}${real_format(val[0])}` } ] })4d:T541,rendered_tree = { var t = tree.render("#tree_container", { height:width, width:height, 'left-right-spacing': 'fit-to-size', 'top-bottom-spacing': 'fit-to-size', 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { if (n.decimal_date_value) { return 1; } return 5; } return 0; }; t.node_label = n=>""; t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = true; t.style_edges ((e,d) => { if (!tree.is_leafnode (d.target)) { e.style ("opacity", d.target.data.bootstrap_values); } else { if (d.target.decimal_date_value) { e.style ('stroke', annotation[subject]['colors'][d.target.decimal_date_value]); } else { e.style ('stroke', 'purple'); } } }); t.style_nodes ((n,d) => { if (tree.is_leafnode (d)) { if (d.decimal_date_value) { n.selectAll ("circle").style ("fill", annotation[subject]['colors'][d.decimal_date_value]).style ("stroke", annotation[subject]['colors'][d.decimal_date_value]); } else { n.selectAll ("circle").style ("fill", "purple").style ("stroke", "purple"); } } }); t.update(); return t; }4e:[] 48:{"id":"100b56ef6e3832cc","slug":"dating-ogv-hiv-strains","title":"Dating OGV HIV strains","thumbnail":"da5ce6035e014bdf27c54edb259160d5cde50d98ce3b19bc9b2a467b68d95cff","access_level":"public","create_time":"$D2019-04-15T12:47:42.343Z","update_time":"$D2019-11-08T19:42:22.551Z","view_time":null,"first_public_time":"$D2019-04-16T00:15:24.278Z","has_unpublished_edits":null,"fork":false,"stars":1,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024","bio":"","followed_by_you":false,"follows_you":false},"version":353,"publish_version":353,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"bio":"","followed_by_you":false,"follows_you":false}],"members":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"role":"editor"}],"comments":[{"id":"16a1d7846333df7b","reply_to_id":null,"content":"How can I get a sample file to see your work? I'm getting a 404 error on this file.","create_time":"$D2020-11-06T20:38:48.884Z","update_time":null,"resolved":false,"user":{"type":"individual","id":"b71d6cb609c0328b","login":"pamsaint","name":"Pam St. Michel","avatar_url":"https://avatars-next.observableusercontent.com/9315a3295478a6fd0974a5b3a2b6b1571bf28ed5a94f86bfa46c48025085ab7a","tier":null}}],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Dating OGV HIV strains","cells":[{"id":0,"value":"md`# Dating OGV HIV strains`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":40,"value":"md`#### View the following subject / region`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":34,"value":"viewof subject = select(_.keys(_.countBy (summary_table, \"Subject\")))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":163,"value":"viewof region = select(_.keys(_.countBy (_.filter (summary_table, (r) => r.Subject == subject), \"Region\")))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":17,"value":"$4c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":178,"value":"viewof width = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":304,"value":"viewof height = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":203,"value":"md`### Combined OGV and NGS tree`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"md`-----`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"(()=>{\n subject;\n return _.map (summary_table, (record) => {\n //var r = {\"Subject\" : record.Subject, \"Region\" : record.Region, \"Seqi\n /*{\"Gene\" : record[0]['gene'], \"Position\": record[0]['position'], \"AA\" : record[0]['aa'], \"Count\" : record[0]['count'], \"Coverage\" : record[0]['coverage'], \"Type\" : record[0]['unusual'] ? \"Unusual\" : \"Usual\", \"Real\" : real_format(record[1][1])};*/\n \n //console.log (r);\n var r = record;\n return r;\n })})()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"summary_table = await d3.csv (\"https://dl.dropbox.com/s/qwrzb8vxt7i9fkm/summary.csv\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"annotation = await d3.json (\"https://dl.dropbox.com/s/cvrbt7rzbn0qk5w/conversion.json\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"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":"$undefined"},{"id":19,"value":"real_format = d3.format (\"2.0f\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":325,"value":"float_format = d3.format (\".3f\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":124,"value":"supp_format = (v) => v == 'N/A' ? v : d3.format (\"3.2p\")(+v)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":68,"value":"int_format=(v) => v == 'N/A' ? v : d3.format (\".0f\")(+v)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":84,"value":"color_code = (id, date) => {\n \n if ('colors' in annotation[id]) {\n return annotation[id]['colors'][annotation[id]['Start2ART']-date];\n } else {\n return d3.interpolateRdBu ((annotation[id]['Start2ART']-date)/annotation[id]['Start2ART']);\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":21,"value":"_=require(\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":"_.keys(_.countBy (summary_table, \"Subject\"))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":36,"value":"import {select} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":136,"value":"render_icon = (value) => {\n value = +value;\n if (value > 0.4 && value <= 0.7) {\n return '';\n } \n if (value > 0.7) {\n return '';\n }\n \n return '';\n \n }\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":340,"value":"render_dna = (value) => {\n if (value.indexOf (\"_DNA\") > 0) {\n return '';\n } \n return '';\n }","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":173,"value":"phylotree=require (\"phylotree@alpha/build/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":196,"value":"$4d","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":200,"value":"tree = {\n var t = new phylotree.phylotree(await d3.text (\"https://raw.githubusercontent.com/spond/misc/master/qvoa-trees/\"+subject+\"/\"+subject+\"_\"+region+\"_all_hap.fasta_combined.nwk\"));\n \n const date_regexp = new RegExp('([0-9]+)WPI');\n const date_extract = (n) => {\n\t const m = date_regexp.exec(n);\n if (m) {\n return m[1];\n }\n return null;\n }; \n \n phylotree.extract_dates (t, (n) => {\n return date_extract (n.data.name);\n }, (d) => {\n // convert WPI into years post-infection\n var date = new Date (2000 + (+d), 0, 1);\n return date;\n }\n );\n \n t.traverse_and_compute(function(node) {\n if (node.decimal_date_value) {\n node.decimal_date_value -= 2000;\n }\n });\n const rtt = phylotree.fit_root_to_tip (t);\n //t.reroot (rtt.root);\n //console.log (t);\n return t;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":149,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W4e","stdlib":"1"}} 24:null