29:null 2a:["$","title",null,{"children":"Alignment screens with aBSREL | Sergei Pond | Observable"}] 2f: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; }30:T4a6,table_data = { let res = _.map (_.toPairs (result_json), (d)=> { let res = { "ID" : d[0] }; let daic = (d)=>(_.get (d, ["absrel"]["fit"]) && _.get (d, ["absrel-mh"]["fit"] ))?d["absrel"]["fit"]["AIC-c"] - d["absrel-mh"]["fit"]["AIC-c"] : null; let branch_count_d = (d)=>"absrel" in d ? _.filter (d["absrel"]["branches"], (v)=>v["p_corr"] <= critical_value).length : null; let branch_count_mh = (d)=>"absrel-mh" in d ? _.filter (d["absrel-mh"]["branches"], (v)=>v["p_corr"] <= critical_value).length : null; let sus = (d,g)=> suspect_branches (g); let inject = [ ["Sequences", ["sequences"]], ["Sites", ["sites"]], ["Δ c-AIC (MH vs resular)", daic], ["Branches aBSREL", branch_count_d], ["Branches aBSREL-MH", branch_count_mh], ["Suspect", sus] //["ABSREL-MH c-AIC", ["absrel-mh","fit","AIC-c"]], //["ABSREL branches", pdiff], //["ABSREL-MH branches", sites], //["Suspect branches", ], ]; _.each (inject, (i)=> { res[i[0]] = _.isFunction (i[1]) ? i[1](d[1], d[0]) :_.get (d[1], i[1]); }); return res; }) return res; };31:[] 2d:{"id":"e0962a30298ceec4","slug":"alignment-screens-with-absrel","title":"Alignment screens with aBSREL","thumbnail":"062fa461021c58cba7fa56daeb70e4efe39c68f7d959a559c3681a6a3d668fdd","access_level":"public","create_time":"$D2022-10-07T15:39:58.002Z","update_time":"$D2022-10-18T19:37:54.972Z","view_time":null,"first_public_time":"$D2022-10-11T12:53:05.114Z","has_unpublished_edits":null,"fork":{"id":"61ca4428b1c669bd","slug":"visualizing-busted-ph-analysis-results","title":"Visualizing BUSTED-PH analysis results","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"},"version":3518,"publish_version":null,"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":0,"collection":null,"type":"notebook","body":{"title":"Alignment screens with aBSREL","cells":[{"id":0,"value":"md`# Alignment screens with aBSREL`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3176,"value":"\nviewof phenotype = select ({\n \"options\" : [\"marine-screen-absrel\"],\n \"value\" : \"marine-screen-absrel\",\n \"title\" : \"Dataset\"\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2156,"value":"md`### Summary of aBSREL analyses\naBSREL results are available for **${_.size (_.filter (result_json, (d)=>\"absrel\" in d))}** alignments, and aBSREL-MH results : for **${_.size (_.filter (result_json, (d)=>\"absrel-mh\" in d))}** alignments\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3267,"value":"viewof search = Inputs.search(table_data)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2809,"value":"table1_title = md`**Table 1** BUSTED-PH results on individual alignments`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2817,"value":"table1 = Inputs.table(search, {\n format: {\n \"Suspect\": (val)=>val.length ? (\"\" + val.length + \" : \" + val.join (\", \")) : \"\",\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2838,"value":"md`\n\n1. ** ID ** : gene / alignment ID\n2. ** Sequences ** : number of sequences in the aligment\n3. ** Sites ** : number of sites in the alignment \n4. ** Δ c-AIC (MH vs regular) ** : does aBSREL with MH outperform regular aBSREL using c-AIC.\n5. ** Branches aBSREL ** : # of branches under selection (p ≤ ${critical_value}) under aBSREL.\n6. ** Branches aBSREL-MH ** : # of branches under selection (p ≤ ${critical_value}) under aBSREL-MH.\n7 ** Suspect branches ** : # and list of branches that may include local alignment errors.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2233,"value":"md`### Gene-by-gene information`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":966,"value":"viewof gene_id = {\n const dd3 = autoSelect ({\n title: \"Gene ID\",\n options: _.keys (result_json)\n \n });\n dd3.input.style.fontSize = \"12px\";\n dd3.input.style.marginTop = \"8px\";\n return dd3;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2236,"value":"md`### Tree for ${gene_id}`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3397,"value":"\nviewof model = select ({\n \"options\" : [\"absrel\",\"absrel-mh\"],\n \"value\" : \"absrel\",\n \"title\" : \"Branch length\"\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1941,"value":"trendLegend = swatches({\n color: species_colors,\n title: \"Viral species\",\n //tickFormat: \"%\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":870,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"md`---`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2701,"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\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"phylotree=require (\"https://dl.dropboxusercontent.com/s/i528j2lqnyzknit/phylotree.js\")\n//require (\"phylotree/build/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"_=require(\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":78,"value":"//resolve(\"phylotree@0.1/phylotree.css\")\n//require (\"https://dl.dropbox.com/s/mjhii51tjy1o5gt/phylotree.js\")\nhtml`\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1905,"value":"tree_object = [new phylotree.phylotree(_.get (result_json, [gene_id,\"tree\"]) || \"()\"), collect_branches (model,\"rates\"),collect_branches (model,\"L\")]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3409,"value":"collect_branches = (model, key)=> {\n return _.chain (result_json[gene_id][model]['branches']).toPairs().map ((d)=>[d[0],d[1][key]]).fromPairs().value();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":127,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":874,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":174,"value":"import {select,checkbox, autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":488,"value":"vegalite = require(\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2288,"value":"float_format = d3.format (\".3g\");","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2321,"value":"report_ratio = (a,b)=> {\n if (a == 0 && b == 0) return 'N.D.';\n if (a == 0) return 'Infinite';\n return float_format (b/a);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1937,"value":"species_colors = d3.scaleOrdinal(d3.schemeCategory10).domain ([..._.sortBy (_.uniq (_.values(tree_object[1])))]);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3228,"value":"critical_value = 0.05","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3471,"value":"suspect_branches = (gene) => {\n let a = result_json[gene][\"absrel\"],\n b = result_json[gene][\"absrel-mh\"];\n if (a && b) {\n let branches = [];\n _.each (a[\"branches\"], (v, br)=> {\n if (v[\"p_corr\"] <= critical_value) {\n if (b[\"branches\"][br][\"p_corr\"] > critical_value && b[\"branches\"][br][\"2H\"] >= 0.1 && b[\"branches\"][br][\"3H\"] >= 1) if (br.indexOf (\"NODE\") < 0) branches.push (br);\n }\n });\n return branches;\n }\n return null;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2785,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3205,"value":"computeFDR = (values)=> {\n const N = values.length;\n return _.chain (values).map ((d,i)=>[i,d]).sortBy (d=>d[1]).map ((d,i)=>[d[0],d[1],Math.min (1,d[1]*(N/(i+1)))]).sortBy (d=>d[0]).value();\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":754,"value":"result_json = await d3.json (\"https://data.hyphy.org/web/busted-ph/\"+phenotype+\".json\");","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1943,"value":"import { legend, swatches } from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2060,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3299,"value":"import {renderNDiscreteDistributions} from \"@spond/omega-plots\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W31","stdlib":"1","titling":"auto"}} 2e:"$2d:body"