29:null 2a:["$","title",null,{"children":"Displaying aBSREL results using branch \"censoring\" | Sergei Pond | Observable"}] 2f:T1162,displayed_tree={ let dim = treeDim.length ? _.map (treeDim.split ("x"), (d)=>+d) : null; let tree = tree_object; var t = tree.render( dim ? { height:dim[0] || 1024, width:dim[1] || 600, 'show-scale' : true, 'is-radial' : false, 'left-right-spacing': 'fit-to-size', 'top-bottom-spacing': 'fit-to-size', 'node_circle_size' : (n)=>0 } : { height:1024, width:800, 'show-scale' : true, '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)) { return 3; } return 1; }; let bl = _.fromPairs (_.map (_.toPairs (dabsrel_json ["branch attributes"][0]), (d)=>[d[0], d[1][branch_length_selector]])); let c10 = d3.scaleOrdinal(d3.schemeDark2); t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = false; const cbl = +censored_length; t.phylotree.branch_length_accessor = n=> { let bll = bl[n.data.name]; if (bll > cbl) { n.data.censored_bl = true; return cbl; } else { n.data.censored_bl = false; } return bll; } t.nodeLabel ((n)=>{ if (n.children && n.children.length) return ""; return n.data.name; }); 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.resortChildren (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); t.style_nodes ((e,n) => { /*if (nodeStates) { e.style ('fill', c10 (nodeStates[n.data.name])); if (binfo[0].length) { e.selectAll ("circle").style ('fill', species_colors (binfo[0])); } } else { if (binfo[0].length) { e.style ('fill', species_colors (binfo[0])); } }*/ //} }); let cutoffp = 0.05; t.style_edges ((e,d) => { let ttext = d.target.data.name; if (dabsrel_json ["branch attributes"][0][d.target.data.name]["Corrected P-value"] <= cutoffp) { e.style ('stroke-width',5); } else { e.style ('stroke-width',null); } if (d.target.data.name in coloration) { e.style ('stroke', color_scale (coloration[d.target.data.name])); ttext += "\n" + branch_color_selector + " = " + coloration[d.target.data.name]; } else { e.style ('stroke', null); } /* if (subs) { sub_count = subs.length; ttext = "Subs at " + subs.join (", "); } if (d.target.data.name in treeTags) { if (treeTags[d.target.data.name][3].length) { ttext += "\nMEME selection at sites " + _.map (treeTags[d.target.data.name][3], (s)=>annotation_json [s].G + "/" + annotation_json [s].S).join (", "); } sub_count = treeTags[d.target.data.name][3].length; } if (nodeStates) { if (nodeStates[d.target.data.name] != nodeStates[d.source.data.name]) { e.style ('stroke-width',5); } else { e.style ('stroke-width',null); } if (d.target.data.name in treeTags) { if ( treeTags[d.target.data.name][3].indexOf (+site2view) >= 0) { e.style ('stroke','darkred'); } } } else { if (d.target.data.name in tree_object[1]) { let binfo = tree_object[1][d.target.data.name]; e.style ('stroke-width', 1 + sub_count); } //e.selectAll("title").text ("p = " + p); } */ if (d.target.data.censored_bl) { e.style ('stroke-dasharray',10); } if (ttext) { e.selectAll("title").text (ttext); } }); t.placenodes(); t.update(); return t; }30:T5ba,function addRegression(Plot) { Plot.regression = function ({ x, y, type, bandwidth, order, ...options }) { type = String(type).toLowerCase(); const regressor = type === "quad" ? reg.regressionQuad() : type === "poly" ? reg.regressionPoly() : type === "pow" ? reg.regressionPow() : type === "exp" ? reg.regressionExp() : type === "log" ? reg.regressionLog() : type === "loess" ? reg.regressionLoess() : reg.regressionLinear(); if (bandwidth && regressor.bandwidth) regressor.bandwidth(bandwidth); if (order && regressor.order) regressor.order(order); const z = options.z || options.stroke; // maybeZ return Plot.transform(options, function (data, facets) { const X = Plot.valueof(data, x); const Y = Plot.valueof(data, y); const Z = Plot.valueof(data, z); regressor.x((i) => X[i]).y((i) => Y[i]); const regFacets = []; const points = []; for (const facet of facets) { const regFacet = []; for (const I of Z ? d3.group(facet, (i) => Z[i]).values() : [facet]) { const reg = regressor(I); for (const d of reg) { const j = points.push(d) - 1; if (z) d[z] = Z[I[0]]; regFacet.push(j); } } regFacets.push(regFacet); } return { data: points, facets: regFacets }; }); }; return Plot; }31:[] 2d:{"id":"ec9dacf338059a17","slug":"displaying-absrel-results-using-branch-censoring","title":"Displaying aBSREL results using branch \"censoring\"","thumbnail":"d424adc933e485ebf34657162f882c88ddc0b1783df5464f231d82b310598ce4","access_level":"public","create_time":"$D2021-01-05T19:38:06.492Z","update_time":"$D2025-03-11T12:48:48.464Z","view_time":null,"first_public_time":"$D2021-01-05T21:05:25.521Z","has_unpublished_edits":null,"fork":{"id":"7cb808b133d2105a","slug":"zav501v2","title":"Visualizing preliminary selection analysis results for evolution of the UK501 clade","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":3552,"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":4,"collection":null,"type":"notebook","body":{"title":"Displaying aBSREL results using branch \"censoring\"","cells":[{"id":0,"value":"md`# Displaying aBSREL results using branch \"censoring\"`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2704,"value":"md`\nLoad an aBSREL result file and present the tree with branches that are too long clipped to a fixed length\n` ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3134,"value":"viewof absrel_results_file = params.get (\"url\") ? localFileInput({accept: \".json\", value : params.get (\"url\"), disable: true}) : localFileInput({accept: \".json\"}) ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2657,"value":"viewof treeDim = text({placeholder : \"1024 x 800\", description: \"Tree dimension (height x width in pixels), leave blank to auto-scale\", submit: \"Resize\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3222,"value":"viewof branch_length_selector = select ({\n options: _.map (_.filter (_.toPairs(dabsrel_json[\"branch attributes\"][\"attributes\"]), (d)=>d[1][\"attribute type\"] == \"branch length\" || d[1][\"attribute type\"] == \"branch label\"), (d)=>d[0]),\n description: \"Branch lengths come from this model\",\n value: \"Full adaptive model\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3283,"value":"viewof branch_color_selector = select ({\n options: _.map (_.filter (_.toPairs(dabsrel_json[\"branch attributes\"][\"attributes\"]), (d)=>d[1][\"attribute type\"] == \"branch label\"), (d)=>d[0]),\n description: \"Branch colors come from this attribute\",\n value: \"Corrected P-value\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3270,"value":"viewof censored_length = text({value : 0.25, description: \"Maximum branch length to display\", submit: \"Update\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2855,"value":"md`Branches that have evidence of episodic selection (p≤0.05) are shown in thicker lines, and the colors are shown based on the coloring attribute above. Branches that have been censored because they are too long are shown as dashed lines. Mouse over branches to view more details about them`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3401,"value":"viewof treeExport = Inputs.textarea({label: \"Newick with displayed branch lengths\", value : exportNewick})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3305,"value":"legend({\n color: color_scale,\n title: branch_color_selector,\n tickFormat: \".2h\",\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3378,"value":"displayed_tree.show()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"html`\n \n

\n`\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3512,"value":"viewof search = Inputs.search(table_data)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3524,"value":"table1_title = md`**Table 1** aBSREL result summary`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3527,"value":"table1 = Inputs.table(search, {\"format\" : {\"prop(ω)\" : (d)=>d3.format (\".2p\")(d)}})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3464,"value":"viewof param = type === \"LOESS\"\n ? Inputs.range([0, 1], { label: \"bandwidth (LOESS)\" })\n : type === \"Poly\"\n ? Inputs.range([1, 5], { label: \"poly order\", value: 3, step: 1 })\n : Object.assign(html`—`, { value: null })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3424,"value":"viewof type = Inputs.select([\"Linear\", \"Quad\", \"Poly\", \"Log\", \"Exp\", \"LOESS\"], {\n label: \"type\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3427,"value":"viewof scale = Inputs.select([\"linear\", \"sqrt\", \"log\"], {\n label: \"scale\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3430,"value":"viewof x = Inputs.select(branch_length_attr, {\n label: \"x\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3432,"value":"viewof y = Inputs.select(branch_length_attr, {\n label: \"y\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3482,"value":"viewof filter = Inputs.text({label: \"Name filter\", placeholder: \"Regexp\", submit: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3449,"value":"Plot.plot({\n height: 640,\n grid: true,\n x: {\n type: scale,\n label: \"\" + x + \" →\"\n },\n y: {\n type: scale,\n label: \"↑ \" + y\n },\n r: {\n range: [0, 20]\n },\n marks: [\n Plot.dot(branch_length_values, {x: x, y: y, fill: \"steelblue\"}),\n Plot.line(\n branch_length_values,\n Plot.regression({\n x: x,\n y: y,\n type,\n bandwidth: param,\n order: param,\n stroke: \"firebrick\"\n })\n )\n ]\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":3027,"value":"md`\n

\n### Data and libraries \n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3138,"value":"dabsrel_json = await get_json (params.get (\"url\"))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3503,"value":"get_json = async (json_source)=> {\n if (json_source) {\n return d3.json (json_source);\n }\n return absrel_results_file.json();\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3321,"value":"color_scale = {\n const v = _.map (coloration);\n let d = d3.extent (v);\n let md = d3.median (v);\n if (d[1] > md*10.) {\n return d3.scaleDiverging([d[0], md, d[1]], d3.interpolateRdBu);\n }\n return d3.scaleSequential([d[0], d[1]], d3.interpolatePiYG);\n \n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3295,"value":"coloration = _.chain (_.toPairs (dabsrel_json[\"branch attributes\"][0]).map (d=>[d[0], d[1][branch_color_selector]])).fromPairs().value()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3459,"value":"branch_length_values = _.filter (_.map (dabsrel_json[\"branch attributes\"][\"0\"], (d,k)=>{d.Name = k; return d}), (d)=>name_filter.exec(d.Name) !== null)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3489,"value":"name_filter = new RegExp (filter)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3519,"value":"table_data = _.map (dabsrel_json[\"branch attributes\"][\"0\"], (d,k)=> {\n if (!d[\"Rate Distributions\"]) return [];\n return {\n 'Name' : k,\n 'p-value (corrected)' : d['Corrected P-value'],\n 'Rates' : d[\"Rate classes\"],\n 'max(ω)' : _.sortBy (d[\"Rate Distributions\"], (r)=>r[1])[0][0],\n 'prop(ω)' : _.sortBy (d[\"Rate Distributions\"], (r)=>r[1])[0][1]\n };\n});","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 (\"phylotree\")\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":3435,"value":"branch_length_attr = _.map (_.filter (_.toPairs (dabsrel_json[\"branch attributes\"][\"attributes\"]), (d)=>d[1][\"attribute type\"] == \"branch length\"), d=>d[0])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3403,"value":"exportNewick = {\n tree_object.branch_length_accessor = (n)=>dabsrel_json[\"branch attributes\"][0][n.data.name] ? dabsrel_json[\"branch attributes\"][0][n.data.name][branch_length_selector] : 0 ;\n return tree_object.getNewick((n)=>dabsrel_json.tested[0][n.data.name] == \"test\" ? \"{TEST}\" : \"\");\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3356,"value":"params = new URLSearchParams(location.search)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1905,"value":"tree_object = new phylotree.phylotree(dabsrel_json[\"input\"][\"trees\"][0])","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":"$undefined"},{"id":3506,"value":"import {localFileInput} from \"@mbostock/localfile\"","pinned":false,"hidden":false,"mode":"ojs","author":"$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":"$undefined"},{"id":174,"value":"import {select,checkbox, autoSelect, text} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3306,"value":"import {legend} from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$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":"$undefined"},{"id":3079,"value":"entropy = (array)=> {\n const nonGap = _.filter (_.toPairs (array), (d)=>d[0] != '-');\n let N = d3.sum (nonGap, (d)=>d[1]);\n const log2 = Math.log (2);\n return -d3.sum (_.map (nonGap, (d)=>d[1]/N * Math.log (d[1]/N) / log2));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1598,"value":"name_fragment = (n)=>{ \n let pieces = n.split ('_');\n if (pieces.length > 3) {\n return pieces[1]+\"/\"+pieces[2];\n }\n return pieces[1];\n};","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3416,"value":"import { Plot as Plot_ } from \"@fil/plot-splom\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3475,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3472,"value":"Plot = addRegression(Plot_)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3469,"value":"reg = require(\"d3-regression@1\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W31","stdlib":"1","titling":"auto"}} 2e:"$2d:body"