31:T820,function multiAutoSelect(config = {}) { const { value, title, description, disabled, autocomplete = "off", placeholder, size, options, list = "variants" } = Array.isArray(config) ? { options: config } : config; const optionsSet = new Set(options); const form = input({ type: "text", title, description, attributes: { disabled }, action: fm => { const addSelectedOption = d => { const ele = html`${d} `; ele.querySelector("button").addEventListener("click", b => { fm.value.splice(fm.value.indexOf(d), 1); renderSelection(); fm.dispatchEvent(new CustomEvent("input")); fm.input.focus(); }); return ele; }; function renderSelection() { fm.output.innerHTML = ""; for (let o of fm.value) { fm.output.appendChild(addSelectedOption(o)); } } fm.input.value = ""; fm.value = value || []; fm.onsubmit = e => e.preventDefault(); fm.input.oninput = function(e) { e.stopPropagation(); if ( optionsSet.has(fm.input.value) && fm.value.indexOf(fm.input.value) === -1 ) { fm.value.push(fm.input.value); renderSelection(); fm.dispatchEvent(new CustomEvent("input")); fm.input.value = ""; } }; renderSelection(); }, form: html` ` }); form.output.style["margin-left"] = "0px"; return form; }32:Tc29,html` `33:[] 2f:{"title":"MULTI-HIT analysis result visualization","cells":[{"id":0,"value":"md`# MULTI-HIT analysis result visualization`","pinned":false,"hidden":false,"mode":"ojs"},{"id":660,"value":"md`Load a MULTIHIT JSON result file `","pinned":false,"hidden":false,"mode":"ojs"},{"id":89,"value":"viewof results_file = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":592,"value":"html`\n\n\n\n\n

\n \n

\n ${results_json.input[\"number of sequences\"]}\n sequences in the alignment\n

\n \n

\n ${results_json.input[\"number of sites\"]}\n sites in the alignment\n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":538,"value":"fig1label=md`**Figure 1**. Evidence Ratios.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":434,"value":"fig1=vegalite ({\n width: 400,\n height: 200,\n \"data\": {\"values\": evidence_ratios},\n \"mark\": {type: \"rule\", tooltip : true},\n \"encoding\": {\n \"facet\": {\n \"field\": \"model\",\n \"type\": \"ordinal\",\n \"columns\": 2\n },\n \"x\": {\"field\": \"site\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, title : \"site\"}},\n \"y\": {\"field\": \"er\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, title : \"Evidence Ratio\"}},\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":577,"value":"fig2_label=md`**Figure 2**. Site Log-Likelihood`","pinned":false,"hidden":false,"mode":"ojs"},{"id":486,"value":"fig2=vegalite ({\n width: 400,\n height: 200,\n \"data\": {\"values\": site_log_likelihood},\n \"mark\": {type: \"point\", tooltip : true},\n \"encoding\": {\n \"facet\": {\n \"field\": \"model\",\n \"type\": \"ordinal\",\n \"columns\": 2\n },\n \"x\": {\"field\": \"site\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, title : \"site\"}},\n \"y\": {\"field\": \"site_log_likelihood\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, title : \"Site Log-Likelihood\"}},\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":689,"value":"fig3_label=md`**Figure 3**. Model Fitting Benchmarks`","pinned":false,"hidden":false,"mode":"ojs"},{"id":728,"value":"fig3=vegalite ({\n width: 800,\n height: 200,\n \"data\": {\"values\": timers},\n \"mark\": {type: \"bar\", tooltip : true, point : false},\n \"encoding\": {\n \"y\": {\"field\": \"model\", \"type\": \"ordinal\", \"axis\" : {\"grid\" : false, title : \"Model\"}, \"sort\": \"-x\"},\n \"x\": {\"field\": \"time\", \"type\": \"quantitative\", \"axis\" : {\"grid\" : false, title : \"Time (seconds)\"}, \"scale\" : {\"type\" :\"sqrt\"}},\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"md`---`","pinned":false,"hidden":false,"mode":"ojs"},{"id":476,"value":"stages = _.size (results_json.improvements)","pinned":false,"hidden":false,"mode":"ojs"},{"id":638,"value":"floatFormat = d3.format (\"2g\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":99,"value":"results_json = await (JSON.parse (await (Files.text(results_file))))","pinned":false,"hidden":false,"mode":"ojs"},{"id":933,"value":"evidence_ratios = _.chain(results_json[\"Evidence Ratios\"]).map((d, k) => [_.map(d[0], (x, i) => { return { model: k, site : i, er:x }})]).flatten().flatten().value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":957,"value":"site_log_likelihood = _.chain(results_json[\"Site Log Likelihood\"]).map((d, k) => [_.map(d[0], (x, i) => { return { model: k, site : i, site_log_likelihood:x }})]).flatten().flatten().value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":970,"value":"timers = _.chain(results_json[\"timers\"]).map((d, k) => { return { model: k, time : d.timer}}).value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":9,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":416,"value":"floatFmt = d3.format (\".2g\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":841,"value":"seqNames = (tree)=> {\n let seq_names = [];\n tree.traverse_and_compute (n=>{\n if (n.children && n.children.length) return;\n seq_names.push (n.data.name);\n });\n return seq_names;\n};","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"_=require(\"lodash\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":711,"value":"totalTreeLength = (tree)=> {\n let L = 0;\n tree.traverse_and_compute ( (n)=> {\n if (tree.branch_length (n)) {\n L += +tree.branch_length (n);\n }\n });\n return L;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":350,"value":"import {legend} from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":78,"value":"phylotree=require (\"https://dl.dropboxusercontent.com/s/i528j2lqnyzknit/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":127,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":432,"value":"vegalite = require (\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":174,"value":"import {select, text, input, autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":833,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":587,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":598,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W33","stdlib":"1","titling":"auto"}