30:T56f,viewof detection_plot = Plot.plot({ style: {"fontSize" : 14, "fontSize-swatches" : 14, "fontFamily" : "Helvetica"}, marginBottom: 40, marginTop: 30, marginLeft : 60, width : 600, height: 600, y: { grid: true, tickFormat: "f", domain: [1e-3,100], label: "Relative rate on labeled branches", "type" : "log", "exponent" : 1., ticks :5, }, x: { grid: true, tickFormat: "f", domain: [1e-3,100], label: "Relative rate on background branches", "type" : "log", "exponent" : 1., ticks: 5 }, color: { legend: true, "type" : "linear", range: crameri_bilbao, interpolate: (start, end) => (t) => d3.interpolateHsl(start, end)(t), label: "-log10 (q-value)", }, marks: [ Plot.ruleY([0]), Plot.ruleX([0]), Plot.line([{'x' : 0.001, 'y': 0.001},{'x' : 100, 'y': 100}], {x: "x", y: "y", "stroke" : "#CCC"}), //Plot.rect([{'x1' : 0.9, 'y1': 0.9, 'x2' : 1, 'y2': 1.}], {'x1' : 'x1', 'y1': 'y1', 'x2' : 'x2', 'y2': 'y2', opacity : 0.2}), Plot.dot(_.filter (gene_data, (d)=>d.FDR <= maxq ), {x: "bg", y: "fg", fill: (d)=>-Math.log10 (Math.max (1e-16, d["FDR"]), 10), r : (d)=>Math.min (100, d.ratio > 1 ? d.ratio :(d.ratio > 0 ? 1/d.ratio : 1000)), opacity : 0.3, stroke : null}), Plot.dot(_.filter (gene_data, (d)=>d.FDR <= maxq ), Plot.pointer({x: "bg", y: "fg", fill: "red"})), ] })31:[] 2e:{"title":"Molerate small background","cells":[{"id":0,"value":"# Molerate small background","pinned":false,"hidden":false,"mode":"md"},{"id":880,"value":"viewof bg_size = Inputs.radio([8, 12, 20], {value: 20, label: \"Background size\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":752,"value":"viewof phenotype = Inputs.select (_.keys (urls), {label : \"Show this phenotype\", value : \"Hairless\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":298,"value":"viewof maxq = Inputs.range([0, 1], {label: \"FDR q-value\", value : 0.1})","pinned":false,"hidden":false,"mode":"ojs"},{"id":317,"value":"** Figure 1** Relative amino-acid rates (using a genome-average tree as a reference) for foreground (endothermy) and background (all else) branches in the tree for individual genes. Points above the diagonal are accelerated on FG relative to BG. The color of each dot shows the FDR-corrected q-value (as -log₁₀ (q)) for the rates being different between FG and BG. The size of the bubble is proportional to `max [FG/BG, BG/FG]`. Mouse-over and click on individual data circles (genes), to see more details and open up detailed result pages.","pinned":false,"hidden":false,"mode":"md"},{"id":344,"value":"detection_plot ? md`Gene ${detection_plot.gene}. Relative rates : FG ${detection_plot.fg.toFixed (2)}, BG ${detection_plot.bg.toFixed (2)}. q-value ${detection_plot.FDR}. Detailed results` : md`Select a bubble to view more details`","pinned":false,"hidden":false,"mode":"ojs"},{"id":27,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":443,"value":"viewof gene_data = Inputs.search (sim_data, {'label' : 'Filter genes'})","pinned":false,"hidden":false,"mode":"ojs"},{"id":323,"value":"Table 1. Detailed gene by gene results","pinned":false,"hidden":false,"mode":"md"},{"id":325,"value":"viewof results = Inputs.table (gene_data, {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":437,"value":"Table 2. Top accelerated genes","pinned":false,"hidden":false,"mode":"md"},{"id":431,"value":"viewof results_accelerated = Inputs.table (_.filter (sim_data, table2_selector), {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n sort: \"ratio\", \n reverse: true,\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":460,"value":"Table 3. Top decelerated genes","pinned":false,"hidden":false,"mode":"md"},{"id":456,"value":"viewof results_decelerated = Inputs.table (_.filter (sim_data, table3_selector [scenario]), {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n sort: \"ratio\", \n reverse: false,\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":629,"value":"Plot.plot({\n style: {\"fontSize\" : 14, \"fontSize-swatches\" : 14, \"fontFamily\" : \"Helvetica\"},\n marginBottom: 40,\n marginTop: 30,\n marginLeft : 60,\n width : 600,\n height: 600,\n y: {\n grid: true,\n tickFormat: \"f\",\n label: \"Relative rate on labeled branches\",\n ticks :5,\n },\n x: {\n grid: true,\n tickFormat: \"f\",\n //domain: [1e-3,100],\n label: \"Relative rate on background branches\",\n \"type\" : \"log\",\n \"exponent\" : 1.,\n ticks: 5\n },\n color: {\n legend: true,\n \"type\" : \"linear\",\n range: crameri_bilbao, \n interpolate: (start, end) => (t) => d3.interpolateHsl(start, end)(t),\n label: \"-log10 (q-value)\",\n },\n marks: [\n Plot.dot(_.filter (gene_data, (d)=>d.FDR <= 0.01 & d.tested >= 4), {x: \"ratio\", y: \"informative\", fill: (d)=>-Math.log10 (Math.max (1e-16, d[\"FDR\"]), 10), r : (d)=>Math.min (100, d.ratio > 1 ? d.ratio :(d.ratio > 0 ? 1/d.ratio : 1000)), opacity : 0.5, stroke : null}),\n ]\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":668,"value":"N = d3.max (sim_data, d=>d.tested)","pinned":false,"hidden":false,"mode":"ojs"},{"id":821,"value":"scenario = 1","pinned":false,"hidden":false,"mode":"ojs"},{"id":659,"value":"tested = _.filter (sim_data, d=>d.tested >= 2).length","pinned":false,"hidden":false,"mode":"ojs"},{"id":664,"value":"passing_fdr = _.filter (sim_data, d=>d.tested >= 2 && d.FDR <= 0.01).length","pinned":false,"hidden":false,"mode":"ojs"},{"id":672,"value":"accelerated = d3.filter (sim_data, table2_selector).length","pinned":false,"hidden":false,"mode":"ojs"},{"id":679,"value":"decelerated = d3.filter (sim_data, table3_selector).length","pinned":false,"hidden":false,"mode":"ojs"},{"id":684,"value":"outliers = d3.filter (sim_data, d=>d.tested >= 2 && d.FDR <= 0.01 && d.informative == 0 && d.outliers == 1).length","pinned":false,"hidden":false,"mode":"ojs"},{"id":397,"value":"urls = ({'Subterranean' : \"https://data.hyphy.org/web/busted-ph/molerate/subter_\" + bg_size + \"bg.csv\",\n 'Hairless' : 'https://data.hyphy.org/web/busted-ph/molerate/hairless_' + bg_size + 'bg.csv'\n })","pinned":false,"hidden":false,"mode":"ojs"},{"id":542,"value":"table2_selector = (d)=>d.FDR <= 0.01 && d.ratio >= 2.0 &&d.tested >= N/2 && d.informative >= N/2 && d.outliers == 0","pinned":false,"hidden":false,"mode":"ojs"},{"id":547,"value":"table3_selector = (d)=>d.FDR <= 0.01 && d.ratio <= .5 && d.tested >= N/2 && d.informative >= N/2 && d.outliers == 0\n ","pinned":false,"hidden":false,"mode":"ojs"},{"id":410,"value":"suffix = ({'Scenario 1' : \".RER.json.gz\",\n 'Scenario 2' : \".RER.json.gz\",\n 'Scenario 3' : \".RER.json.gz\",\n 'Scenario 4' : \".RER.json.gz/\",\n 'Scenario 5' : \".RER.json.gz\"\n })","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"sim_data = {\n let pvalue_data = summary_data; \n const pvalue_column = 'p';\n let rd = _.sortBy (_.map (_.filter (pvalue_data, (d)=>_.isNumber (_.get (d, pvalue_column))), (d)=>d), (d)=>d[pvalue_column]);\n _.each (rd, (d,i)=> {\n d[\"FDR\"] = d[pvalue_column]*rd.length/(i+1);\n });\n return rd;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":777,"value":"summary_data = await d3.csv(urls[phenotype], autoType);","pinned":false,"hidden":false,"mode":"ojs"},{"id":843,"value":"function autoType(row) {\n const parsed = {};\n for (const [key, value] of Object.entries(row)) {\n if (value === \"\") parsed[key] = null;\n else if (!isNaN(value)) parsed[key] = +value;\n else if (value === \"true\" || value === \"false\") parsed[key] = value === \"true\";\n else parsed[key] = value;\n }\n return parsed;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":623,"value":"crameri_bilbao = crameri [0].schemes[4].scheme[12]","pinned":false,"hidden":false,"mode":"ojs"},{"id":615,"value":"import {schemes_by_tag as crameri} from \"@nitaku/fabio-crameris-color-schemes\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":754,"value":"params = new URLSearchParams(location.search)","pinned":false,"hidden":false,"mode":"ojs"},{"id":766,"value":"pako = require('pako@2.1.0/dist/pako.min.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":757,"value":"import {localFileInput} from \"@mbostock/localfile\"","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W31","stdlib":"1","titling":"auto"}