28:null 29:["$","title",null,{"children":"Molerate summary view | ACME Computational Molecular Evolution Group | Observable"}] 2e: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"})), ] })2f:T471,urls = ({'Sugar Consuming 4' : "https://dl.dropbox.com/scl/fi/8jigqy22wtiv46xyi89ov/sackton-birds-results.csv?rlkey=jimgpyhioym0jx2qcp79k3iwx", 'UCSC subterranean' : 'https://dl.dropbox.com/scl/fi/nnk0n4s5zwgjubpnp3p6m/subter.csv?rlkey=kop7zgfrk8tbuox43n7p4fgml', 'Zoonomia subterranean' : 'https://data.hyphy.org/web/RER/results-molerate-subter-zoonomia.csv', 'Zoonomia marine' : 'https://data.hyphy.org/web/RER/results-molerate-marine.csv', 'UCSC hairless' : 'https://dl.dropbox.com/scl/fi/qhklsn1ddkl9h41qv2ef4/hairless.csv?rlkey=cpamrulzsd6m4vatrgp09qs0x', 'UCSC marine' : 'https://dl.dropbox.com/scl/fi/e8jowpzu976i98hy3zocc/marine.csv?rlkey=rbh0unxijnlehuq7g3hp2spd9', 'UCSC random' : 'https://dl.dropbox.com/scl/fi/i94f1p8kjl1aowm63o71i/random.csv?rlkey=sqw1ltjbmvlbq3b2rqkici6rm', 'UCSC marine-all' :'https://dl.dropbox.com/scl/fi/mjmjzrg1f4246t0bvkato/results-marine-all.csv?rlkey=7b543ym5ro09aanhfs3j99ttd', 'UCSC subterranean / nucleotide' : 'https://dl.dropbox.com/scl/fi/pio5b7zhy3ohcjo4fbgww/subter-nuc.csv?rlkey=0fx7g38vdvqpzjl2v2qzb4oxl' })30:[] 2c:{"id":"61e40a0d939fa19a","slug":"molerate-summary","title":"Molerate summary view","thumbnail":"932f4e71b5c5c9578e19177028e8c71654495d5b261d76c61ff0c59025a07080","access_level":"public","create_time":"$D2025-03-31T22:42:16.074Z","update_time":"$D2025-04-01T18:07:50.247Z","view_time":null,"first_public_time":"$D2025-03-31T22:42:40.878Z","has_unpublished_edits":null,"fork":true,"stars":0,"starred":false,"owner":{"type":"team","id":"7ada8a89538f700a","login":"hyphy","name":"ACME Computational Molecular Evolution Group","avatar_url":"https://avatars-next.observableusercontent.com/c49d98d47337d40736a6fb1a598558be99c1e5fbeea48e7cac329854f99ccb98","tier":"education_2026"},"version":819,"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"},{"type":"team","id":"7ada8a89538f700a","login":"hyphy","name":"ACME Computational Molecular Evolution Group","avatar_url":"https://avatars-next.observableusercontent.com/c49d98d47337d40736a6fb1a598558be99c1e5fbeea48e7cac329854f99ccb98","tier":"education_2026","role":"viewer"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"Molerate summary view","cells":[{"id":0,"value":"# Molerate summary view","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":763,"value":"load_prompt = md`Load a MoleRate CSV summary file `","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":752,"value":"viewof results_file = params.get (\"url\") ? localFileInput({accept: [\".csv\",\".gz\"], value : params.get (\"url\"), disable: true}) : localFileInput({accept: [\".csv\",\".gz\"]}) ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":298,"value":"viewof maxq = Inputs.range([0, 1], {label: \"FDR q-value\", value : 0.1})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":317,"value":"** Figure 1** Relative amino-acid rates (using a genome-average tree as a reference) for foreground (endothermy) and background (all else) branches in the tree for individual genes. Points above the diagonal are accelerated on FG relative to BG. The color of each dot shows the FDR-corrected q-value (as -log₁₀ (q)) for the rates being different between FG and BG. The size of the bubble is proportional to `max [FG/BG, BG/FG]`. Mouse-over and click on individual data circles (genes), to see more details and open up detailed result pages.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"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 ${detection_plot.FDR}. Detailed results` : md`Select a bubble to view more details`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":27,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":443,"value":"viewof gene_data = Inputs.search (sim_data, {'label' : 'Filter genes'})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":323,"value":"Table 1. Detailed gene by gene results","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":325,"value":"viewof results = Inputs.table (gene_data, {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":437,"value":"Table 2. Top accelerated genes","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":431,"value":"viewof results_accelerated = Inputs.table (_.filter (sim_data, table2_selector), {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n sort: \"ratio\", \n reverse: true,\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":460,"value":"Table 3. Top decelerated genes","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":456,"value":"viewof results_decelerated = Inputs.table (_.filter (sim_data, table3_selector [scenario]), {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n sort: \"ratio\", \n reverse: false,\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":629,"value":"Plot.plot({\n style: {\"fontSize\" : 14, \"fontSize-swatches\" : 14, \"fontFamily\" : \"Helvetica\"},\n marginBottom: 40,\n marginTop: 30,\n marginLeft : 60,\n width : 600,\n height: 600,\n y: {\n grid: true,\n tickFormat: \"f\",\n label: \"Relative rate on labeled branches\",\n ticks :5,\n },\n x: {\n grid: true,\n tickFormat: \"f\",\n //domain: [1e-3,100],\n label: \"Relative rate on background branches\",\n \"type\" : \"log\",\n \"exponent\" : 1.,\n ticks: 5\n },\n color: {\n legend: true,\n \"type\" : \"linear\",\n range: crameri_bilbao, \n interpolate: (start, end) => (t) => d3.interpolateHsl(start, end)(t),\n label: \"-log10 (q-value)\",\n },\n marks: [\n Plot.dot(_.filter (gene_data, (d)=>d.FDR <= 0.01 & d.tested >= 4), {x: \"ratio\", y: \"informative\", fill: (d)=>-Math.log10 (Math.max (1e-16, d[\"FDR\"]), 10), r : (d)=>Math.min (100, d.ratio > 1 ? d.ratio :(d.ratio > 0 ? 1/d.ratio : 1000)), opacity : 0.5, stroke : null}),\n ]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":668,"value":"N = d3.max (sim_data, d=>d.tested)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":659,"value":"tested = _.filter (sim_data, d=>d.tested >= 2).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":664,"value":"passing_fdr = _.filter (sim_data, d=>d.tested >= 2 && d.FDR <= 0.01).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":672,"value":"accelerated = d3.filter (sim_data, table2_selector).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":679,"value":"decelerated = d3.filter (sim_data, table3_selector).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":684,"value":"outliers = d3.filter (sim_data, d=>d.tested >= 2 && d.FDR <= 0.01 && d.informative == 0 && d.outliers == 1).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":397,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":542,"value":"table2_selector = (d)=>d.FDR <= 0.01 && d.ratio >= 2.0 &&d.tested >= N/2 && d.informative >= N/2 && d.outliers == 0","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":547,"value":"table3_selector = (d)=>d.FDR <= 0.01 && d.ratio <= .5 && d.tested >= N/2 && d.informative >= N/2 && d.outliers == 0\n ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":410,"value":"suffix = ({'Scenario 1' : \".RER.json.gz\",\n 'Scenario 2' : \".RER.json.gz\",\n 'Scenario 3' : \".RER.json.gz\",\n 'Scenario 4' : \".RER.json.gz/\",\n 'Scenario 5' : \".RER.json.gz\"\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"sim_data = {\n let pvalue_data = summary_data; 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