29:null 2a:["$","title",null,{"children":"Amino-acid rate acceleration/deceleration for Endothermy lineages: | Avery Selberg | Observable"}] 2f:T4d8,viewof detection_plot = Plot.plot({ style: {"fontSize" : 14, "fontSize-swatches" : 14, "fontFamily" : "Helvetica"}, marginBottom: 40, marginTop: 30, marginLeft : 50, width : 600, height: 600, y: { grid: true, tickFormat: "f", label: "Relative rate in foreground", "type" : "log", "exponent" : 1., ticks :5, }, x: { grid: true, tickFormat: "f", label: "Relative rate in background", "type" : "log", "exponent" : 1., ticks: 4 }, color: { legend: true, "type" : "linear", label: "-log10 (q-value)", scheme: 'rdpu', reverse: false }, marks: [ Plot.ruleY([0]), Plot.ruleX([0]), Plot.line([{'x' : 0.01, 'y': 0.01},{'x' : 10, 'y': 10}], {x: "x", y: "y", "stroke" : "Gray"}), //Plot.rect([{'x1' : 0.9, 'y1': 0.9, 'x2' : 1, 'y2': 1.}], {'x1' : 'x1', 'y1': 'y1', 'x2' : 'x2', 'y2': 'y2', opacity : 0.2}), Plot.dot(_.filter (sim_data, (d)=>d.FDR <= maxq), {x: "bg", y: "fg", fill: (d)=>-Math.log10 (Math.max (1e-16, d["FDR"]), 10), r : (d)=>d.ratio > 1 ? d.ratio : 1/d.ratio, opacity : .9, stroke : "black"}), Plot.dot(_.filter (sim_data, (d)=>d.FDR <= maxq), Plot.pointer({x: "bg", y: "fg", fill: "red"})), //Plot.frame() ] })30:[] 2d:{"id":"fc3586cd66a3036b","slug":"rer_hyphy_endothermy","title":"Amino-acid rate acceleration/deceleration for Endothermy lineages:","thumbnail":"0b9439a743ed42dc13b8655ae21cfa3c7a29e141286ee4a8fa5dafbc985c3115","access_level":"public","create_time":"$D2024-04-30T21:08:58.188Z","update_time":"$D2024-12-18T17:28:17.515Z","view_time":null,"first_public_time":"$D2024-04-30T21:49:44.055Z","has_unpublished_edits":null,"fork":true,"stars":0,"starred":false,"owner":{"type":"team","id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":"starter_2024"},"version":628,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null}],"members":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null,"role":"editor"},{"type":"team","id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":4,"collection":{"id":"2eb706d35ccd0bc3","slug":"endothermy","title":"Endothermy","owner":{"id":"c1465becab0bcdf5","login":"averyselberg","name":"Avery Selberg"}},"type":"notebook","body":{"title":"Amino-acid rate acceleration/deceleration for Endothermy lineages:","cells":[{"id":0,"value":"# Amino-acid rate acceleration/deceleration for Endothermy lineages: \n#### June 6th data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":402,"value":"viewof scenario = Inputs.select (_.sortBy (_.keys (urls)))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":298,"value":"viewof maxq = Inputs.range([0, 1], {label: \"FDR q-value\", step: 0.01, value : 0.05})","pinned":false,"hidden":false,"mode":"ojs","author":"$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":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$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 (sim_data, {\n format :{\n \"gene\" : (d)=>html`${d}`\n },\n columns: [\"gene\", \"fg\", \"bg\", \"ratio\", \"p\", \"FDR\", \"B\"],\n header : {\n \"gene\" : \"Gene\",\n \"fg\" : \"FG rel. rate\",\n \"bg\" : \"BG rel. rate\",\n \"ratio\" : \"FG/BG ratio\",\n \"p\" : \"p-value FG = BG\",\n \"FDR\" : \"q-value FG = BG\",\n \"B\" : \"# branches\"\n }\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":555,"value":"slow_genes = _.filter (sim_data, (d)=>d.FDR <= maxq && d.ratio < 1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":622,"value":"fast_genes = _.filter (sim_data, (d)=>d.FDR <= maxq && d.ratio > 1)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":542,"value":"acc_multiple_branch = _.filter(results, (d) => d.B > 1 && d.FDR <= maxq) ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":397,"value":"/*urls = ({'Scenario 1' : \"https://data.hyphy.org/web/fish/RER_res043024/scenario_1/\",\n 'Scenario 2' : \"https://data.hyphy.org/web/fish/RER_res043024/scenario_2/\",\n 'Scenario 3' : \"https://data.hyphy.org/web/fish/RER_res043024/scenario_3/\",\n 'Scenario 4' : \"https://data.hyphy.org/web/fish/RER_res043024/scenario_4/\" ,\n }) */\nurls = ({'Scenario 1' : \"https://data.hyphy.org/web/fish/RER_res060624/sc1/\",\n 'Scenario 2' : \"https://data.hyphy.org/web/fish/RER_res060624/sc2/\",\n 'Scenario 3' : \"https://data.hyphy.org/web/fish/RER_res060624/sc3/\",\n 'Scenario 4' : \"https://data.hyphy.org/web/fish/RER_res060624/sc4/\" ,\n })\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":410,"value":"suffix = ({'Scenario 1' : \".fasta.RER.json.gz\",\n 'Scenario 2' : \".fasta.RER.json.gz\",\n 'Scenario 3' : \".fasta.RER.json.gz\",\n 'Scenario 4' : \".fasta.RER.json.gz/\",\n 'Scenario 5' : \".fasta.RER.json.gz\"\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"sim_data = {\n let pvalue_data = await d3.csv (urls[scenario] + \"summary.csv\", d3.autoType); \n const pvalue_column = 'p';\n let rd = _.sortBy (_.map (_.filter (pvalue_data, (d)=>_.isNumber (_.get (d, pvalue_column))), (d)=>d), (d)=>d[pvalue_column]);\n _.each (rd, (d,i)=> {\n d[\"FDR\"] = d[pvalue_column]*rd.length/(i+1);\n try {\n let nulls = _.map (d.null.split (\",\"), e=>+e);\n let alts = _.map (d.alternative.split (\",\"), e=>+e);\n let BC = _.filter (nulls, (e,i)=> {\n return e <= 0.05 && alts[i] <= 0.05;\n });\n d[\"B\"] = BC.length;\n } catch {}\n //let alts = _.map (d.alternative.split (\",\"), e=>+e);\n });\n return rd;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":507,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W30","stdlib":"1","titling":"auto"}} 2e:"$2d:body"