2f:T4f2,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: color_scheme, reverse: reverse_colors }, 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 : color_opacity, stroke : "black"}), Plot.dot(_.filter (sim_data, (d)=>d.FDR <= maxq), Plot.pointer({x: "bg", y: "fg", fill: "red"})), //Plot.frame() ] })30:T52d,viewof color_scheme = Inputs.select(new Map([["Turbo", 'turbo'], ["Violet-yellow", 'viridis'], ["Black-pink-white", 'magma'],["Black-red-yellow", 'inferno'], ["Violet-pink-yellow'", 'plasma'], ["Navy-yellow", 'cividis'], ["Turbo", 'turbo'], ["Violet-yellow", 'viridis'], ["Black-pink-white", 'magma'],["Black-red-yellow", 'inferno'], ["Violet-pink-yellow", 'plasma'], ["Navy-yellow", 'cividis'], ["Cube_helix", 'cubehelix'], ["Warm_colors", 'warm'], ["Cool_colors", 'cool'], ["Blue-green", 'bugn'],["Blue-purple", 'bupu'], ["Green-blue'", 'gnbu'], ["Orange-red", 'orrd'], ["Purple-blue", 'pubu'], ["Purple-blue-green", 'pubugn'], ["Purple-red", 'purd'],["Red-purple", 'rdpu'], ["Yellow-green", 'ylgn'], ["Yellow-green-blue", 'ylgnbu'], ["Yellow-orange-brown", 'ylorbr'], ["Yellow-orange-red", 'ylorrd'], ["Brown-bluegreen", 'brbg'], ["purple-green", 'prgn'],["Pink-green", 'piyg'], ["Purple-orange", 'puor'], ["Red-blue", 'rdbu'], ["Red-gray", 'rdgy'], ["Red-yellow-blue", 'rdylbu'], ["Red-yellow-green", 'rdylgn'],["Spectral", 'spectral'], ["Blues", 'blues'], ["Greens", 'greens'], ["Greys", 'greys'], ["Oranges", 'oranges'], ["Purples", 'purples'], ["Reds", 'reds'],["Rainbow", 'rainbow'], ["Sinebow", 'sinebow'], ]), {value: 'rdpu', label: "Colors"}) //viewof color_scheme = Inputs.select (new Map(['red-purple', 'rdpu']))31:[] 2d:{"title":"RER-Hyphy Results","cells":[{"id":0,"value":"# RER-Hyphy Results","pinned":false,"hidden":false,"mode":"md"},{"id":402,"value":"viewof scenario = Inputs.select (_.sortBy (_.keys (urls)))","pinned":false,"hidden":false,"mode":"ojs"},{"id":670,"value":"viewof csvfile = Inputs.file({label: \"CSV file\", accept: \".csv\"})","pinned":false,"hidden":false,"mode":"ojs"},{"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"},{"id":317,"value":"** Figure 1** Relative amino-acid rates (using a genome-average tree as a reference) for foreground (pheonotype) 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":"$2f","pinned":false,"hidden":false,"mode":"ojs"},{"id":636,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":646,"value":"viewof reverse_colors = Inputs.toggle({label: \"Reverse colors?\", value: true})","pinned":false,"hidden":false,"mode":"ojs"},{"id":663,"value":"viewof color_opacity = Inputs.range([0, 1], {label: \"Color opacity\", step: 0.01, value : 0.7})","pinned":false,"hidden":false,"mode":"ojs"},{"id":763,"value":"viewof search_results = Inputs.search (sim_data)","pinned":false,"hidden":false,"mode":"ojs"},{"id":323,"value":"Table 1. Detailed gene by gene results","pinned":false,"hidden":false,"mode":"md"},{"id":325,"value":"viewof results = Inputs.table (only_search_results, {\n format :{\n \"gene\" : (d)=>html`${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"},{"id":761,"value":"viewof gene_id = Inputs.select(_.map(only_search_results, d=> d.gene), {label: \"Show this gene:\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":759,"value":"viewof ind_branch = Inputs.table (branch_pvals)","pinned":false,"hidden":false,"mode":"ojs"},{"id":555,"value":"slow_genes = _.filter (sim_data, (d)=>d.FDR <= maxq && d.ratio < 1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":622,"value":"fast_genes = _.filter (sim_data, (d)=>d.FDR <= maxq && d.ratio > 1)","pinned":false,"hidden":false,"mode":"ojs"},{"id":542,"value":"acc_multiple_branch = _.filter(results, (d) => d.B > 1 && d.FDR <= maxq) ","pinned":false,"hidden":false,"mode":"ojs"},{"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 = ({'PhylogramHyphy' : \"https://data.hyphy.org/web/rer/Aintzane/\",\n 'Upload file' : 'Upload file'\n })\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":410,"value":"suffix = ({'PhylogramHyphy' : \".fasta.json.gz\",\n //'Scenario 2' : \".fasta.RER.json.gz\",\n //'Scenario 3' : \".fasta.RER.json.gz\",\n })","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"sim_data = {\n const pvalue_column = 'Proportional:Proportional Partitioned p-val';\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"},{"id":672,"value":"import {localFileInput} from \"@mbostock/localfile\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":771,"value":"branch_pvals = {\n let chosen_gene = _.filter(pvalue_data, d=> d.gene === gene_id )[0]\n let branch_list = chosen_gene['branch'].split (\",\")\n let null_list = chosen_gene['null'].split (\",\")\n let alt_list = chosen_gene['alternative'].split(',')\n let to_return = []\n return _.map(branch_list, (branch, i) => ({\n Branch: branch,\n 'Single branch (null)': null_list[i],\n 'All but this branch (alternative)': alt_list[i],\n}));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":766,"value":"only_search_results = {\n var data = []\n for(var i = 0;i< search_results.length;i++){\n data.push(search_results[i])\n }\n return data\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":781,"value":"_.map(only_search_results, d=> d.gene)","pinned":true,"hidden":false,"mode":"ojs"},{"id":727,"value":"pvalue_data = scenario != 'Upload file' ? await d3.csv (urls[scenario] + \"combined_update.csv\", d3.autoType) : await csvfile.csv({typed: true});","pinned":false,"hidden":false,"mode":"ojs"},{"id":507,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W31","stdlib":"1","titling":"auto"}