31:T44a,table(_.map (RELAX_summary, (data,key) => { var r = {"Alignment" : key, "Seqs": data["input"]["number of sequences"], "Sites" : data["input"]["number of sites"], "p-value" : d3v5.format (".2g")(data["test"]["p-value"])}; get_k (data, r); return r; }).sort ((a,b) => {return (+a["p-value"])-(+b["p-value"]);}), {limit: 1024,columns: [ 'Alignment', 'Seqs', 'Sites', { key: 'p-value', name: 'LRT p-value', render: val => {if (val < 0.05) return `${val}`; return `${val}`;} }, { key: 'K', name: `K_"K"`, render: val => {if (val > 1) return `${val}`; return `${val}`;} }, { key: 'NEF', name: `K_"NEF"`, render: val => {if (val > 1) return `${val}`; return `${val}`;} }, { key: 'H', name: `K_"H"`, render: val => {if (val > 1) return `${val}`; return `${val}`;} } ]})32:T587,rate_distribution = (plot_data, plot_title) => { var data_by_group = {}; _.each (plot_data, (rates) => { _.each (rates["relaxation or intensification parameter"], (value, key) => { if (key != "EF") { if (!(key in data_by_group)) { data_by_group [key] = []; } data_by_group[key].push (value); } }); }); data_by_group = _.map (data_by_group, (x,k) => {return { y : _.clone (x), boxpoints: 'suspectedoutliers', jitter: 0.3, pointpos: 0, type: 'box', boxmean : true, opacity : 0.5, notched : true, marker:{ color: 'rgb(50,50,50)', }, name: "Branch set " + k }}); console.log (data_by_group); var layout = { title: plot_title, font:{ family: 'Arial', size : 24 }, showlegend: false, xaxis: { tickangle: 0, type: "category", autorange : true, title: "Branch Group", titlefont: { size : 24 }, tickfont: { size : 18 } }, yaxis: { range: [0,5], gridwidth: 0, nticks : 5, tickmode : "auto", title: "Intensification/relaxation parameter", titlefont: { size : 24 }, tickfont: { size : 18 } }, width : 1000, height: 600 }; const div = DOM.element('div'); plotly.newPlot(div, data_by_group, layout); return div; }33:[] 2f:{"title":"Multiple group RELAX analysis","cells":[{"id":0,"value":"md`# Multiple group RELAX analysis\n\nThis page summarizes the analysis of **${number_of_trees}** alignments with branches partitioned into multiple groups (M=4 in this case). The standard RELAX analysis has been extended to estimate M-1 intensification / relaxation parameters _K_ for each of the groups, except for one (_EF_), which is held as the reference. A significant test result, with the p-value derived using the LRT with χ² distribution with M-1 degrees of freedom, implies that **some** of the _K_ values are different from each other, but does not determine **which** ones.\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":55,"value":"md`**Table 1** Analysis results sorted by p-value. Relaxation/Intensification parameters for each branch group relative to **EF** are shown.` ","pinned":false,"hidden":false,"mode":"ojs"},{"id":31,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":246,"value":"md`**Figure 2.** Distribution of inferred relaxation/intensifcation parameters by branch group (all relative to the **EF** group) and censored at K = 5 to improve readability`","pinned":false,"hidden":false,"mode":"ojs"},{"id":255,"value":"rate_distribution (_.map (RELAX_summary, v => {return v[\"test\"]}),\"\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":75,"value":"viewof fileview = DOM.select(_.map(RELAX_summary, (v,k) => {return k}))","pinned":false,"hidden":false,"mode":"ojs"},{"id":88,"value":"viewof height = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":90,"value":"viewof width = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":131,"value":"md`**Figure 3.** Tree for \\`${fileview}\\` colored by group and scaled by input branch lengths. NEF, H, K, EF`","pinned":false,"hidden":false,"mode":"ojs"},{"id":129,"value":"render_tree (tree(d3.layout.newick_parser(RELAX_summary[fileview][\"input\"][\"trees\"][\"0\"])), RELAX_summary[fileview][\"labels\"])","pinned":false,"hidden":false,"mode":"ojs"},{"id":59,"value":"md`#### Dependancies`","pinned":false,"hidden":false,"mode":"ojs"},{"id":19,"value":"_ = window._ = await require(\"lodash@4\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":23,"value":"d3v5 = require(\"https://d3js.org/d3.v5.min.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":21,"value":"RELAX_summary=await d3v5.json(\"https://dl.dropbox.com/s/zj0m6gimnyo3s6h/summary.json\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"number_of_trees = _.keys (RELAX_summary).length","pinned":false,"hidden":false,"mode":"ojs"},{"id":29,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":66,"value":"get_k = (d,o) => {\n _.each ([\"K\",\"H\",\"NEF\"], g => {\n if (g in d[\"test\"][\"relaxation or intensification parameter\"]) {\n o [g] = d3v5.format (\".4f\") (d[\"test\"][\"relaxation or intensification parameter\"][g]);\n } else {\n o [g] = \"None\";\n }\n \n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":86,"value":"d3 = {\n const d3 = window.d3 = await require(\"d3@3\");\n await require(\"phylotree@v0.2.0-alpha.1\").catch(() => {});\n return d3;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":97,"value":"html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":122,"value":"plotly=require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":210,"value":"tree = {\n return d3.layout.phylotree()\n .options({\n 'left-right-spacing': 'fit-to-size', // fit to given size top-to-bottom\n 'top-bottom-spacing': 'fit-to-size', // fit to given size left-to-right\n 'selectable': false, // make nodes and branches not selectable\n 'collapsible': false, // turn off the menu on internal nodes\n 'transitions' : false // turn off animations\n })\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":124,"value":"render_tree = (parsed_tree, labels) => {\n //var parsed_tree = tree(d3.layout.newick_parser(RELAX_summary[fileview][\"input\"][\"trees\"][\"0\"])).size([height, width]);\n const svg = d3.select(DOM.svg(width, height));\n parsed_tree\n .svg(svg)\n .size([height, width])\n .style_edges (function (element, data) {\n if (data.target.name in labels) {\n element.style (\"stroke\", group_colors(labels[data.target.name]));\n element.style (\"stroke-width\", \"5px\");\n } else {\n element.style (\"stroke\", null);\n element.style (\"stroke-width\", null);\n }\n })\n .layout();\n \n return svg.node();\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":138,"value":"group_colors = d3v5.scaleOrdinal(d3v5.schemeCategory10).domain (['NEF','K','H','EF'])","pinned":false,"hidden":false,"mode":"ojs"},{"id":251,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W33","stdlib":"1","titling":"auto"}