31:T112b,{ let dim = treeDim.length ? _.map (treeDim.split ("x"), (d)=>+d) : null; let tree = tree_object; var t = tree.render("#tree_container_0", dim ? { height:dim[0] || 1024, width:dim[1] || 600, 'show-scale' : true, 'is-radial' : false, 'left-right-spacing': 'fit-to-size', 'top-bottom-spacing': 'fit-to-size', 'node_circle_size' : (n)=>0 } : { //height:1024, width:800, 'show-scale' : true, 'left-right-spacing': 'fit-to-size', //'top-bottom-spacing': 'fit-to-size', 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { return 3; } return 1; }; let bl = _.fromPairs (_.map (_.toPairs (absrel_json ["branch attributes"][0]), (d)=>[d[0], d[1][branch_length_selector]])); let c10 = d3.scaleOrdinal(d3.schemeDark2); t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = false; const cbl = +censored_length; t.phylotree.branch_length_accessor = n=> { let bll = bl[n.data.name]; if (bll > cbl) { n.data.censored_bl = true; return cbl; } else { n.data.censored_bl = false; } return bll; } t.node_label ((n)=>{ if (n.children && n.children.length) return ""; return n.data.name; }); function sort_nodes (asc) { tree.traverse_and_compute (function (n) { var d = 1; if (n.children && n.children.length) { d += d3.max (n.children, function (d) { return d["count_depth"];}); } n["count_depth"] = d; }); tree.resort_children (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); t.style_nodes ((e,n) => { /*if (nodeStates) { e.style ('fill', c10 (nodeStates[n.data.name])); if (binfo[0].length) { e.selectAll ("circle").style ('fill', species_colors (binfo[0])); } } else { if (binfo[0].length) { e.style ('fill', species_colors (binfo[0])); } }*/ //} }); let cutoffp = 0.05; t.style_edges ((e,d) => { let ttext = d.target.data.name; if (absrel_json ["branch attributes"][0][d.target.data.name]["Corrected P-value"] <= cutoffp) { e.style ('stroke-width',5); } else { e.style ('stroke-width',null); } if (d.target.data.name in coloration) { e.style ('stroke', color_scale (coloration[d.target.data.name])); ttext += "\n" + branch_color_selector + " = " + coloration[d.target.data.name]; } else { e.style ('stroke', null); } /* if (subs) { sub_count = subs.length; ttext = "Subs at " + subs.join (", "); } if (d.target.data.name in treeTags) { if (treeTags[d.target.data.name][3].length) { ttext += "\nMEME selection at sites " + _.map (treeTags[d.target.data.name][3], (s)=>annotation_json [s].G + "/" + annotation_json [s].S).join (", "); } sub_count = treeTags[d.target.data.name][3].length; } if (nodeStates) { if (nodeStates[d.target.data.name] != nodeStates[d.source.data.name]) { e.style ('stroke-width',5); } else { e.style ('stroke-width',null); } if (d.target.data.name in treeTags) { if ( treeTags[d.target.data.name][3].indexOf (+site2view) >= 0) { e.style ('stroke','darkred'); } } } else { if (d.target.data.name in tree_object[1]) { let binfo = tree_object[1][d.target.data.name]; e.style ('stroke-width', 1 + sub_count); } //e.selectAll("title").text ("p = " + p); } */ if (d.target.data.censored_bl) { e.style ('stroke-dasharray',10); } if (ttext) { e.selectAll("title").text (ttext); } }); t.placenodes(); t.update(); return t; }32:[] 2f:{"title":"Displaying aBSREL results using branch \"censoring\"","cells":[{"id":0,"value":"md`# Displaying aBSREL results using branch \"censoring\"`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2704,"value":"md`\nLoad a Datamonkey.org aBSREL result and present the tree with branches that are too long clipped to a fixed length\n` ","pinned":false,"hidden":false,"mode":"ojs"},{"id":3134,"value":"viewof absrel_json_url = text({placeholder : \"Paste in datamonkey job id to load\", submit: \"Load\", description: \"Paste in the part of the job URL shown with XX: http://datamonkey.org/absrel/XX\", \"title\" : \"Datamonkey aBSREL job ID\", \"value\" : params.get(\"id\")})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2657,"value":"viewof treeDim = text({placeholder : \"1024 x 800\", description: \"Tree dimension (height x width in pixels), leave blank to auto-scale\", submit: \"Resize\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":3222,"value":"viewof branch_length_selector = select ({\n options: _.map (_.filter (_.toPairs(absrel_json[\"branch attributes\"][\"attributes\"]), (d)=>d[1][\"attribute type\"] == \"branch length\"), (d)=>d[0]),\n description: \"Branch lengths come from this model\",\n value: \"Full adaptive model\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":3283,"value":"viewof branch_color_selector = select ({\n options: _.map (_.filter (_.toPairs(absrel_json[\"branch attributes\"][\"attributes\"]), (d)=>d[1][\"attribute type\"] == \"branch label\"), (d)=>d[0]),\n description: \"Branch colors come from this attribute\",\n value: \"Corrected P-value\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":3270,"value":"viewof censored_length = text({value : 0.25, description: \"Maximum branch length to display\", submit: \"Update\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2855,"value":"md`Branches that have evidence of episodic selection (p≤0.05) are shown in thicker lines, and the colors are shown based on the coloring attribute above. Branches that have been censored because they are too long are shown as dashed lines. Mouse over branches to view more details about them`","pinned":false,"hidden":false,"mode":"ojs"},{"id":3305,"value":"legend({\n color: color_scale,\n title: branch_color_selector,\n tickFormat: \".2h\",\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"tree=html`\n \n

\n`\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":870,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":3027,"value":"md`\n

\n### Data and libraries \n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":3138,"value":"absrel_json = await d3.json (\"https://datamonkey.org/absrel/5fea72d670baba7af141c189/results\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":3321,"value":"color_scale = {\n const v = _.map (coloration);\n let d = d3.extent (v);\n let md = d3.median (v);\n if (d[1] > md*10.) {\n return d3.scaleDiverging([d[0], md, d[1]], d3.interpolateRdBu);\n }\n return d3.scaleSequential([d[0], d[1]], d3.interpolatePiYG);\n \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":3295,"value":"coloration = _.chain (_.toPairs (absrel_json[\"branch attributes\"][0]).map (d=>[d[0], d[1][branch_color_selector]])).fromPairs().value()","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"md`---`","pinned":false,"hidden":false,"mode":"ojs"},{"id":9,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":11,"value":"phylotree=require (\"https://dl.dropbox.com/s/i528j2lqnyzknit/phylotree.js\")\n//require (\"phylotree/build/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":13,"value":"_=require(\"lodash\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":78,"value":"//resolve(\"phylotree@0.1/phylotree.css\")\n//require (\"https://dl.dropbox.com/s/mjhii51tjy1o5gt/phylotree.js\")\nhtml`\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":3356,"value":"params = new URLSearchParams(location.search)","pinned":true,"hidden":false,"mode":"ojs"},{"id":1905,"value":"tree_object = new phylotree.phylotree(absrel_json[\"input\"][\"trees\"][0])","pinned":false,"hidden":false,"mode":"ojs"},{"id":127,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":874,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":174,"value":"import {select,checkbox, autoSelect, text} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":3306,"value":"import {legend} from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":2288,"value":"float_format = d3.format (\".3g\");","pinned":false,"hidden":false,"mode":"ojs"},{"id":3079,"value":"entropy = (array)=> {\n const nonGap = _.filter (_.toPairs (array), (d)=>d[0] != '-');\n let N = d3.sum (nonGap, (d)=>d[1]);\n const log2 = Math.log (2);\n return -d3.sum (_.map (nonGap, (d)=>d[1]/N * Math.log (d[1]/N) / log2));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1598,"value":"name_fragment = (n)=>{ \n let pieces = n.split ('_');\n if (pieces.length > 3) {\n return pieces[1]+\"/\"+pieces[2];\n }\n return pieces[1];\n};","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}