31:T1d4d,genome_view = vegalite({ "$schema": "https://vega.github.io/schema/vega-lite/v5.json", "config": { "view": { "stroke": null }, }, "vconcat": [ { "layer": [ { "height": 125, "width": 750, "data" : {"values" : fragments}, "mark" : {"type" : "bar"}, "transform": [ { "calculate": "(datum['7'] % 2 == 0) ? -30 : -40", "as": "y" }, { "calculate": "(datum['7'] % 2 == 0) ? -40 : -50", "as": "y2" } ], "encoding" : { "x" : {"field" : "1", "type": "quantitative","axis": null}, "x2" : {"field" : "2", "type": "quantitative","axis": null}, "y" : {"field" : "y", "type": "quantitative","axis": null}, "y2" : {"field" : "y2", "type": "quantitative","axis": null}, "stroke" : { "condition": {"test": "datum['3'] <= 0.05", "value": "black"}, "value" : null }, "fill" : {"field" : "6", //"condition": {"test": "datum['3'] > 0.05", "value": "white"}, "legend" : {"title" : "dN/dS", "orient" : "bottom"}, "type" : "quantitative", "scale": {"scheme": "lightmulti", "type" : "sqrt", "domain" : [0,4]}}, } }, { "data" : {"values" : fragments}, "mark" : {"type" : "text", "align" : "left", "fontSize" : 9, "dx" : 2}, "transform": [ { "calculate": "(datum['7'] % 2 == 0 && datum['7'] != 6) ? -35 : -45", "as": "y" }, { "calculate": "(datum['1'])", "as": "x_m" }, ], "encoding" : { "x" : {"field" : "x_m", "type": "quantitative","axis": null}, "y" : {"field" : "y", "type": "quantitative","axis": null}, "angle" : {"value" : 0}, "text" : {"field" : "5", "align" : "right", "baseline" : "bottom", "legend" : null, "type" : "nominal", "condition": {"test": "datum['3'] > 0.05 && datum['4'] == 0 || datum ['7'] == 7", "value": ""}, } } }, //================================ { "data" : {"values" : conserved_sites}, "transform": [{ "calculate": "3", "as": "y" }, { "calculate": "6", "as": "y2" }], "mark": { type: "rule" }, "encoding": { "x": { "field": "0", "type": "quantitative", "axis": null, }, "y": { "field": "y", "type": "quantitative", "axis": null, }, "y2": { "field": "y2", "type": "quantitative", "axis": null, }, "size" : {"value" : 0.05}, "color" : {"value" : "black"} } }, { "data" : {"values" : negative_sites}, "transform": [{ "calculate": "30", "as": "y" }, { "calculate": "35", "as": "y2" }], "mark": { type: "rule" }, "encoding": { "x": { "field": "0", "type": "quantitative", "axis": null, }, "y": { "field": "y", "type": "quantitative", "axis": null, }, "y2": { "field": "y2", "type": "quantitative", "axis": null, }, "size" : {"value" : 0.01}, "color" : {"value" : "grey"}, "opacity" : {"value" : 0.5} } }, { "data" : {"values" : selected_sites}, "transform": [{ "calculate": "38", "as": "y" }, { "calculate": "43", "as": "y2" }], "mark": { type: "rule" }, "encoding": { "x": { "field": "coordinate", "type": "quantitative", "axis": null, }, "y": { "field": "y", "type": "quantitative", "axis": null, }, "y2": { "field": "y2", "type": "quantitative", "axis": null, }, "size" : {"value" : 1}, "color" : {"field" : "meme_weight", "type": "quantitative", "legend" : null, "scale": {"scheme": "lightgreyred"}} } }, { "data": { "values": gene_coordinates }, "transform": [{ "calculate": "(datum['3'] % 2) ? -1 : 1", "as": "coloring" }, { "calculate": "(datum['3'] % 2) ? -5 : 0", "as": "y" }, { "calculate": "(datum['3'] % 2) ? 10 : 15", "as": "y2" } ], "mark": { "type": "bar", "stroke": "#000", tooltip : false, }, "encoding": { "x": { "field": "0", "type": "quantitative", "axis": null }, "x2": { "field": "2" }, "y": { "field": "y", "type": "quantitative", "axis": null }, "y2": { "field": "y2" }, "fill": { "value" : null }, "opacity": { "value": "0.5" } } }, { "data": { "values": gene_coordinates }, "transform": [ { "calculate": "-10 + ((datum['3'] % 2) ? -5 : 0) + (datum['3'] == 4 ? 25 : 0) + (datum['3'] == 6 ? 25 : 0) + (datum['3'] == 8 ? 32 : 0) + (datum['3'] == 9 ? -7 : 0) ", "as": "y" }, { "calculate": "(datum['0'])+50 + (datum['3'] == '4' ? -50: 0) + (datum['3'] == '5' ? 200: 0) + (datum['3'] == '10' ? 300: 0)", "as": "x" }], "mark": { "type": "text", "fontSize": 9, "baseline": "bottom", "tooltip" : false, "align" : "left" }, "encoding": { "x": { "field": "x", "type": "quantitative", }, "y": { "field": "y", "type": "quantitative" }, "text": { "field": "1", "legend" : null, }, } } ] }, /*{ "layer": [ { "height": 20, "width": 750, "data" : {"values" : srv}, "mark" : {"type" : "rule"}, "encoding" : { "x" : {"field" : "0", "type": "quantitative","axis": null}, "y" : {"field" : "1", "type": "quantitative","axis": null}, "size" : {"value" : 0.05}, "color" : {"value" : "grey"} } } ] }*/ ], //"resolve": {"scale": {"y": "shared"}}, })32:T680,html`

${name_fragment(fragments_with_selection[0])}	${name_fragment(fragments_with_selection[1])}	${name_fragment(fragments_with_selection[2])}	${name_fragment(fragments_with_selection[3])}	${name_fragment(fragments_with_selection[4])}

${name_fragment(fragments_with_selection[5])}	${name_fragment(fragments_with_selection[6])}	${name_fragment(fragments_with_selection[7])}	${name_fragment(fragments_with_selection[8])}	${name_fragment(fragments_with_selection[9])}

${name_fragment(fragments_with_selection[10])}

` 33:T59b,vegalite ({ "data": { "values": _.filter (busted_distributions, (d)=>d.file == segment_id) }, "encoding": { "theta": {"field": "proportion", "type": "quantitative", "stack": true}, "color": {"field": "omega", "type": "quantitative", //"sort": "descending", "title" : "dN/dS", "scale": { "domain" : [0,4], "type" : "sqrt", "clamp" : true, //"domainMid": 1, "scheme": "lightmulti" } }}, "layer" : [ { "mark": {"type": "arc", "innerRadius": 40, "outerRadius" : 60, tooltip : true, padAngle : 0.0, strokeWidth : 1, strokeOpacity: 1}, "encoding" : { "stroke" : {value : "black"}, } }, { "mark": {"type": "text", "outerRadius" : 70, "fontSize" : 18}, "encoding": { "color" : {"value" : "black"}, "text": { "field": "omega", "type": "nominal", "format" : ".2f", "condition": {"test": "datum['omega'] <= 1.", "value": ""}, } } }, { "mark": {"type": "text", "outerRadius" : 20, "fontSize" : 18}, "encoding": { "color" : {"value" : "black"}, "text": { "field": "proportion", "type": "nominal", "format" : ".2p", "condition": {"test": "datum['omega'] <= 1.", "value": ""}, } } } ], "view": {"stroke": null} }) 34:T62a,table (busted_distribution_summary, { limit: 5000, enableCSVDownload: true, sort: true, enableFilter: false, columns: [ { key: 'file', name: 'Segment' }, { key: 'omega1', name: '⍵1', render : (val)=>d3.format (".3g") (val) }, { key: 'proportion1', name: 'p1', render : (val)=>d3.format (".3p") (val) }, { key: 'omega2', name: '⍵2', render : (val)=>d3.format (".3g") (val) }, { key: 'proportion2', name: 'p2', render : (val)=>d3.format (".3p") (val) }, { key: 'omega3', name: '⍵3', render : (val)=>d3.format (".3g") (val) }, { key: 'proportion3', name: 'p3', render : (val)=>d3.format (".3p") (val) }, { key : 'p', name : 'p-value', render : (val)=>val <= 0.05 ? '' + d3.format (".3g") (val) + '' : d3.format (".3g") (val) }, { key : 'q', name : 'q-value', render : (val)=>val <= 0.2 ? '' + d3.format (".3g") (val) + '' : d3.format (".3g") (val) }, { key : 'lambda', name : 'HMM switching parameter', render : (val)=>d3.format (".3g") (val) } ] });35:T122e,{ return _.map (trees, (td, i)=> { let tree = td[0]; var t = tree.render("#tree_container_" + i, { height:200, width:175, 'show-scale' : true, 'left-right-spacing': 'fit-to-size', 'top-bottom-spacing': 'fit-to-size', 'show-scale' : false, //'internal-names' : true, 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { return 1; } return 1; }; var c10 = d3.scaleOrdinal(d3.schemeCategory10); //t.node_label = n=>n.data.name.substr (0,3); t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = false; t.font_size = 14; t.phylotree.branch_length_accessor = n=> { //console.log (summary_json[segment_id]); let bl = td[1]["lengths"][n.data.name]; if (bl > 0.25) { n.data.censored_bl = true; return 0.25; } else { n.data.censored_bl = false; } return bl; } const name_regularized = (n)=> { if (n == "Wuhan") return "SARS-CoV-2"; if (n == "Pangolin") return "Pangolin CoV"; return n; }; t.node_label ((n)=>{ if (tree.is_leafnode (n)) { if (td[1]["tested"][n.data.name] == "test"){ return name_regularized(n.data.name.split ("_").slice (0,1).join ("")); } } return ""; }); 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"];}); } else { if (name_regularized(n.data.name.split ("_").slice (0,1).join ("")) == "SARS-CoV-2") { console.log ("WUHAN"); d = 10000; } /* if (n.data.name.indexOf ("RATG13") >= 0) { n.data.kind = "BAT"; } else { if (n.data.name.indexOf ("PANGOLIN") >= 0) { if (n.data.name.indexOf ("2017") >= 0) { n.data.kind = "PANGOLIN 2017"; } else { n.data.kind = "PANGOLIN 2019"; } } else { n.data.kind = "SC2"; } }*/ //console.log (n.data.kind); } n["count_depth"] = d; }); tree.resort_children (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); tree.traverse_and_compute ((n) => { //if (!tree.is_leafnode (n)) { if ("notshown" in n) { delete n["notshown"]; } n.notshown = true; //} }); tree.traverse_and_compute ((n) => { if (td[1]["tested"][n.data.name] == "test") { n.notshown = false; } if (n.parent) { n.parent.notshown = n.parent.notshown && n.notshown; } }); tree.traverse_and_compute ((n) => { //if (!tree.is_leafnode (n) && !n.tagged_view && n.parent && n.parent.tagged_view) { //n.notshown = true; //} }); t.style_nodes ((e,n) => { if (n.data.name in td[1]["branches"]) { e.selectAll ("text").style ("font-size","13px"); } }); t.style_edges ((e,d) => { //console.log (site); if (d.target.data.name in td[1]["branches"]) { let binfo = td[1]["branches"][d.target.data.name]; let p = binfo["absrel"]['p']; if (p != null) { p = Math.max (1e-8,p); /*if (p <= 0.05) { e.style ('stroke-width' , '3px') }*/ //e.style ('stroke-width', Math.sqrt (1 + binfo['meme'].length)); } else { p = 1; } if (td[1]["tested"][d.target.data.name] == "test") { e.style ('stroke', "#DDDDDD"); e.style ('stroke-width', 3); if (p <= 0.05) { e.style ('stroke', "darkred"); } else { e.style ('opacity', 0.5); } } else { e.style ('stroke', "#DDDDDD"); } if (d.target.data.censored_bl) { e.style ('stroke-dasharray',10); } e.selectAll("title").text ("p = " + p); } }); t.placenodes(); t.update(); return t; }); }36:T634,fragments = { let result = _.sortBy(_.flatten (_.map (summary_json, (d,k)=> { let ranges = _.filter (d.map, (i)=>i>=0); let my_range = []; ranges.push (1e100); let last_check = ranges[0]; _.reduce (ranges, (accumulator, value)=> { if (value - accumulator == 3) { return value; } else { let tag = k.split ("_"); if (tag.length > 3) { tag = tag[1]+"/"+tag[2]; } else { tag = tag[1]; } my_range.push ([k, last_check, accumulator + 2, d["BUSTED-HMM"].test["p-value"], _.filter (d.branches,(b)=>_.isNumber (b.absrel.p) && b.absrel.p <=0.05).length, tag, d["BUSTED-HMM"]["mean"]["Rate Distributions"]["non-synonymous/synonymous rate ratio for *test*"][0][0]]); last_check = value; return value; } }, ranges[0]-3); return my_range; } ), true), (d)=>d[1]); let index = {}; let count = 0; _.each (result, (d) => { d.push (count++); }); return result; }37:[] 2f:{"title":"Visualizing selection analysis results for CoV evolution in bats","cells":[{"id":0,"value":"md`# Visualizing selection analysis results for CoV evolution in bats\n\nLoad a \\`JSON\\` file with summary results, select a specific site, using the summary table as a guide, and view the tree with branches colored by empirical Bayes factor support for episodic selecion at specific branches.\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":627,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":966,"value":"viewof segment_id = {\n const dd3 = select({\n title: \"View this gene\",\n options: _.map (_.uniqBy (fragments,\"0\"), (g)=>g[0])\n \n });\n dd3.input.style.fontSize = \"30px\";\n dd3.input.style.marginTop = \"8px\";\n return dd3;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":1081,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":870,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1693,"value":"md`**Table 1** List of sites found to be under selection by MEME in the nCOV clade`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1028,"value":"table (selected_sites,\n {\n limit: 5000,\n enableCSVDownload: true,\n sort: true,\n enableFilter: false,\n columns: [\n {\n key: 'coordinate',\n name: 'Genomic coordinate'\n },\n {\n key: 'gene',\n name: 'Gene/ORF'\n \n },\n {\n key: 'site',\n name: 'Site'\n },\n {\n key : 'meme_weight',\n name : 'Fraction of sites with omega>1',\n render : (val)=>d3.format (\".3p\") (val)\n },\n {\n key : 'p',\n name : 'p-value',\n render : (val)=>d3.format (\".3g\") (val)\n }\n ]\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":1697,"value":"md`**Table 2** List of ⍵ distributions inferred for non-recombinant segments under BUSTED[S]-HMM`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1663,"value":"$34","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":30,"value":"trees = {\n var t = _.map (fragments_with_selection, (m)=>[new phylotree.phylotree(summary_json[m].tree),summary_json[m]]);\n return t;\n}","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":127,"value":"$35","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} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":488,"value":"vegalite = require(\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":684,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":681,"value":"summary_json = await d3.json (\"https://dl.dropbox.com/s/as3vwdggvpgpggf/summary-2.json\");","pinned":false,"hidden":false,"mode":"ojs"},{"id":1152,"value":"busted_distributions = _.flatten (_.map (summary_json, (d,k)=>{\n return _.map (d[\"BUSTED-HMM\"][\"fit\"][\"Rate Distributions\"][\"Test\"], (dd)=>{\n return {\n file: k,\n omega: dd.omega,\n proportion: dd.proportion,\n p: d[\"BUSTED-HMM\"][\"test\"][\"p-value\"]\n };\n });\n})); ","pinned":false,"hidden":false,"mode":"ojs"},{"id":1666,"value":"busted_distribution_summary = {\n let bds = _.sortBy (_.map (summary_json, (d,k)=>{\n let dd = d[\"BUSTED-HMM\"][\"fit\"][\"Rate Distributions\"][\"Test\"];\n return {\n file: name_fragment (k),\n omega1: dd[0].omega,\n proportion1: dd[0].proportion,\n omega2: dd[1].omega,\n proportion2: dd[1].proportion,\n omega3: dd[2].omega,\n proportion3: dd[2].proportion,\n p: d[\"BUSTED-HMM\"][\"test\"][\"p-value\"],\n lambda: d[\"BUSTED-HMM\"][\"fit\"][\"Rate Distributions\"][\"HMM rate switching parameter\"]\n };\n }), (d)=>d.p); \n return _.map (bds, (record, i)=> {\n record['q'] = record['p'] * bds.length / (i+1); \n return record;\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":764,"value":"conserved_sites = _.map (_.filter (_.map (annotation_json, (v,k)=>[k,v]), (s)=>_.size (s[1].baa.nCOV)==1), (d)=>[+d[0]])","pinned":false,"hidden":false,"mode":"ojs"},{"id":780,"value":"selected_sites = _.map (_.filter (_.map (annotation_json, (v,k)=>[k,v]), (s)=>s[1].bMEME.p<=0.05), (d)=>{return {'coordinate' : +d[0]+1,'p' : d[1].bMEME.p,'meme_weight' : d[1].bMEME[\"w+\"],'gene': d[1].G, 'site' : d[1].S};})","pinned":false,"hidden":false,"mode":"ojs"},{"id":798,"value":"negative_sites = _.map (_.filter (_.map (annotation_json, (v,k)=>[k,v]), (s)=>_.size (s[1].bcdn.nCOV) > 1 && s[1].bFEL.p<=0.05 && s[1].bFEL.a > s[1].bFEL.b), (d)=>[+d[0], d[1].bFEL.b / d[1].bFEL.a])","pinned":false,"hidden":false,"mode":"ojs"},{"id":823,"value":"srv = _.map (_.map (annotation_json, (v,k)=>[k,v]), (s)=>[+s[0],s[1].busted[\"max-hmm-rate\"]])","pinned":false,"hidden":false,"mode":"ojs"},{"id":754,"value":"annotation_json = await d3.json (\"https://dl.dropbox.com/s/875f9isn5s87cpo/descriptions.json\");","pinned":false,"hidden":false,"mode":"ojs"},{"id":629,"value":"gene_coordinates = _.map ([\n [266,'ORF1a',13483],\n [13471, 'ORF1b',21555],\n [21563,'S',25385],\n [25393,'ORF3a',26220],\n [26245,'E',26472],\n [26523,'M',27191],\n [27202,'ORF6',27387],\n [27394,'ORF7a',27759],\n [27756,'ORF7b',27887],\n [27894,'ORF8',28259],\n [28274,'N',29533],\n [29558,'ORF10',29674]\n], (d,i)=>{\n d.push (i);\n return d;\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1535,"value":"fragments_with_selection = _.map (_.sortBy (_.filter (_.map (summary_json, (d,k)=>[k,d]), (s)=>(s[1][\"BUSTED-HMM\"].test[\"p-value\"]<=.05 || _.filter (s[1].branches,(b)=>_.isNumber (b.absrel.p) && b.absrel.p <=0.05).length)), (s)=>s[1].map[0]), (s)=>s[0])","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":"$W37","stdlib":"1","titling":"auto"}