28:null 29:["$","title",null,{"children":"Visualizing selection analysis results for evolution of human CoV | Sergei Pond | Observable"}] 2e:T1d8f,genome_view = vegalite({ "$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" : "Mean dN/dS SARS-CoV-2", "orient" : "bottom"}, "type" : "quantitative", "scale": {"scheme": "lightmulti", "type" : "sqrt", "domain" : [0,3], "clamp" : true}}, } }, { "data" : {"values" : fragments}, "mark" : {"type" : "text", "align" : "left", "fontSize" : 9, "dx" : 2}, "transform": [ { "calculate": "(datum['7'] % 2 == 0) ? -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", tooltip : true, }, "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", tooltip : true, }, "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", tooltip : true, }, "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"}}, })2f:T449,md`Site **${site2view}** is in segment *${site2segment[site2view]}* and is codon ${site2alignment[site2view]} in the overall alignment.
FEL p-value ${float_format (annotation_json[site2view].bFEL.p)}, ω = ${report_ratio (annotation_json[site2view].bFEL.a, annotation_json[site2view].bFEL.b)}
MEME p-value ${float_format (annotation_json[site2view].bMEME.p)}, ω + = ${report_ratio (annotation_json[site2view].bMEME["a"], annotation_json[site2view].bMEME["b+"])}, p = ${float_format (annotation_json[site2view].bMEME["w+"])}, **${annotation_json[site2view].bMEME.br}** selected branches
Contrast-FEL report: ${cfel_site_report(site2view)}
**Amino-acid composition**

OC43: ${freq_report (annotation_json [site2view].aa["OC43"])}
HKU1: ${freq_report (annotation_json [site2view].aa["HKU1"])}
SARS: ${freq_report (annotation_json [site2view].aa["SARS"])}
SARS-CoV-2: ${freq_report (annotation_json [site2view].aa["SARS-CoV-2"])}

**Substitutions** ${subs_site_report(rendered_tree.subs)} `30:T593,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) }, ] });31:T11c1,rendered_tree = { let tree = tree_object[0]; var t = tree.render("#tree_container_0", { //height:1024, width:800, 'show-scale' : true, 'left-right-spacing': 'fit-to-size', //'top-bottom-spacing': 'fit-to-size', //'internal-names' : true, 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { return 3; } return 1; }; let siteID = summary_json[site2segment [site2view]? site2segment [site2view] : segment_id].subs[site2view]; let nodeStates = null; if (siteID) { nodeStates = {}; let node_labels = siteID; function recurse_node (node) { if (node.data.name in node_labels) { nodeStates[node.data.name] = node_labels[node.data.name]; } else { nodeStates[node.data.name] = nodeStates[node.parent.data.name]; } _.each (node.children, (c)=>recurse_node(c)); } recurse_node(tree.nodes); if (doAA) { for (let node in nodeStates) { nodeStates[node] = nodeStates[node] in translation_table ? translation_table[nodeStates[node]] : '?'; } } } let c10 = d3.scaleOrdinal(d3.schemeDark2); //var c10 = d3.scaleOrdinal(d3.schemeDark2); //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"] = nodeStates ? true : false; t.font_size = 8; t.spacing_x (7); t.phylotree.branch_length_accessor = n=> { //console.log (summary_json[segment_id]); let bl = tree_object[1][n.data.name][2]; if (bl > 0.25) { n.data.censored_bl = true; return 0.25; } else { n.data.censored_bl = false; } return bl; } t.node_label ((n)=>{ if (nodeStates) { return nodeStates[n.data.name];// + " (" + n.data.name + ")"; } return n.data.name; //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"];}); } 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) && !n.tagged_view && n.parent && n.parent.tagged_view) { //n.notshown = true; //} }); t.style_nodes ((e,n) => { if (n.data.name in tree_object[1]) { let binfo = tree_object[1][n.data.name]; 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 substitution_counts = {}; t.style_edges ((e,d) => { //console.log (site); if (nodeStates) { if (nodeStates[d.target.data.name] != nodeStates[d.source.data.name]) { let from = nodeStates[d.target.data.name] < nodeStates[d.source.data.name] ? nodeStates[d.target.data.name] : nodeStates[d.source.data.name]; let to = nodeStates[d.target.data.name] > nodeStates[d.source.data.name] ? nodeStates[d.target.data.name] : nodeStates[d.source.data.name]; if (!(from in substitution_counts)){ substitution_counts[from] = {}; } substitution_counts[from][to] = 1 + (substitution_counts[from][to] || 0); e.style ('stroke-width',5); } } else { if (d.target.data.name in tree_object[1]) { let binfo = tree_object[1][d.target.data.name]; if (binfo[0].length) { e.style ('stroke-color', species_colors (binfo[0].length)); } } //e.selectAll("title").text ("p = " + p); } if (d.target.data.censored_bl) { e.style ('stroke-dasharray',10); } }); t.subs = substitution_counts; t.placenodes(); t.update(); return t; }32:T5ac,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 == 0) { return value; } else { let tag = k.split ("_"); if (tag.length > 3) { tag = tag[1]+"/"+tag[2]; } else { tag = tag[1].split (".")[0]; } my_range.push ([k, last_check, accumulator + 2, d["busted"]["p"], 0, tag, d["rates"]["mean-omega"]["SARS-CoV-2"] ]); 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; }33:T576,plotPie = (data)=>vegalite ({ "data": { "values": data }, "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:[] 2c:{"id":"9700f64f8bf5f171","slug":"beta-cov-analysis","title":"Visualizing selection analysis results for evolution of human CoV","thumbnail":"90c2febb3c9205632717a45acabee96e8c36c458e98b5e8eb0ec21562d1ba056","access_level":"public","create_time":"$D2020-11-17T15:22:49.365Z","update_time":"$D2022-04-07T17:52:51.000Z","view_time":null,"first_public_time":"$D2020-11-23T17:27:07.138Z","has_unpublished_edits":null,"fork":{"id":"4f04bdd107c6841c","slug":"visualizing-selection-analysis-results-for-cov-evolution","title":"Visualizing selection analysis results for CoV evolution in bats","owner":{"id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond"}},"stars":0,"starred":false,"owner":{"type":"team","id":"9bf992815a7b66f2","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":"starter_2024"},"version":2518,"publish_version":2518,"role":null,"authored":false,"authors":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null}],"members":[{"type":"individual","id":"f439ea11e6786e12","login":"spond","name":"Sergei Pond","avatar_url":"https://avatars-next.observableusercontent.com/23c8c466a3ef27f1444c95a9ed8e52bcf08888403b6d4efbd039319b0761c13d","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":4,"collection":null,"type":"notebook","body":{"title":"Visualizing selection analysis results for evolution of human CoV","cells":[{"id":0,"value":"md`# Visualizing selection analysis results for evolution of human CoV\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2156,"value":"md`**Overview of selection regimes on the human CoV genomes.**

\nSee https://www.biorxiv.org/content/10.1101/2021.05.24.445313v1 for details.\n\nFrom top to bottom\n\n- Sites found to be under positive selection by MEME on internal branches (colored by the % of branches under selection). \n- Sites found to be under negative selection by FEL on internal branches. \n- SARS-CoV-2 partial genome; ticks in th middle of the bars show sites that are conserved on the amino-acid level by all 4 species. \n- Non-recombinant fragments inferred by GARD; colors: mean dN/dS on the SARS-CoV-2 clade on the fragment; black outline -- segment is under positive selection in SARS-CoV-2 sequences.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":627,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2167,"value":"md`Mean dN/dS and total branch length for each of the CoV species along GARD non-recombinant fragments`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1807,"value":"segment_profile = vegalite({\n\t\"$schema\": \"https://vega.github.io/schema/vega-lite/v5.json\",\n\t\"config\": {\n\t\t\"view\": {\n\t\t\t\"stroke\": null\n\t\t},\n\t},\n \"data\" : {\"values\" : selection_profile},\n \"mark\" : {\"type\" : \"line\", \"clip\": true, \"tooltip\": {\"content\": \"data\"}},\n \"width\" : 300,\n \"height\" : 50,\n \"encoding\": {\n \"facet\": {\n \"field\": \"s\",\n \"type\": \"ordinal\",\n \"columns\": 2,\n \"title\" : \"Species\",\n }, \n \"x\" : {\"field\" : \"x\", \"type\": \"quantitative\", \"axis\": {\"title\" : \"Coordinate\"}}, \n \"y\" : {\"field\" : \"omega\", \"type\": \"quantitative\", \"scale\": {\"domain\" : [0,2], \"clip\": true}, \"axis\": {\"title\" : \"Mean dN/dS\"}}, \n //\"color\" : {\"field\" : \"s\", \"legend\" : {\"title\" : \"Species\"}}\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1826,"value":"segment_profile_T = vegalite({\n\t\"$schema\": \"https://vega.github.io/schema/vega-lite/v5.json\",\n\t\"config\": {\n\t\t\"view\": {\n\t\t\t\"stroke\": null\n\t\t},\n\t},\n \"data\" : {\"values\" : selection_profile},\n \"mark\" : {\"type\" : \"line\", \"clip\": true},\n \"width\" : 300,\n \"height\" : 50,\n \"encoding\": {\n \"facet\": {\n \"field\": \"s\",\n \"type\": \"ordinal\",\n \"columns\": 2,\n \"title\" : \"Species\"\n }, \n \"x\" : {\"field\" : \"x\", \"type\": \"quantitative\", \"axis\": {\"title\" : \"Coordinate\"}}, \n \"y\" : {\"field\" : \"T\", \"type\": \"quantitative\", \"scale\": {\"domain\" : [0,2], \"clip\": true}, \"axis\": {\"title\" : \"Tree length\"}}, \n //\"color\" : {\"field\" : \"s\", \"legend\" : {\"title\" : \"Species\"}}\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2140,"value":"md`Individual sites where Contrast-FEL identified significant differences in selective pressures between pairs of viral species, or overall (mouse over to view)`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2098,"value":"cfel_profile = vegalite({\n\t\"$schema\": \"https://vega.github.io/schema/vega-lite/v5.json\",\n\t\"config\": {\n\t\t\"view\": {\n\t\t\t\"stroke\": null\n\t\t},\n\t},\n \"data\" : {\"values\" : cfel_sites},\n \"mark\" : {\"type\" : \"tick\", \"size\" : 10, \"thickness\" : 2, \"tooltip\": {\"content\": \"data\"}},\n \"width\" : 700,\n \"height\" : 150,\n \"encoding\": { \n \"x\" : {\"field\" : \"site\", \"type\": \"quantitative\", \"axis\": {\"title\" : \"Coordinate\", \"grid\" : false}}, \n \"y\" : {\"field\" : \"type\", \"type\": \"nominal\", \"axis\": {\"title\" : \"\"}}, \n \"color\" : {\"field\" : \"p\", \"type\": \"quantitative\", \"legend\" : {\"title\" : \"p-value\"}, \"scale\": {\"type\" : \"linear\", \"domain\" : [0.05,0]}}\n }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2233,"value":"md`### Segment information`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":966,"value":"viewof segment_id = {\n const dd3 = select({\n title: \"View this segment\",\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","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2137,"value":"md`ω distribution inferred for SARS-CoV-2 (independent of others) on this segment by BUSTED`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2134,"value":"plotPie (_.filter (busted_distributions, (d)=>d.file == segment_id))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2280,"value":"md`ω distributions inferred for individual species on this segment by RELAX. The RELAX p-value is **${float_format(summary_json[segment_id][\"relax\"][\"p\"])}** and the relaxation/intensification parameters (relative to OC43; >1 : intensified, < 1: relaxed) were ${_.map (summary_json[segment_id][\"relax\"][\"K\"], (d,k)=>\"**\" + k + \"**: \" + float_format(d)).join (\", \")}.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2224,"value":"html`

\n\n \n \n \n \n \n\n \n \n\n \n \n\n\n\n\n\n \n

OC43	HKU1
${await plotPie (_.filter (relax_distributions, (d)=>d.file == segment_id && d.species == \"OC43\"))}	${await plotPie (_.filter (relax_distributions, (d)=>d.file == segment_id && d.species == \"HKU1\"))}
SARS	SARS-CoV-2
${await plotPie (_.filter (relax_distributions, (d)=>d.file == segment_id && d.species == \"SARS\"))}	${await plotPie (_.filter (relax_distributions, (d)=>d.file == segment_id && d.species == \"SARS-CoV-2\"))}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2236,"value":"md`### Site-level information`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1972,"value":"\nviewof site2view = autoSelect({\n options: _.flatten ([\"Overall for \" + segment_id,_.map (site2segment, (s,k)=>k)]),\n title: `View this site (in SARS-CoV-2 reference coordinates)`,\n placeholder: \"Select a site (or overall)\"\n})\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2067,"value":"viewof doAA = checkbox({\n options: [{ value: \"toggle\", label: \"Amino-acids\" }]\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2301,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1941,"value":"trendLegend = swatches({\n color: species_colors,\n title: \"Viral species\",\n //tickFormat: \"%\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"html`\n \n

\n`\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":870,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2239,"value":"md`### Summary tables`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1693,"value":"md`**Table 1** List of ${selected_sites.length} sites found to be under selection by MEME along internal branches, as well as biochemical properties that are _important_ at this site (via the PRIME method)`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1028,"value":"table (selected_sites,\n {\n limit: 5000,\n enableCSVDownload: true,\n sort: true,\n enableFilter: false,\n columns: [\n {\n key: 'coordinate',\n name: 'Coordinate (SARS-CoV-2)'\n },\n {\n key: 'gene',\n name: 'Gene/ORF'\n \n },\n {\n key: 'site',\n name: 'Codon (in alignment)'\n },\n {\n key : 'meme_weight',\n name : '% of branches with ω>1',\n render : (val)=>d3.format (\".3p\") (val)\n },\n {\n key : 'p',\n name : 'p-value',\n render : (val)=>d3.format (\".3g\") (val)\n },\n {\n key : 'prime',\n name : 'Properties',\n render : (val)=>_.map (val, (d)=>{if (d[2]) return d[0] + (d[2]>0 ? \" (constrained) \" : \" (changing)\"); else return 'overall';}).join (\", \")\n }\n ]\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2244,"value":"md`**Table 2** List of ${negative_sites.length} sites found to be under negative selection by FEL along internal branches`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2249,"value":"table (negative_sites,\n {\n limit: 5000,\n enableCSVDownload: true,\n sort: true,\n enableFilter: false,\n columns: [\n {\n key: '0',\n name: 'Coordinate (SARS-CoV-2)'\n },\n {\n key: '3',\n name: 'Codon (in alignment)'\n },\n {\n key : '1',\n name : 'dN/dS',\n render : (val)=>d3.format (\".3g\") (val)\n },\n {\n key : '2',\n name : 'p',\n render : (val)=>d3.format (\".3g\") (val)\n }\n ]\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2173,"value":"md`**Table 3** BUSTED selection results on the SARS-CoV-2 clade across segments`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1663,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"md`---`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"d3 = require (\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"phylotree=require (\"https://dl.dropboxusercontent.com/s/i528j2lqnyzknit/phylotree.js\")\n//require (\"phylotree/build/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"_=require(\"lodash\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":78,"value":"//resolve(\"phylotree@0.1/phylotree.css\")\n//require (\"https://dl.dropbox.com/s/mjhii51tjy1o5gt/phylotree.js\")\nhtml`\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1905,"value":"tree_object = [new phylotree.phylotree(summary_json[site2segment [site2view]? site2segment [site2view] : segment_id][\"tree\"]), summary_json[site2segment [site2view]? site2segment [site2view] : segment_id][\"tree_tags\"]]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2481,"value":"rendered_tree.subs","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":127,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":874,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":174,"value":"import {select,checkbox, autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":488,"value":"vegalite = require(\"vega-embed\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1793,"value":"selection_profile = {\n let summary = [];\n _.each (fragments, (d,i)=> {\n _.each ([\"HKU1\",\"OC43\",\"SARS\",\"SARS-CoV-2\"], (s)=> {\n let T = summary_json[d[0]].rates[\"T\"][s];\n if (T > 0) {\n summary.push ({'segment' : i+1, 'x': d[1], 'omega' : summary_json[d[0]].rates[\"mean-omega\"][s], 'T' : T, 's': s});\n summary.push ({'segment' : i+1, 'x': d[2], 'omega' : summary_json[d[0]].rates[\"mean-omega\"][s], 'T' : T, 's': s});\n\n } else {\n summary.push ({'segment' : i+1, 'x': d[1], 'T' : T, 's': s});\n summary.push ({'segment' : i+1, 'x': d[2], 'T' : T, 's': s});\n\n }\n })});\n return summary;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":684,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2288,"value":"float_format = d3.format (\".3g\");","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":681,"value":"summary_json = await d3.json (\"https://dl.dropboxusercontent.com/s/rwq7e3jow4pzu0h/summary.json\");","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2217,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1876,"value":"prime_annotation = _.map (summary_json[_.first (_.keys(summary_json))][\"prime-properties\"], (d)=>d.split (\" \")[2])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2321,"value":"report_ratio = (a,b)=> {\n if (a == 0 && b == 0) return 'N.D.';\n if (a == 0) return 'Infinite';\n return float_format (b/a);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1929,"value":"species = _.sortBy (_.filter (_.uniq (_.map (summary_json[_.first (_.keys(summary_json))][\"tree_tags\"], (d)=>d[0])), (d)=>d.length))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1937,"value":"species_colors = d3.scaleOrdinal(d3.schemeCategory10).domain (species);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1152,"value":"busted_distributions = _.flatten (_.map (summary_json, (d,k)=>{\n return _.map (d[\"rates\"][\"busted\"][\"Test\"], (dd)=>{\n return {\n file: k,\n omega: dd.omega,\n proportion: dd.proportion,\n p: d[\"busted\"][\"p\"]\n };\n });\n})); ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2230,"value":"relax_distributions = _.flatten (_.map (summary_json, (d,k)=>{\n return _.flatten (_.map (d[\"rates\"][\"relax\"], (dd2,kk)=>{\n \n return _.map (dd2, (dd)=>{return {\n file: k,\n species: kk,\n omega: dd.omega,\n proportion: dd.proportion,\n p: d[\"relax\"][\"p\"]\n }\n });\n }))})); ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1666,"value":"busted_distribution_summary = {\n let bds = _.sortBy (_.map (summary_json, (d,k)=>{\n let dd = d[\"rates\"][\"busted\"][\"Test\"];\n return {\n file: k,\n omega1: dd[0].omega,\n proportion1: dd[0].proportion,\n omega2: dd[1].omega,\n proportion2: dd[1].proportion,\n omega3: dd[2].omega,\n proportion3: dd[2].proportion,\n p: d[\"busted\"][\"p\"],\n };\n }), (d)=>d.p); \n return _.map (bds, (record, i)=> {\n record['q'] = record['p'] * bds.length / (i+1); \n return record;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":764,"value":"conserved_sites = _.filter (_.map (annotation_json, (v,k)=>[k,v]), (s)=>_.uniq (_.flatten (_.map (species, (sp)=>_.uniq (_.keys (s[1].aa[sp]))))).length == 1, (d)=>[+d[0]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2195,"value":"site2segment = {\n let r = {};\n _.each (summary_json, (d,s)=> {\n _.each (d.map, (c)=> {\n if (c >= 0) {\n r[c] = s; \n }\n });\n });\n \n return r;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2407,"value":"site2alignment = {\n let r = {};\n let offset = 1;\n let last_segment = \"\";\n let only_sites = _.sortBy (_.map (annotation_json, (d,k)=>[k,d.index]), (s)=>+s.k);\n _.each (only_sites, (d)=> {\n if (site2segment[d[0]] != last_segment) {\n if (last_segment.length) {\n offset += summary_json [last_segment].map.length;\n }\n last_segment = site2segment[d[0]];\n }\n r [d[0]] = offset + d[1];\n });\n \n return r;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":780,"value":"selected_sites = _.map (_.filter (_.map (annotation_json, (v,k)=>[k,v]), (s)=>s[1].bMEME.p<=0.05), (d)=>{return {'coordinate' : +d[0],'p' : d[1].bMEME.p,'meme_weight' : d[1].bMEME[\"w+\"],'gene': d[1].G, 'site' : site2alignment[d[0]], 'fel_p' : d[1].bFEL.p, 'fel_n' : d[1].bFEL.b < d[1].bFEL.a, 'prime' : _.map(_.filter (_.map (d[1].prime.p, (p,i)=>[i,p,i>0 ? d[1].prime['lambda'][i-1] : null]), (pr)=>pr[1]<0.05), (d)=>{if (d[0]>0) d[0] = prime_annotation [d[0]-1]; else d [0] = \"Overall\"; return d;})};})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":798,"value":"negative_sites = _.map (_.filter (_.map (annotation_json, (v,k)=>[k,v]), (s)=>_.size (s[1].cdn[\"SARS-CoV-2\"]) > 1 && s[1].bFEL.p<=0.05 && s[1].bFEL.a > s[1].bFEL.b), (d)=>[+d[0], d[1].bFEL.b / d[1].bFEL.a, d[1].bFEL.p, site2alignment[d[0]]])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2084,"value":"cfel_sites = {\n let result = [];\n _.each (_.chain (annotation_json).map ((d,k)=>[k,d]).filter ((d)=>d[1].bCFEL.pp > 0 && d[1].bCFEL.pp <= 0.05).value (), ((d)=> { _.each (d[1].bCFEL.p,(v,p)=>{\n if (v <= 0.05) {\n result.push ({'site' : d[0], 'type' : p, 'p' : v});\n }\n })}));\n return result;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2078,"value":"site_report = annotation_json [site2view]\n ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2339,"value":"freq_report = (freqs)=> {\n return _.map (_.sortBy (_.map (freqs, (f,a)=>[a,f]), (d)=>-d[1]), (d)=> d[0] + \"_{\" + d[1] + \"}\").join (\" \");\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2486,"value":"subs_site_report = (sub_data)=> {\n // collect unique values of targets\n if (_.size (sub_data) == 0) {\n return \"No substitutions at this site\";\n }\n \n let all_targets = new Set();\n\n _.each (sub_data, (t)=> {\n _.each (t, (ignore, tt)=> all_targets.add (tt));\n });\n all_targets = _.sortBy ([...all_targets]);\n\n let all_sources = _.sortBy (_.map (sub_data, (v,k)=>k));\n \n return \"\"+_.map (all_targets, (d)=>\"\").join (\"\") + \"\" + \n _.map (all_sources, (k)=> {\n return \"\";\n }).join (\"\") + \"

From/To	\" + (d.length == 3 ? d + \"(\" + translation_table [d] + \")\" : d) + \"
\" + (k.length == 3 ? k + \"(\" + translation_table [k] + \")\" : k) + \"	\" + _.map (all_targets, (t)=> sub_data[k][t] \|\| \"-\").join (\"	\") + \"

\";\n \n \n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2354,"value":"cfel_site_report = (d)=> {\n const site_data = annotation_json[d][\"bCFEL\"];\n return \"\" + _.map (species, (sp)=>\"\"). join (\"\") + \"

Species	ω	Substitutions
\" + sp + \"	\" + report_ratio (site_data.a, site_data.b[sp]) + \"	\" + site_data.s[sp] +\"

\" + \n \"\" +\n _.map (site_data.p, (p,k)=> {return \"\"}).join (\"\")\n +\"

Pair	p-value
\" + k + \"	\" + float_format(p) + \"

\";\n}\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":754,"value":"annotation_json = await d3.json (\"https://dl.dropboxusercontent.com/s/juyb58p52uc98bq/annotation.json\");","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"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","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"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","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1943,"value":"import { legend, swatches } from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2060,"value":"import {translation_table} from \"@spond/usual-vs-unusual-mutation-analyses\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W34","stdlib":"1","titling":"auto"}} 2d:"$2c:body"