31:T5fa,vegalite ({ "layer" : [{ "data": {"values": _.filter (raw_data, (d)=>d.kind == 3 && d.ER32 > 5)}, "transform" : [ {"filter" : "datum.L < 1"} ], "mark": "bar", height: 360, width: 400, "encoding": { "color" : {"value" : "gray"}, "opacity" : {"value" : 0.75}, "x": { "bin": {"step": 0.01}, "field": "L", "type": "quantitative", "axis":{ "title" : "Branch Length", grid : false, titleFontSize: 20, labelFontSize: 14, format : "r" } }, "y": { "aggregate": "count", "type": "quantitative", "scale": {"type": "sqrt"}, "axis":{ "title" : "Substitution Count", grid : false, titleFontSize: 20, labelFontSize: 14, format : "r" } } } }, { "data": {"values": _.filter (raw_data, (d)=>d.kind == 3 && d.ER32 < 1)}, "transform" : [ {"filter" : "datum.L < 1"} ], "mark": "bar", height: 360, width: 400, "encoding": { "color" : {"value" : "red"}, "opacity" : {"value" : 0.5}, "x": { "bin": {"step": 0.01}, "field": "L", "type": "quantitative", "axis":{ grid : false, titleFontSize: 20, labelFontSize: 14, format : "r" } }, "y": { "aggregate": "count", "type": "quantitative", } } }] } ) 32:T9ce,substitution_info = (data, cut)=>{ cut = cut || 500; let codons = {}; let links = {}; let count_by_codon = {}; let idx = {}; let c = 0; _.each (translation_table, (aa,i)=>{ idx[aa] = c/20.; c++; }); _.each (data, (d)=> { _.each ([d.from, d.to], (c)=> { if (! (c in codons)) { codons[c] = {len : 0, color: codon_colors (idx[translation_table[c]]), label: c, id: "codon-" + c, aa : translation_table[c]}; if (! (c in count_by_codon)) count_by_codon[c] = 0; } codons[c].len ++; }); let lower = d.from < d.to ? d.from : d.to, higher = d.from < d.to ? d.to : d.from; if (! (lower in links)) { links[lower] = {}; } if (! (higher in links[lower])) { links[lower][higher] = 0; } links[lower][higher]++; }); let filtered_links = []; _.each (links, (l1,c1)=> { if (codons[c1].len>=cut) { _.each (l1, (l2, c2)=> { if (codons[c2].len>=cut) { let link_info = { 'count' : l2, 'source': { 'id' : 'codon-' + c1, 'start': count_by_codon[c1], 'end': count_by_codon[c1] + l2, 'codon' : c1 }, 'target': { 'id' : 'codon-' + c2, 'start': count_by_codon[c2], 'end': count_by_codon[c2] + l2, 'codon' : c2 }, 'color' : codon_colors (translation_table[c1]) }; count_by_codon[c2]+=l2; count_by_codon[c1]+=l2; filtered_links.push (link_info); } }); } }); let ret = [_.map (_.filter (codons, (c)=>c.len >= cut)).sort ((a,b)=>a.aa < b.aa ? -1 : a.aa > b.aa ? 1 : 0, (c)=>c),filtered_links]; let text = []; _.each (ret[0], (c) => { text.push ({ block_id: c.id, value: translation_table [c.label], position: 0 }); }); ret.push (text); //return _.filter (codons, (c)=>c.len > 500); return ret; } 33:[] 2f:{"title":"Multihit paper empirical results for substitutions","cells":[{"id":0,"value":"md`# Multihit paper empirical results for substitutions`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2285,"value":"table(\n top10,\n {\n enableCSVDownload: true,\n columns: [\n { \n key: '1',\n name: 'From',\n render: val => (val + \" (\" + translation_table[val] + \")\")\n },\n { \n key: '2',\n name: 'To',\n render: val => (val + \" (\" + translation_table[val] + \")\")\n },\n { \n key: '0',\n name: 'Count'\n },\n { \n key: '3',\n name: 'Fraction',\n render: val => percentage (val)\n\n }\n ]\n }\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":2159,"value":"md`Figure 1. Triple hit changes with ER (3H+:2H)>5; minimum 500 events per codon`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2240,"value":"{\n var container = html`

`;\n yield container;\n var subs = new Circos({\n container: '#chart1',\n width: 700,\n height: 700,\n})\n let data = substitution_info (source_data,500);\n \n \n subs.layout(data[0], configuration);\n subs.chords ('flow',data[1], {color: 'grey', opacity: 0.25});\n subs.text('aa', data[2], {\n innerRadius: 230,\n outerRadius: 300,\n style: {\n 'font-size': 20,\n fill: 'black',\n opacity: 1\n },\n events: {}\n });\n\n subs.render();\n\n \n return container;\n \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2315,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":2365,"value":"samples = [_.map (_.filter (raw_data, (d)=>d.kind == 3 && d.ER32 > 5), (d)=>d.L),_.map (_.filter (raw_data, (d)=>d.kind == 3 && d.ER32 < 1), (d)=>d.L)]","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"md`------`","pinned":false,"hidden":false,"mode":"ojs"},{"id":19,"value":"sim_data = {\n let cutoff = 0.01;\n var data = raw_data;\n _.each (raw_data, (d)=>{\n d.call21 = d[\"2v1\"] <= cutoff;\n d.call32 = d[\"3v2\"] <= cutoff;\n d.call3v3si = d[\"3v3si\"] <= cutoff;\n d.call3siv2 = d[\"3siv2\"] <= cutoff; \n d.call3v1 = d[\"3v1\"] <= cutoff;\n d[\"3v2_LRT\"] = d[\"3v2LRT\"];\n });\n return data;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":287,"value":"raw_data = await d3.csv (\"https://dl.dropbox.com/s/o5gr7ry05f8i4gq/summary_subs.csv\", d3.autoType)","pinned":false,"hidden":false,"mode":"ojs"},{"id":2249,"value":"source_data = _.filter (raw_data, (d)=>d.kind == 3 && d.ER32 > 5)","pinned":false,"hidden":false,"mode":"ojs"},{"id":2254,"value":"top10 = {\n let flat_array = []\n _.each (substitution_info (source_data, 250)[1],(d)=> {\n flat_array.push ([d.count, d.source.codon, d.target.codon,d.count / source_data.length])\n });\n return flat_array.sort ((a,b)=>-a[0]+b[0]).slice (0,11);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1964,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":2038,"value":"substitution_info (_.filter (raw_data, (d)=>d.kind == 2 && d.ER21 > 10), 2000)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1987,"value":"key_gen = (from, to)=>{\n if (from <= to) {\n return from + \"(\" + translation_table[from] + \") : \" + to + \"(\" + translation_table[to] + \")\";\n } \n return to + \"(\" + translation_table[to] + \") : \" + from + \"(\" + translation_table[from] + \")\";\n\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":9,"value":"d3 = require(\"d3\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1984,"value":"translation_table = {\n var code = d3.csvParse (\"Codon,AA\\nTTT,F\\nTCT,S\\nTAT,Y\\nTGT,C\\nTTC,F\\nTCC,S\\nTAC,Y\\nTGC,C\\nTTA,L\\nTCA,S\\nTAA,*\\nTGA,*\\nTTG,L\\nTCG,S\\nTAG,*\\nTGG,W\\nCTT,L\\nCCT,P\\nCAT,H\\nCGT,R\\nCTC,L\\nCCC,P\\nCAC,H\\nCGC,R\\nCTA,L\\nCCA,P\\nCAA,Q\\nCGA,R\\nCTG,L\\nCCG,P\\nCAG,Q\\nCGG,R\\nATT,I\\nACT,T\\nAAT,N\\nAGT,S\\nATC,I\\nACC,T\\nAAC,N\\nAGC,S\\nATA,I\\nACA,T\\nAAA,K\\nAGA,R\\nATG,M\\nACG,T\\nAAG,K\\nAGG,R\\nGTT,V\\nGCT,A\\nGAT,D\\nGGT,G\\nGTC,V\\nGCC,A\\nGAC,D\\nGGC,G\\nGTA,V\\nGCA,A\\nGAA,E\\nGGA,G\\nGTG,V\\nGCG,A\\nGAG,E\\nGGG,G\\n\");\n var mapped_code = {};\n _.each (code, (v,k) => {mapped_code[v.Codon] = v.AA;});\n return mapped_code;\n}\n\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":2030,"value":"configuration = ({\n innerRadius: 250,\n outerRadius: 300,\n cornerRadius: 0,\n gap: 0.04, // in radian\n labels: {\n display: true,\n position: 'center',\n size: '14',\n color: 'black',\n radialOffset:60,\n },\n ticks: {\n display: false,\n },\n events: {}\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2048,"value":"codon_colors = d3.scaleSequential(d3.interpolateRainbow)","pinned":false,"hidden":false,"mode":"ojs"},{"id":2027,"value":"Circos = require('circos@2.1.0/dist/circos.es6.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":2080,"value":"_ = require (\"lodash\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":2246,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":2302,"value":"percentage = d3.format (\".2p\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":2319,"value":"vegalite = require(\"vega-embed@3\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":2336,"value":"_.map (source_data, (d)=>d.L)","pinned":true,"hidden":false,"mode":"ojs"},{"id":2359,"value":"genstats = require('https://bundle.run/genstats@0.0.1')","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W33","stdlib":"1","titling":"auto"}