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el_2013-12-30:0.0900704):0.37545,Oman_2874_2013_KT156561_human_2013-12-28:0.460041):0.131001,((Oman_2285_2013_KT156560_human_2013-10-28:0.270194,AbuDhabi_UAE_9_2013_KP209312_human_2013-11-15:0.319509):0,((((UAE_D1164.11_2014_KP719929_camel_2014-06:0.0552323,D1164.1_14_KX108937_camel_2014-06-02:0.0196159):0.0658481,UAE_D1164.9_2014_KP719927_camel_2014-06:0.12108):0,UAE_D1164.14_2014_KP719930_camel_2014-06:0.12108):0,UAE_D1164.10_2014_KP719928_camel_2014-06:0.12108):0.779251):0.153724):0.339468):0.222637,UAE-FRA1_1627-2013_BAL_KJ361500_human_2013-04-26:0.479174):0,Taif_2_2013_KJ156896_human_2013-06-12:0.607941):0.115397,Asir_2_2013_KJ156863_human_2013-08-05:0.871283):0,KSA-376_KJ713299_camel_2013-11:1.15074):0.0726869,Buraidah_1_2013_KF600630_human_2013-05-13:0.713833):0.239331):0.143753):0.287363,Riyadh_1_2012_KF600612_human_2012-10-23:0.83138):0.346806):2.26417,(Jordan-N3_2012_KC776174_human_2012-04-15:2.21434,EMC_2012_JX869059_human_2012-06-13:2.37554):0.706156):0.665307,(((Camel_Egypt_NRCE-HKU271__camel_2013-12-30:0.0166023,Camel_Egypt_NRCE-HKU270__camel_2013-12-30:0.0166023):3.8139,NRCE-HKU205_KJ477102_camel_2013-11-15:3.70721):0.0817865,Egypt_NRCE-NC163_2014_KU740200_camel_2014-12-17:4.87667):1.38115):0.138606);"32:T4ca,function computeRootToTipOtherRoot (tree, node, coming_from, shared_distance, distance_to_new_root) { var my_bl = tree.branch_length () (node); var go_up = false; if (!coming_from) { shared_distance = node.rtt; distance_to_new_root = 0; go_up = true; } if (node.children) { for (var c = 0; c < node.children.length; c++) { if (node.children[c] != coming_from) { computeRootToTipOtherRoot (tree, node.children[c], node, shared_distance, distance_to_new_root); } else { go_up = true; } } } node.rtta = node.rtt - shared_distance + distance_to_new_root; if (go_up) { shared_distance -= my_bl; distance_to_new_root += my_bl; } if (node.parent && go_up) { computeRootToTipOtherRoot (tree, node.parent, node, shared_distance, distance_to_new_root); } }33:T64f,function linear_fit (data) { var ss = data.reduce (function (p,c) {return c[2] + p}, 0), // sample count sx = data.reduce (function (p,c) {return c[2]*c[0] + p}, 0), // sum X sy = data.reduce (function (p,c) {return c[2]*c[1] + p}, 0), // sum Y sxoss = sx/ss, syoss = sy/ss; var fitB = 0, st2 = 0, vary = 0; data.forEach (function (point) { var t = point[0] - sxoss; st2 += point[2] * t * t; fitB += point[2] * t * point[1]; vary += point[2] * (point[1]-syoss)*(point[1]-syoss); }); fitB /= st2; var a = (sy - sx * fitB) / ss; var varres = 0; data.forEach (function (point) { var t = point[1] - a - fitB * point[0]; varres += point[2] * t * t; }); var normvarres = Math.sqrt (varres / (ss - 2)); return {'intercept' : a, 'slope' : fitB, 'r2': 1 - varres / vary, 'var (intercept)' : Math.sqrt ((1+sx*sx/(ss*st2))/ss), 'var (slope)' : Math.sqrt (1/st2) }; }34:T4a7,function rtt(tree) { var plot_data = []; var linear_data = []; computeRootToTip (tree,tree.get_nodes()[0]); var max_r2 = 0; var best_node = 0; // To return if best node is the root already tree.traverse_and_compute (function (node) { if (d3.layout.phylotree.is_leafnode (node)) { linear_data.push ([node.numeric_date, node.rtta, node.copy_number]); } }); var best_fit = linear_fit (linear_data); tree.traverse_and_compute (function (node) { if (d3.layout.phylotree.is_leafnode (node)) { //if (node.numeric_date == 0) { computeRootToTipOtherRoot (tree, node, null, 0, 0); linear_data = []; tree.traverse_and_compute (function (node) { if (d3.layout.phylotree.is_leafnode (node)) { linear_data.push ([node.numeric_date, node.rtta, node.copy_number]); } }); var fit = linear_fit (linear_data); var r2 = fit["r2"]; if (r2 > max_r2) { max_r2 = r2; best_node = node; best_fit = fit; } //} } }); return {"root": best_node, "fit": best_fit}; }35:T4ae,snpmats = { var snpa = mathjs.zeros(testal.number_of_sequences, testal.number_of_sites, 'sparse'); var snpc = mathjs.zeros(testal.number_of_sequences, testal.number_of_sites, 'sparse'); var snpg = mathjs.zeros(testal.number_of_sequences, testal.number_of_sites, 'sparse'); var snpt = mathjs.zeros(testal.number_of_sequences, testal.number_of_sites, 'sparse'); var snpn = mathjs.zeros(testal.number_of_sequences, testal.number_of_sites, 'sparse'); var i,j,b; for(i=0;i 1 && isLeapYear(d)) doy++;\n return(doy);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":133,"value":"function decimalDate(d) {\n var year = d.getFullYear();\n var doy = dayOfYear(d);\n var ndays = 365;\n if(isLeapYear(d)){\n ndays = 366;\n }\n return(year+doy/ndays);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":284,"value":"md`Annotate the nodes by copy number`","pinned":false,"hidden":false,"mode":"ojs"},{"id":286,"value":"annotateCopyNumber = {\n tree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n node.copy_number = 1;\n }\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":667,"value":"md`## Tree display`","pinned":false,"hidden":false,"mode":"ojs"},{"id":42,"value":"treedisplay = {\n const width = 800;\n const height = 600;\n const nodeSize = 1;\n const selectable = true;\n const collapsible = true;\n const transitions = true;\n const radial = false;\n const svg = d3.select(DOM.svg(width, height));\n \n tree.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': selectable, // nodes and branches not selectable?\n 'collapsible': collapsible, // menu on internal nodes?\n 'transitions' : transitions // animations?\n })\n .svg(svg)\n .size([height, width])\n .node_circle_size(nodeSize);\n \n tree.layout();\n \n if(radial){\n \ttree.radial(radial).placenodes().update();\n }\n return svg.node();\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":669,"value":"md`## Tree export`","pinned":false,"hidden":false,"mode":"ojs"},{"id":670,"value":"tree.json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":256,"value":"md`## Root to tip`","pinned":false,"hidden":false,"mode":"ojs"},{"id":62,"value":"{\n var linear_data = [];\n tree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n linear_data.push ([node.numeric_date, node.rtt, 1]);\n }\n });\n return linear_data;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"function computeRootToTip (tree,node) {\n if (node.parent!=null) {\n node.rtt = node.parent.rtt + tree.branch_length () (node);\n }\n else {\n node.rtt = 0;\n }\n \n if (node.children!=null) {\n for (var c = 0; c < node.children.length; c++) {\n computeRootToTip (tree,node.children[c]);\n }\n \n }\n }","pinned":false,"hidden":false,"mode":"ojs"},{"id":153,"value":"nodes = tree.get_nodes()","pinned":false,"hidden":false,"mode":"ojs"},{"id":148,"value":"nodes[0]","pinned":false,"hidden":false,"mode":"ojs"},{"id":52,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":57,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":54,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":146,"value":"rttfit = rtt(tree)","pinned":false,"hidden":false,"mode":"ojs"},{"id":291,"value":"rtree = cloneDeep(tree)","pinned":false,"hidden":false,"mode":"ojs"},{"id":309,"value":"rcomputeDates = {\n rtree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n var dt = node.name.split(\"_\").slice(-1)[0];\n if(dt.length==7){\n dt = dt+\"-15\";\n }\n if(dt.length==4){\n dt = dt+\"07-01\";\n }\n var m = new Date(dt);\n node.date = m;\n node.numeric_date = decimalDate(m);\n }\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":293,"value":"rtree.reroot(rttfit[\"root\"])","pinned":false,"hidden":false,"mode":"ojs"},{"id":203,"value":"md`Plot RTT`","pinned":false,"hidden":false,"mode":"ojs"},{"id":205,"value":"td = {\n var td = [];\n rtree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n td.push(node.date);\n }\n });\n return td; \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":302,"value":"tdd = {\n var tdd = [];\n rtree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n tdd.push(node.numeric_date);\n }\n });\n return tdd; \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":208,"value":"rd = {\n var rd = [];\n rtree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n rd.push(node.rtt);\n }\n });\n return rd; \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":217,"value":"tn = {\n var tn = [];\n rtree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n tn.push(node.name);\n }\n });\n return tn; \n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":225,"value":"ts = {\n var states = [];\n rtree.traverse_and_compute (function (node) {\n if (d3.layout.phylotree.is_leafnode (node)) {\n var nm = node.name;\n if(nm.indexOf(\"camel\")!=-1){\n states.push(\"camel\");\n }else{\n states.push(\"human\");\n }\n }\n });\n return states;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":333,"value":"pred = tdd.map(function(x) {return rttfit[\"fit\"][\"intercept\"]+rttfit[\"fit\"][\"slope\"]*x;})","pinned":false,"hidden":false,"mode":"ojs"},{"id":213,"value":"rttplot = {\n \n var colors = {\"human\": \"blue\", \"camel\": \"red\"};\n \n var trace = {\n type: \"scatter\",\n mode: \"markers\",\n x: td,\n y: rd,\n text: tn,\n marker: {\n size: 5,\n color: ts.map(x=>colors[x])\n },\n name: \"Observed\"\n }\n \n var ptrace = {\n type: \"scatter\",\n mode: \"line\",\n x: td,\n y: pred,\n marker: {\n size: 5,\n color: \"black\"\n },\n name: \"Fitted\"\n }\n \n var data = [trace, ptrace];\n \n var layout = {\n title: 'Root to tip',\n width: 800\n };\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":407,"value":"md`## Tip lengths`","pinned":false,"hidden":false,"mode":"ojs"},{"id":409,"value":"tiplengths = {\n var tl = [];\n tree.traverse_and_compute(function(node){\n if (d3.layout.phylotree.is_leafnode (node)) {\n tl.push(parseFloat(node.attribute));\n };\n }, \"post-order\");\n return tl;\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":422,"value":"md`## Pairwise distances between tips`","pinned":false,"hidden":false,"mode":"ojs"},{"id":426,"value":"rootdist = {\n var tn = [];\n tree.traverse_and_compute(function(node){\n if (d3.layout.phylotree.is_leafnode (node)) {\n tn.push(node.name);\n };\n }, \"post-order\");\n var ntips = tn.length;\n var d = [];\n for(var i=0;i{return binom(x,2)})","pinned":false,"hidden":false,"mode":"ojs"},{"id":390,"value":"function ne(a,t,r) {\n var result = [];\n var tm = [];\n for (var i = 1; i < (a.length-1); i++){\n result.push(binom(a[i],2)*(t[i]*t[i-1])/r);\n tm.push(t[i]);\n };\n return {\"t\":tm,\"ne\":result};\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":392,"value":"effsize=ne(att.a,att.t,1.0)","pinned":false,"hidden":false,"mode":"ojs"},{"id":396,"value":"neplot = {\n \n var trace = {\n type: \"scatter\",\n mode: \"step\",\n x: effsize.t,\n y: effsize.ne,\n }\n \n var data = [trace];\n \n var layout = {\n title: 'Ne over time',\n width: 800,\n yaxis: {\n type: 'log',\n autorange: true\n }\n };\n \n const div = DOM.element('div');\n Plotly.newPlot(div, data, layout);\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":446,"value":"md`## Read FASTA and calculate SNP distance using sparse methods`","pinned":false,"hidden":false,"mode":"ojs"},{"id":628,"value":"mutable testfasta = \"\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":634,"value":"url = \"https://raw.githubusercontent.com/veg/alignment.js/master/dist/fasta/Flu.fasta\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":448,"value":"loadfasta = d3.text(url,(error,x)=>{mutable testfasta = x;})","pinned":false,"hidden":false,"mode":"ojs"},{"id":451,"value":"testal = aljs.fastaParser(testfasta)","pinned":false,"hidden":false,"mode":"ojs"},{"id":479,"value":"BASES=[\"A\",\"C\",\"G\",\"T\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":454,"value":"profile = {\n var i,j;\n var profile=[];\n for(i=0;i{return BASES[x];})","pinned":false,"hidden":false,"mode":"ojs"},{"id":482,"value":"md`Make separate sparse matrices for each state e.g. A,C,G,T`","pinned":false,"hidden":false,"mode":"ojs"},{"id":497,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":525,"value":"sharedsnps={\n var d = mathjs.multiply(snpmats[0],mathjs.transpose(snpmats[0]));\n var i;\n for(i=1;i<5;i++){\n d = mathjs.add(d,mathjs.multiply(snpmats[i],mathjs.transpose(snpmats[i])));\n }\n return d;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":582,"value":"function getcol(M,i){\n return mathjs.flatten(M.subset(mathjs.index(mathjs.range(0, M._size[0]),i)));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":575,"value":"function getrow(M,i){\n return mathjs.flatten(M.subset(mathjs.index(i, mathjs.range(0, M._size[1]))));\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":612,"value":"sum_snps = {\n var sum_snps=snpmats[0];\n var i;\n for(i=1;i<4;i++){\n sum_snps = mathjs.add(sum_snps,snpmats[i]);\n }\n return sum_snps;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":532,"value":"total_snps={\n var result = [];\n var i;\n for(i=0;i {});\n return d3;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":14,"value":"phylocss = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":289,"value":"cloneDeep = require('https://bundle.run/lodash.clonedeep@4.5.0')","pinned":false,"hidden":false,"mode":"ojs"},{"id":322,"value":"hash = require('object-hash@1.3.0/dist/object_hash.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":76,"value":"moment = require('moment@2.22.2/moment.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":211,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":243,"value":"numjs=require('https://bundle.run/numericjs@1.2.6')","pinned":false,"hidden":false,"mode":"ojs"},{"id":444,"value":"aljs = require('https://bundle.run/alignment.js@1.0.10')","pinned":false,"hidden":false,"mode":"ojs"},{"id":494,"value":"mathjs = require('https://bundle.run/mathjs')","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W36","stdlib":"1","titling":"auto"}