summary = { let prior_dates = []; let support_format = d3.format (".2g"); let tabulate_for_date = (selection_info, this_date) => { let T = []; let for_plotting = []; let selectors = []; let epitopes = {}; _.each (selection_info, (record, gene)=> { let tree_object = new phylotree.phylotree (record['tree']); _.each (record['selection'], (info, site) => { let site_score = 0; let genomic_site = record.map[+site]+1; let ref_coord_start = _.find (gene_coordinates(this_date), (d)=> d[1] == gene)[0] + (genomic_site-1)*3; let prc = for_plotting.length; let plot_record = {'position' : ref_coord_start, 'gene' : gene, 'site_in_gene' : genomic_site}; let ref_coord = "" + ref_coord_start + "-" + (ref_coord_start+2) + ""; let peptide_site = _.find (peptide_coordinates, (d)=> (genomic_site >= d[1] && genomic_site <= d[2] && d[3] == gene)); let site_record = { 'site' : gene + " " + genomic_site + (peptide_site ? "
" + peptide_site[0] + " " + (genomic_site - peptide_site[1] + 1) : "") + "
Genomic " + ref_coord, 'classification' : {'fel' : info['fel'] <= record.p , 'meme' : info['meme'] <= record.p, 'fraction' : info['meme-fraction'], 'kind' : info['kind'], 'branches' : info['meme-branches'] }, 'substitutions' : info['substitutions'], 'position' : ref_coord_start }; if (peptide_site) { plot_record['peptide'] = peptide_site[0] + " " + (genomic_site - peptide_site[1] + 1); } if ((site_record['classification']['fel']||site_record['classification']['meme'])) { site_score += 1; if (info['kind'] == "negative") { plot_record.kind = "Selection"; plot_record.type = "Negative"; for_plotting.push (_.clone(plot_record)); } else { plot_record.kind = "Selection"; plot_record.type = "Positive"; for_plotting.push (_.clone(plot_record)); } } else { plot_record.type = "Neutral"; } if (site_record['classification']['branches'] > 1) { site_score++; plot_record.kind = "Multiple Clades"; for_plotting.push (_.clone(plot_record)); } if ('MAF' in record) { if (info.MAF >= record.MAF) { site_record['classification']['MAF'] = info.MAF; site_score++; plot_record.kind = "Common Variant"; for_plotting.push (_.clone(plot_record)); } } if ('trend' in info) { if (info['trend'] >= 3) { site_record['classification']['trend'] = true; site_score++; plot_record.kind = "Increasing frequency"; for_plotting.push (_.clone(plot_record)); } } if (gene in shift_genes) { ref_coord_start++; } if ((ref_coord_start-1) in comparative_annotation) { site_record['comp'] = comparative_annotation[ref_coord_start-1]; if ('hla' in site_record['comp']) { let ec = _.size (site_record['comp']['hla']); if (ec) { site_record['classification']['hla'] = site_record['comp']['hla']; site_score++; plot_record.kind = "Predicted CTL epitope"; for_plotting.push (_.clone(plot_record)); } } if ('bFEL' in site_record['comp']) { if ( site_record['comp']['bFEL']['p'] <= record.p || site_record['comp']['bMEME']['p'] <= record.p || site_record['comp']['bCFEL']['p'] <= record.p) { if (site_record['comp']['bFEL']['p'] <= record.p) { site_record['classification']['betas'] = ((site_record['comp']['bFEL']['a'] < site_record['comp']['bFEL']['b']) ? "Positively" : "Negatively") + " selected in the closely related bat/pangolin clade";} else {site_record['classification']['betas'] = "";} if (site_record['comp']['bMEME']['p'] <= record.p) { if (site_record['classification']['betas'].length) { site_record['classification']['betas'] += "\n"; } site_record['classification']['betas'] += "Episodic positive selection in the closely related bat/pangolin clade"; } if (site_record['comp']['bCFEL']['p'] <= record.p) { if (site_record['classification']['betas'].length) { site_record['classification']['betas'] += "\n"; } site_record['classification']['betas'] = site_record['comp']['bCFEL']['b-nCOV'] > site_record['comp']['bCFEL']['b'] ? "Higher dN/dS in the closely related bat/pangolin clade" : "Lower dN/dS in the closely related bat/pangolin clade"; } site_score++; plot_record.kind = "Selected in animals"; for_plotting.push (_.clone(plot_record)); } } } let composition = _.sortBy(_.map (info['composition'], (v,k) => [k,v]), (d)=>-d[1]); if ('evolutionary_support' in info) { let support_by_residue = {}; _.each (info['evolutionary_support'], (e)=>{ if (! (e.aa in support_by_residue)) { support_by_residue[e.aa] = 0; } support_by_residue[e.aa] += e.support; }); _.each (composition, (d, i) => { if (d[0] in support_by_residue) { d[2] = support_by_residue[d[0]]; } else { d[2] = 0; } }); if (_.every (composition, (d,i)=> (i == 0 || d[2] > 0 || d[1] == 1 || d[0].length > 1))) { site_record['classification']['evo_support'] = true; //site_score++; } else { site_record['classification']['evo_support'] = false; site_score++; plot_record.kind = "Unexpected residues"; for_plotting.push (_.clone(plot_record)); } } site_record ['composition'] = { 'composition' : _.map (composition, (d,i)=>{ let style_string = ''; let support_text = ''; if (d.length>2 && d[0].length == 1 && d[0] != '-') { if (d[2] > 0.1) { style_string = 'style="color:darkgreen"'; support_text = "Very high evolutionary credibility"; } else { if (d[2] > 0.001) { style_string = 'style="color:#c2a90f"'; support_text = "High evolutionary credibility"; } else { if (d[2] > 0.0) { style_string = 'style="color:#ff8c00"'; support_text = "Medium evolutionary credibility"; } else { style_string = 'style="color:darkred"'; support_text = "Low evolutionary credibility"; } } } } return "" + (d[0] == '-' ? '[-]' : d[0]) + "_{" + d[1] + "}"; } ).join (""), 'variants' : site_record['variants'] = _.filter (intra_host, (d)=>d[0] == gene && d[3] >= ref_coord_start && d[3] <= ref_coord_start + 2 && genomic_site)}; if ('prime' in info) { site_record ['composition']['prime'] = info['prime']; } if (site_record ['composition'].variants.length > 0) { site_record['classification']['variants'] = site_record ['composition'].variants.length; site_score++; plot_record.kind = "Intra-host variants"; for_plotting.push (_.clone(plot_record)); } let substitutions = {}; let internal_node_names = {}; tree_object.traverse_and_compute ((n)=> { if (!tree_object.is_leafnode (n)) { internal_node_names [n.data.name] = 1; } }); let root_name = _.find (info['labels'], (n, k)=>{ return !(k in internal_node_names); }); info['labels']['root'] = (root_name); tree_object.traverse_and_compute ((n)=> { if (n.parent) { function gen_label (f,t) { var aac = (a)=>a.length <= 4 ? a : "MIX"; return f[1]+"("+aac(f[0])+"):"+t[1]+"("+aac(t[0])+")"; } let from_state = info['labels'][n.parent.data.name]; let to_state = info['labels'][n.data.name]; if (from_state[1] != to_state[1]) { let sub_key = from_state[1] < to_state[1] ? gen_label (from_state,to_state) : gen_label (to_state,from_state); if (! (sub_key in substitutions)) { substitutions[sub_key] = { 'leaves' : 0, 'internal' : 0, 'from_codon' : from_state[1], 'to_codon' : to_state[1], 'position' : _.map ( _.filter ( _.map (from_state[1], (c,i)=>{ return [c != to_state[1][i],i] }), (d)=>d[0]), (d)=>d[1])}; } if (tree_object.is_leafnode (n)) { substitutions[sub_key]['leaves'] ++; } else { substitutions[sub_key]['internal'] ++; } } } }); substitutions = _.sortBy (_.map (substitutions, (v,k)=> { v.key = k; return v; }), (d)=> -d['leaves']-100*d['internal']); site_record['expanded_subs'] = substitutions; site_record['annotation'] = []; _.each ([ref_coord_start,ref_coord_start+1,ref_coord_start+2], (c)=> { if (c in annotation_data) { site_record['annotation'].push (annotation_data[c]); } }); site_record['score'] = site_score; for (let i = prc; i < for_plotting.length; i++) { for_plotting[i]['score'] = site_score; } site_record['for_plot'] = _.clone(plot_record); site_record['for_plot'].score = site_score; T.push (site_record); selectors.push ([gene, genomic_site, +site+1,site_score]); epitopes [gene+"/"+genomic_site] = site_record['classification']['hla']; }); }); return {'table' : _.sortBy (T,(d)=>-d.score), 'selectors' : _.sortBy (selectors,(d)=>-d[3]), 'plot' : for_plotting, 'epitopes' : epitopes}; }; let current_data = tabulate_for_date (selection_data[0], use_date); let all_dates_before_this = _.sortBy (_.filter (analysis_dates, (d)=> d < use_date)); if (all_dates_before_this.length > 0) { let prior_summaries = {}; _.each (all_dates_before_this, (d)=>{ prior_summaries[d] = tabulate_for_date (all_selection_data[d], d); }); _.each (current_data.table, (row)=>{ let previously_found = []; _.each (prior_summaries, (d,v) => { if (_.find (d.table, (r)=>r.position == row.position)) { previously_found.push(v); } }); row.prior = [previously_found , all_dates_before_this.length]; if (previously_found.length==0) { let new_flag = row.for_plot; new_flag.kind = "New"; current_data.plot.push (new_flag); } }); } return current_data; }