by_gene_plot = { let variants = []; _.each (comparative_data, (site, key)=> { let plot_object = { 'gene' : site["G"], 'coord' : +site["S"], 'type' : null, 'kind' : null }; function add_point (kind, type) { plot_object['type'] = type || "Variable"; plot_object['kind'] = kind; variants.push (_.clone ( plot_object)); }; let cdn_variants = _.sortBy (_.filter (site['cdn'], (v,k)=> {return k.indexOf ('-') < 0 && k != 'NNN'})); if (cdn_variants.length > 1) { add_point ("Nucleotide"); if (_.some (cdn_variants, (v,i) => {return v>=2&&i {return k != '-'})); if (aa_variants.length > 1) { add_point ("AA SNP"); if (_.some (aa_variants, (v,i) => {return v>=2&&i{ if (c in intra_host) { ihv = _.extend (ihv, intra_host[c]); } }); _.each (ihv, (v,k)=> { add_point ("Intrahost " + k,"Intrahost variants"); }); if (site["evo"]) { let nuc = {'A': 1, 'C': 1, 'G' :1, 'T': 1}; cdn_variants = _.filter (_.map (site['cdn'], (c,k)=>[k,c]), (c)=>_.every (c[0], (n)=>{return (n in nuc);})); if (_.some (cdn_variants, (c)=> { if (c[0] in site["evo"]) { return false; } if (site["G"] == "S") console.log (c, site); return c[1] >= 5; })) { add_point ("Unexpected codons","Adaptive"); } } }); return variants; }