var node_size = function (div) {

    var scale = d3.scale.linear()
        .domain(extent(species_data, "Protein-coding genes"))
        .range([2, 10]);


        var node_size = function (node) {
            if (node.node_name()) {
                return scale(species_data[node.node_name()]['Protein-coding genes']);
            }
            return 2;
        };

    var tree = tnt.tree()
        .data(tnt.tree.parse_newick(newick))
        .node_display(tnt.tree.node_display.circle()
            .size(node_size)
            .fill("white")
        )
        .layout(tnt.tree.layout.vertical()
            .width(700)
            .scale(true)
        )
        .label(tnt.tree.label.text()
            .fontsize(12)
            .text(function (node) {
                return node.node_name();
            })
        );

    tree(div);
};

function extent (data, attr) {
    var min;
    var max;
    for (var sp in species_data) {
        if (species_data.hasOwnProperty(sp)) {
            if ((species_data[sp] !== undefined) && (species_data[sp][attr] !== undefined)) {
                var val = species_data[sp][attr];
                if ((min === undefined) || (val < min)) min = val;
                if ((max === undefined) || (val > max)) max = val;
            }
        }
    }
    return [min, max];
}

var newick = "(((((((Mus musculus:0.0845,Rattus norvegicus:0.0916):0.2567,Oryctolagus cuniculus:0.2157):0.0153,(((((Pan troglodytes:0.0067,Homo sapiens:0.0067):0.0022,Gorilla gorilla:0.0088):0.0097,Pongo abelii:0.0183):0.0143,Macaca mulatta:0.0375):0.0220,Callithrix jacchus:0.0661):0.0891):0.0206,(((Felis catus:0.0986,Canis familiaris:0.1025):0.0498,Equus caballus:0.1094):0.0107,((Ovis aries:0.0618,Bos taurus:0.0618):0.0869,Sus scrofa:0.1073):0.0403):0.0329):0.2584,Monodelphis domestica:0.3408):0.0717,Ornithorhynchus anatinus:0.4566):0.1095,(((Gallus gallus:0.0414,Meleagris gallopavo:0.0414):0.1242,Taeniopygia guttata:0.1715):0.3044,Anolis carolinensis:0.4989):0.1700)";

var species_data = {
    'Homo sapiens' : {
        'Chromosome pairs' : 23,
        'Protein-coding genes' : 20805,
        'Genome length' : 3.1,
        'Ensembl date' : new Date(2001, 07),
        'Cuteness factor' : 6
    },
    'Tetraodon nigroviridis' : {
        'Chromosome pairs' : 21,
        'Protein-coding genes' : 19602,
        'Genome length' : 0.36,
        'Ensembl date' : new Date(2004, 09),
        'Cuteness factor' : 10
    },
    'Monodelphis domestica' : {
        'Chromosome pairs' : 11,
        'Protein-coding genes' : 21327,
        'Genome length' : 3.6,
        'Ensembl date' : new Date(2005, 11),
        'Cuteness factor' : 9
    },
    'Mus musculus' : {
        'Chromosome pairs' : 20,
        'Protein-coding genes' : 23148,
        'Genome length' : 2.7,
        'Ensembl date' : new Date(2002,01),
        'Cuteness factor' : 7
    },
    'Ornithorhynchus anatinus' : {
        'Chromosome pairs' : 26,
        'Protein-coding genes' : 21698,
        'Genome length' : 2.1,
        'Ensembl date' : new Date(2006,12),
        'Cuteness factor' : 9
    },
    'Pan troglodytes' : {
        'Chromosome pairs' : 24,
        'Protein-coding genes' : 18759,
        'Genome length' : 3.3,
        'Ensembl date' : new Date(2004,05),
        'Cuteness factor' : 6
    },
    'Macaca mulatta' : {
        'Chromosome pairs' : 21,
        'Protein-coding genes' : 21905,
        'Genome length' : 3.1,
        'Ensembl date' : new Date(2005,12),
        'Cuteness factor' : 6
    },
    'Ovis aries' : {
        'Chromosome pairs' : 27,
        'Protein-coding genes' : 20921,
        'Genome length' : 2.6,
        'Ensembl date' : new Date(2013,12),
        'Cuteness factor' : 6
    },
    'Sus scrofa' : {
        'Chromosome pairs' : 19,
        'Protein-coding genes' : 21630,
        'Genome length' : 2.8,
        'Ensembl date' : new Date(2009,09),
        'Cuteness factor' : 5
    },
    'Ciona intestinalis' : {
        'Chromosome pairs' : 14,
        'Protein-coding genes' : 16658,
        'Genome length' : 0.1,
        'Ensembl date' : new Date(2005,05),
        'Cuteness factor' : 3
    },
    'Rattus norvegicus' : {
        'Chromosome pairs' : 21,
        'Protein-coding genes' : 22941,
        'Genome length' : 2.9,
        'Ensembl date' : new Date(2002,11),
        'Cuteness factor' : 5
    },
    'Anolis carolinensis' : {
        'Chromosome pairs' : 14,
        'Protein-coding genes' : 18596,
        'Genome length' : 1.8,
        'Ensembl date' : new Date(2009,03),
        'Cuteness factor' : 7
    },
    'Bos taurus' : {
        'Chromosome pairs' : 30,
        'Protein-coding genes' : 19994,
        'Genome length' : 2.7,
        'Ensembl date' : new Date(2005,07),
        'Cuteness factor' : 6
    },
    'Pongo abelii' : {
        'Chromosome pairs' : 24,
        'Protein-coding genes' : 20424,
        'Genome length' : 3.4,
        'Ensenbl date' : new Date(2011,04),
        'Cuteness factor' : 8
    },
    'Callithrix jacchus' : {
        'Chromosome pairs' : 23,
        'Protein-coding genes' : 20993,
        'Genome length' : 2.9,
        'Ensembl date' : new Date(2009,09),
        'Cuteness factor' : 8
    },
    'Equus caballus' : {
        'Chromosome pairs' : 32,
        'Protein-coding genes' : 20449,
        'Genome length' : 2.5,
        'Ensembl date' : new Date(2008,03),
        'Cuteness factor' : 6
    },
    'Taeniopygia guttata' : {
        'Chromosome pairs' : 40,
        'Protein-coding genes' : 17488,
        'Genome length' : 1.2,
        'Ensembl date' : new Date(2009,03),
        'Cuteness factor' : 8
    },
    'Gasterosteus aculeatus' : {
        'Chromosome pairs' : 22,
        'Protein-coding genes' : 20787,
        'Genome length' : 0.46,
        'Ensembl date' : new Date(2006,08),
        'Cuteness factor' : 3
    },
    'Gallus gallus' : {
        'Chromosome pairs' : 39,
        'Protein-coding genes' : 15508,
        'Genome length' : 1,
        'Ensembl date' : new Date(2004,06),
        'Cuteness factor' : 4
    },
    'Felis catus' : {
        'Chromosome pairs' : 19,
        'Protein-coding genes' : 19493,
        'Genome length' : 2.5,
        'Ensembl date' : new Date(2007,02),
        'Cuteness factor' : 9
    },
    'Gorilla gorilla' : {
        'Chromosome pairs' : 24,
        'Protein-coding genes' : 20962,
        'Genome length' : 3,
        'Ensembl date' : new Date(2008,12),
        'Cuteness factor' : 4
    },
    'Oryctolagus cuniculus' : {
        'Chromosome pairs' : 22,
        'Protein-coding genes' : 19293,
        'Genome length' : 2.7,
        'Ensembl date' : new Date(2006,08),
        'Cuteness factor' : 10
    },
    'Meleagris gallopavo' : {
        'Chromosome pairs' : 40,
        'Protein-coding genes' : 14125,
        'Genome length' : 1.1,
        'Ensembl date' : new Date(2010,03),
        'Cuteness factor' : 2
    },
    'Canis familiaris' : {
        'Chromosome pairs' : 39,
        'Protein-coding genes' : 19856,
        'Genome length' : 2.4,
        'Ensembl date' : new Date(2004,12),
        'Cuteness factor' : 6
    }
};