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emepyc/README.md

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Different node sizes
Raw
README.md

Example of TnT Tree with different node sizes.

Raw
index.html
<!DOCTYPE html>
<head>
<link rel="stylesheet" href="http://tntvis.github.io/tnt.tree/build/tnt.tree.css" type="text/css" />
<style>
#mydiv {
margin-top : 50px;
}
</style>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script src="http://tntvis.github.io/tnt.tree/build/tnt.tree.min.js"></script>
<script src="node_size.js"></script>
</head>
<body>
<div id="mydiv"></div>
<script>
node_size(document.getElementById("mydiv"));
</script>
</body>
Raw
node_size.js
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
}
};
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