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targetGeneTree.js
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targetGeneTree.js
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var ensemblRestApi = require("tnt.ensembl");
var tnt_tree = require("tnt.tree");
var tree_tooltips = require("./tooltips.js");
var tree_legend = require("./legend.js");
var RSVP = require('rsvp');
var targetGeneTree = function () {
"use strict";
var id;
var width = 600;
var proxy = "";
// var species = [
// 9606, // human
// 10090, // mouse
// 9823, // pig
// 9615, // dog
// 9544, // macaque
// // 9541, // crab-eating macaque --- NOT IN ENSEMBL
// 10116, // rat
// 10141, // guinea pig
// 9986, // rabbit
// 8364, // frog
// 7955, // zebrafish
// ];
var colorScale = d3.scale.linear()
.domain([0,100])
.range(["#CBDCEA", "#005299"]);
var tooltips = tree_tooltips();
var legend = tree_legend();
var species = legend.selectedSpecies();
var render = function (div) {
var labelPic = tnt_tree.label.img()
.src (function (node) {
if (node.is_leaf()) {
var data = node.data();
var spName = data.taxonomy.scientific_name.replace(/ /g, "_");
return "/imgs/species/" + spName + ".png";
}
})
.width(function (d) {
return 30;
})
.height(function (d) {
return 30;
});
var labelText = tnt_tree.label.text()
.text(function (node) {
if (node.is_leaf()) {
return node.data().sequence.name || node.data().id.accession;
} else {
return "";
}
})
.height(function (d) {
return 35;
})
.color(function (node) {
if (node.property("taxonomy").scientific_name === "Homo sapiens") {
return "#005299";
}
return "#333333";
})
.fontsize(10);
var label = tnt_tree.label.composite()
.add_label (labelPic)
.add_label (labelText);
var tree_vis = tnt_tree();
tree_vis
.on("click", tooltips.node)
.layout(tnt_tree.layout.vertical()
.width(width)
.scale(true)
)
.node_display(tree_vis.node_display()
.fill(function (node) {
var data = node.data();
var thisId = data.id;
if (thisId && thisId.accession === id) {
return "red";
}
if (node.is_leaf()) {
if (data.homology) {
return colorScale(data.homology.percId);
} else {
return "#FFFFFF";
}
}
return "#BBBBBB";
})
.size(5)
)
.label(label);
var rest = ensemblRestApi();
if (proxy) {
rest
.proxyUrl(proxy);
}
var homologsUrl = rest.url.homologues({
"id": id,
"target_taxons": species,
"format": "full"
});
var homologsPromise = rest.call(homologsUrl);
// .catch(function (err) {
// console.warn (err);
// });
var genetreeUrl = rest.url.gene_tree({
"member_id" : id,
"sequence" : "none",
"species": ["human"]
});
var genetreePromise = rest.call(genetreeUrl);
// .catch(function (err) {
// console.warn (err);
// });
RSVP.all([homologsPromise, genetreePromise])
.then (function (resps) {
// Homologues Data
var homologues = resps[0].body.data[0].homologies;
var homologuesInfo = parseHomologues(homologues);
// GeneTree
var genetreeData = resps[1].body.tree;
tree_vis.data(genetreeData);
var root = tree_vis.root();
sortTree(root);
var subtree = pruneTree(root, species, homologuesInfo);
tree_vis.data(subtree.data());
tree_vis(div);
var treeDiv = d3.select(div).select("div");
// Update the tree when the species are selected / deselected
legend
.update(function (species) {
var subtree = pruneTree(root, species, homologuesInfo);
tree_vis.data(subtree.data());
tree_vis.update();
});
legend(treeDiv.node());
});
RSVP.on("error", function (reason) {
console.warn (reason);
});
};
render.id = function (newId) {
if (!arguments.length) {
return id;
}
id = newId;
return this;
};
render.width = function (w) {
if (!arguments.length) {
return width;
}
width = w;
return this;
};
render.proxy = function (p) {
if (!arguments.length) {
return proxy;
}
proxy = p;
return this;
};
function pruneTree (root, species, homologiesInfo) {
var leaves = root.get_all_leaves();
var retainedLeaves = leaves.filter(function (node) {
var taxid = node.property('taxonomy').id;
return species.indexOf(taxid) >=0 ;
});
addHomologies(retainedLeaves, homologiesInfo);
var subtree = root.subtree(retainedLeaves);
return subtree;
}
function parseHomologues (homologues) {
var info = {};
for (var i=0; i<homologues.length; i++) {
var homolog = homologues[i];
info[homolog.target.id] = {
"cigarLine" : homolog.target.cigar_line,
"percId" : homolog.target.perc_id,
"percPos" : homolog.target.perc_pos,
"species" : homolog.target.species,
"taxonId" : homolog.target.taxon_id,
"level" : homolog.taxonomy_level,
"type" : homolog.type,
"dn_ds" : homolog.dn_ds
};
}
return info;
}
function addHomologies (leaves, homologiesInfo) {
leaves.map (function (leaf) {
var leafData = leaf.data();
leafData.homology = homologiesInfo[leafData.id.accession] || undefined;
});
}
function sortTree (root) {
root.sort (function (node1, node2) {
return hasThisGene(node2) - hasThisGene(node1);
});
}
function hasThisGene(node) {
return node.present (function (n) {
return n.is_leaf() && n.property("id").accession === id;
});
}
return render;
};
module.exports = exports = targetGeneTree;