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Tree and Tracks updates
Raw
README.md

Example of TnT visualisation showing how to update the tree and the board (tracks) based on user input. Click on internal nodes of the tree to collapse them.

Raw
data.js
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'blocks' : [
{
start : 153,
end : 165
}
]
}
};
Raw
index.html
<!DOCTYPE html>
<head>
<link rel="stylesheet" href="http://tntvis.github.io/tnt/build/tnt.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/build/tnt.min.js"></script>
<script src="data.js"></script>
<script src="render.js"></script>
</head>
<body>
<div id="mydiv"></div>
<script>
render(document.getElementById("mydiv"));
</script>
</body>
Raw
render.js
function render (div) {
// The height of tree labels and tracks
var height = 30;
// Create vis, tree and board
var vis = tnt();
var tree = tnt.tree();
var board = tnt.board();
// helper function
var get_highest_val = function (node, prop) {
var highest = 0;
node.apply(function (n) {
if (n.property(prop) === "") {
return;
}
var val = parseInt (n.property(prop));
if (val > highest) {
highest = val;
}
});
return highest;
};
// Swap tracks
var sel = d3.select(div)
.append("select")
.on("change", function () {
var cond;
if (this.value === 'Forward') {
cond = function (node1, node2) {
var highest1 = get_highest_val(node1, '_id');
var highest2 = get_highest_val(node2, '_id');
return highest1 - highest2;
};
}
if (this.value === 'Reverse') {
cond = function (node1, node2) {
var highest1 = get_highest_val(node1, '_id');
var highest2 = get_highest_val(node2, '_id');
return highest2 - highest1;
};
}
tree.root().sort(cond);
vis.update();
});
sel
.append("option")
.attr("selected", 1)
.text("Forward");
sel
.append("option")
.text("Reverse");
// TREE SIDE
// Configure the tree
var newick = "(((((homo_sapiens:9,pan_troglodytes:9)207598:34,callithrix_jacchus:43)314293:52,mus_musculus:95)314146:215,taeniopygia_guttata:310)32524:107,danio_rerio:417)117571:135;";
tree
.data (tnt.tree.parse_newick (newick))
.layout (tnt.tree.layout.vertical()
.width(430)
.scale(false)
)
.label (tnt.tree.label.text()
.text(function (node) {
return node.data().name;
})
.fontsize(12)
.height(height)
);
// collapse nodes on click
tree.on("click", function(node){
node.toggle();
vis.update();
});
// BOARD SIDE
board
.from(0)
.to(4000)
.width(300)
.zoom_out(4000)
.max(4000);
var display_select = d3.select(div)
.append("select")
.on("change", function () {
switch (this.value) {
case 'blocks' :
vis.track(track_blocks);
break;
case 'line' :
vis.track(track_lines);
break;
}
});
display_select
.append("option")
.attr("value", "line")
.text("lines")
.attr("selected", 1);
display_select
.append("option")
.attr("value", "blocks")
.text("blocks");
var track_lines = function (leaf_node) {
var leaf = leaf_node.data();
var sp = leaf.name;
return tnt.board.track()
.color("#EBF5FF")
.data (tnt.board.track.data.sync()
.retriever (function () {
return data[sp] ? data[sp].line : [];
})
)
.display(tnt.board.track.feature.area()
.color("steelblue")
.index(function (d) {
return d.pos;
})
);
};
var track_blocks = function (leaf_node) {
var leaf = leaf_node.data();
var sp = leaf.name;
return tnt.board.track()
.color("#EBF5FF")
.data (tnt.board.track.data.sync()
.retriever (function () {
return data[sp] ? data[sp].blocks : [];
})
)
.display (tnt.board.track.feature.ensembl()
.color ('steelblue')
.index (function (d) {
return d.start;
})
);
};
var axis_top = tnt.board.track()
.height(0)
.color("white")
.display(tnt.board.track.feature.axis()
.orientation("top")
);
var axis_bottom = tnt.board.track()
.height(18)
.color("white")
.display(tnt.board.track.feature.axis()
.orientation("bottom")
);
vis
.tree(tree)
.board(board)
.top(axis_top)
.bottom(axis_bottom)
.track(track_lines);
vis(div);
}
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