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Root-to-tip for intra-host HIV-1 data
Raw
README.md

Root-to-tip regression for intrahost HIV-1 phylogenies.

In this example, we read in trees with branch lengths (FastTree2), based on haplotypes and counts reported in Lorenzo-Redondo et al, construct root-to-tip distances for time-stamped tips, and regress those on time to obtain crude evolutionary rate estimates.

The initial rooting of the tree is obtained by considering all time-point 0 sequences and selecting one that maximizes R2 (regardless of the slope). The user can perform arbitrary rerooting and see what the effect on the regression slope is.

Further, 1000 simulated perturbation of haplotype counts are considered for a given rooting: the estimated frequency of each haplotype (encoded in the tip name) is multiplied by a random number from [0.05-10] distributed uniformly. The proportion of perturbations with positive inferred regression slopes is shown on the chart.

Raw
index.html
<!DOCTYPE html>
<html lang='en'>
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Security-Policy" content="upgrade-insecure-requests">
<link href="//veg.github.io/phylotree.js/phylotree.css" rel="stylesheet">
<link rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<link rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap-theme.min.css">
<script src="//code.jquery.com/jquery.js"></script>
<script src="//netdna.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
<script src="//d3js.org/d3.v3.min.js"></script>
<script src="//phylotree.hyphy.org/phylotree.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script>
<style>
.date-text {
padding: 0.25em;
text-align: center;
}
.dot {
stroke: #000;
opacity : 0.1;
}
.size-bubble, .size-bubble * {
fill: #CCC;
shape-rendering: crispEdges;
stroke: black;
stroke-width: 1px;
}
.size-label {
display: block;
text-align : center;
font-family: sans-serif;
font-size: 9pt;
}
.fit-label {
text-anchor : start;
font-family: sans-serif;
font-size: 7pt;
}
.axis text {
font: 14px sans-serif;
}
.axis path, .axis line {
fill: none;
stroke: #000;
shape-rendering: crispEdges;
}
.fit {
fill: none;
stroke-width: 2px;
stroke: red;
}
.fit-no-counts {
opacity: 0.1;
stroke: gray;
}
@media print
{
.no-print, .no-print *
{
display: none !important;
}
}
</style>
</head>
<body>
<nav class="navbar navbar-default" role="navigation">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-ex1-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a id = "menu-title" class="navbar-brand" href="#"></a>
</div>
<div class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Tree to display <b class="caret"></b></a>
<ul class="dropdown-menu" id = 'tree_selector'>
<li><a href="#" data-tree = "js1774-gag.tre" data-tag = "JS1774 gag"></a></li>
<li><a href="#" data-tree = "sm1727-gag.tre" data-tag = "SM1727 gag"></a></li>
<li><a href="#" data-tree = "tm1679-gag.tre" data-tag = "TM1679 gag"></a></li>
<li><a href="#" data-tree = "js1774-pol-1.tre" data-tag = "JS1774 pol (PR)"></a></li>
<li><a href="#" data-tree = "js1774-pol-2.tre" data-tag = "JS1774 pol (RT)"></a></li>
<li><a href="#" data-tree = "sm1727-pol-1.tre" data-tag = "SM1727 pol (PR)"></a></li>
<li><a href="#" data-tree = "sm1727-pol-2.tre" data-tag = "SM1727 pol (RT)"></a></li>
<li><a href="#" data-tree = "tm1679-pol-1.tre" data-tag = "TM1679 pol (PR)"></a></li>
<li><a href="#" data-tree = "tm1679-pol-2.tre" data-tag = "TM1679 pol (RT)"></a></li>
</ul>
</li>
<li>
<a href="#" data-toggle="modal" data-target="#newick_modal">Input Newick</a>
</li>
</ul>
<form class="navbar-form navbar-left">
<div class="checkbox navbar-btn">
<label class="navbar-link">
<input type="checkbox" id="layout">
Radial layout
</label>
</div>
</form>
</div><!-- /.navbar-collapse -->
</nav>
<div class = "container">
<div class = "row" style = "margin-top: 1em">
<div class = "col-md-2" id="date-legend">
</div>
<div class = "col-md-2" id="compartment-legend">
</div>
<div class = "col-md-2" id="size-legend">
</div>
<div class = "col-md-6">
<svg id="rtt_display"></svg>
</div>
</div>
<div class = "row">
<div class = "col-md-12">
<svg id="tree_display"></svg>
</div>
</div>
</div>
<div class="modal" id = 'newick_modal'>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
<h4 class="modal-title">Newick string to render</h4>
</div>
<div class="modal-body" id = 'newick_body'>
<textarea id = 'nwk_spec' autofocus = true placeholder = "" style = 'width: 100%; height: 100%' rows = 20 selectionStart = 1 selectionEnd = 1000>(a : 0.1, (b : 0.11, (c : 0.12, d : 0.13) : 0.14) : 0.15)</textarea>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-primary" id = 'validate_newick'>Display this tree</button>
</div>
</div><!-- /.modal-content -->
</div><!-- /.modal-dialog -->
</div><!-- /.modal -->
<script>
// use these formats for parsing and displaying sampling dates
var date_in = d3.time.format("%Y%m%d"),
date_out = d3.time.format("%B %d, %Y");
// default scheme to color by date
var coloring_scheme = d3.scale.category10();
// different shapes for labeling compartments
var compartment_labels = d3.scale.ordinal().range(["circle", "square", "diamond", "cross", "triangle-up"]);
// global tree object
var tree;
// bubble size scale
var size_scale = d3.scale.pow ().exponent (0.4).range ([1,6]).clamp (false).domain ([0,1]);
var rescaled_size;
// determines the size of a node "bubble"
function bubbleSize(node) {
if (node && node.copy_number) {
return size_scale(node.copy_number);
}
return 1;
}
function nodeStyler(container, node) {
if (d3.layout.phylotree.is_leafnode(node)) {
var existing_circle = container.selectAll("circle");
if (existing_circle.size() == 1) {
existing_circle.remove();
}
if (node.copy_number) {
existing_circle = container.selectAll("path.node_shape").data([node.compartment]);
existing_circle.enter().append("path").classed("node_shape", true);
var bubble_size = tree.node_bubble_size(node);
var label = existing_circle.attr("d", function(d) {
return d3.svg.symbol().type(compartment_labels(d)).size(bubble_size * bubble_size)();
}).selectAll ("title").data ([node.copy_number]);
label.enter().append("title");
label.text ("" + node.copy_number + " copies");
existing_circle.style("stroke-width", "1px").style("stroke", "black");
if (node.text_angle) {
existing_circle.attr("transform", function(d) {
return "rotate(" + node.text_angle + ") translate(" + (node.text_align == "end" ? -1 : 1) * bubble_size / 2 + ",0)";
});
} else {
existing_circle.attr("transform", function(d) {
return "translate(" + bubble_size / 2 + ",0)";
});
}
}
}
if (node.date) {
var node_color = coloring_scheme (node.date);
container.selectAll("circle").style("fill", node_color);
container.selectAll("path").style("fill", node_color);
container.style("fill", node_color);
}
}
function drawATree(newick) {
tree = d3.layout.phylotree()
.svg(d3.select("#tree_display"))
.options({
'selectable': false,
// make nodes and branches not selectable
'collapsible': true,
// turn off the menu on internal nodes
'transitions': false,
// turn off d3 animations.
'draw-size-bubbles': true,
// draw node size bubbles
'annular-limit': 0.5,
// controls how much of the overall diameter can be taken by
// empty "annular" space
'max-radius': 512
// maximum radial layout radius
})
.node_span(bubbleSize)
.style_nodes(nodeStyler)
.node_circle_size (2) // do not draw clickable circles for internal nodes
.branch_name (function () {return ""}) // no leaf names
.layout_handler (function (tree) {
plotRTT (tree, "rtt_display", 350,350)
}
)
;
/* the next call creates the tree object, and tree nodes */
tree(d3.layout.newick_parser(newick));
/* parse tip names which are assumed to be like this:
6_PB_DNA_1_37-52
splitting on '_' yields
-- TimePoint; parsed and used to assign *colors* to edges/nodes and to draw root-to-tip distances
-- compartment; parsed and used to assign *shapes* to nodes in combination with the DNA/RNA source
-- source;
-- clone ID; ignored
-- another ID; ignored
-- copy number; parsed and used to scale "bubbles" on leaves
tips which do not conform to this naming convention are labeled as "reference",
and annotated using a special character.
*/
var unique_compartments = {},
unique_dates = {};
var copy_number_range = [1e100,0],
attributed_node = null;
_.each(tree.get_nodes(), function(value, key) {
var attributes = value.name.split('_');
if (attributes.length == 5) {
attributed_node = value;
value.compartment = attributes[1] + ' ' + attributes[2];
value.copy_number = parseFloat(attributes[4].split ('-')[1]);
copy_number_range[0] = Math.min (copy_number_range[0], value.copy_number);
copy_number_range[1] = Math.max (copy_number_range[1], value.copy_number);
value.numeric_date = parseInt (attributes[0]);
value.date = "Month " + attributes[0];
unique_compartments[value.compartment] = 1;
unique_dates[value.date] = 1;
} else {
value.is_reference = true;
}
});
size_scale.domain (copy_number_range);
coloring_scheme.domain (_.keys(unique_dates).sort());
compartment_labels.domain (_.keys(unique_compartments).sort());
if ($("#layout").prop("checked")) {
tree.radial (true);
}
tree.placenodes().layout();
var rescale = tree.node_bubble_size(attributed_node) / size_scale (attributed_node.copy_number) * 0.5;
rescaled_size = _.compose (function (d) {return d*rescale}, size_scale);
// create a legend for sizes
// power of 10 ticks
var size_bubbles = _.map (d3.range (Math.floor (Math.log(copy_number_range[0])/Math.log (10)), Math.ceil (Math.log(copy_number_range[1])/Math.log (10))),
function (v) {return Math.pow (10,v);});
d3.select ("#size-legend").selectAll (".row").remove();
var reference_sizes = d3.select ("#size-legend").selectAll (".row").data (_.map (size_bubbles, function (d) {return [d];}));
reference_sizes.enter().append ("div").classed ("row", true).selectAll (".col-md-2").data (function (d) {return [d];}).enter().append ("div").classed ("col-md-2", true);
var max_size = rescaled_size (size_bubbles[size_bubbles.length - 1]);
reference_sizes.selectAll (".col-md-2").each (function (d) {
var circle_size = rescaled_size (d);
d3.select (this).append ("svg").attr ("width", 2*max_size + 4).attr ("height", 2*circle_size + 4).append ("circle").classed("size-bubble", true).attr ("r", circle_size).attr ("cx", max_size+2).attr ("cy", circle_size+2);
d3.select (this).append ("span").classed ("size-label", true).style ("width", "" + (2*max_size+4) + "px").text (d);
});
// create a legend for compartments
d3.select ("#compartment-legend").selectAll (".row").remove();
var compartment_depictions = d3.select ("#compartment-legend").selectAll (".row").data (compartment_labels.domain());
compartment_depictions.enter().append ("div").classed ("row", true).selectAll (".col-md-2").data (function (d) {return [d];}).enter().append ("div").classed ("col-md-2", true);
compartment_depictions.exit().remove();
compartment_depictions.selectAll (".col-md-2").each (function (d) {
d3.select (this).append ("svg").attr ("width", 2*max_size + 4).attr ("height", 2*max_size + 4).append ("path").classed("size-bubble", true).attr("d", function(d) {
return d3.svg.symbol().type(compartment_labels(d)).size(max_size * max_size)();
}).attr ("transform", "translate( " + max_size + "," + max_size + ")");
d3.select (this).append ("span").classed ("size-label", true).style ("width", "" + (2*max_size+4) + "px").text (d);
});
// create a legend for dates
d3.select ("#date-legend").selectAll (".row").remove();
var date_colors = d3.select ("#date-legend").selectAll (".row").data (coloring_scheme.domain());
date_colors.enter().append ("div").classed ("row", true);
date_colors.exit().remove();
date_colors.each (function (d) {
d3.select(this).style ("background-color", coloring_scheme (d)).classed ("date-text", true).text (d).style ("color", d3.rgb(coloring_scheme (d)).hsl().l < 0.5 ? "white" : "black");
});
// UI handlers
$("#layout").on("click", function(e) {
tree.radial($(this).prop("checked")).placenodes().update();
});
var best_node = plotRTT (tree, "rtt_display", 350,350, true);
tree.reroot (best_node).update();
}
function computeRootToTip (node) {
if (node.parent) {
node.rtt = node.parent.rtt + tree.branch_length () (node);
}
else {
node.rtt = 0;
}
if (node.children) {
for (var c = 0; c < node.children.length; c++) {
computeRootToTip (node.children[c]);
}
}
}
function computeRootToTipOtherRoot (node, coming_from, shared_distance, distance_to_new_root) {
var my_bl = tree.branch_length () (node);
var go_up = false;
if (!coming_from) {
shared_distance = node.rtt;
distance_to_new_root = 0;
go_up = true;
}
if (node.children) {
for (var c = 0; c < node.children.length; c++) {
if (node.children[c] != coming_from) {
computeRootToTipOtherRoot (node.children[c], node, shared_distance, distance_to_new_root);
} else {
go_up = true;
}
}
}
node.rtta = node.rtt - shared_distance + distance_to_new_root;
if (go_up) {
shared_distance -= my_bl;
distance_to_new_root += my_bl;
}
if (node.parent && go_up) {
computeRootToTipOtherRoot (node.parent, node, shared_distance, distance_to_new_root);
}
}
function loadTreeFromURL(url) {
d3.text(url, function(error, newick) {
drawATree(newick);
});
}
function plotRTT (tree, tag, w, h, auto_root) {
computeRootToTip (tree.get_nodes()[0]);
if (auto_root) {
var max_r2 = 0;
var best_node = 0;
tree.traverse_and_compute (function (node) {
if (d3.layout.phylotree.is_leafnode (node)) {
if (node.numeric_date == 0) {
computeRootToTipOtherRoot (node, null, 0, 0);
linear_data = [];
tree.traverse_and_compute (function (node) {
if (d3.layout.phylotree.is_leafnode (node)) {
linear_data.push ([node.numeric_date, node.rtta, node.copy_number]);
}
});
var fit_with_counts = linear_fit (linear_data)["r2"];
if (fit_with_counts > max_r2) {
max_r2 = fit_with_counts;
best_node = node;
}
}
}
});
return best_node;
}
var margin = {top: 20, right: 80, bottom: 45, left: 65},
width = w - margin.left - margin.right,
height = h - margin.top - margin.bottom;
var x = d3.scale.linear()
.range([20, width-20]);
var y = d3.scale.linear()
.range([height, 0]);
var xAxis = d3.svg.axis()
.scale(x)
.orient("bottom");
var yAxis = d3.svg.axis()
.scale(y)
.orient("left");
var plot_here = d3.select ("#" + tag);
plot_here.attr ("width", w).attr("height", h);
plot_here.selectAll ("g").remove();
var svg = plot_here.append ("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
var plot_data = [];
var linear_data = [];
tree.traverse_and_compute (function (node) {
if (d3.layout.phylotree.is_leafnode (node)) {
plot_data.push (node);
linear_data.push ([node.numeric_date, node.rtt, 1]);
}
});
xAxis.tickValues (_.keys(_.countBy (linear_data, function (d) {return d[0];})).sort());
x.domain(d3.extent(plot_data, function(d) { return d.numeric_date; })).nice();
y.domain(d3.extent(plot_data, function(d) { return d.rtt; })).nice();
svg.append("g")
.attr("class", "x axis")
.attr("transform", "translate(0," + height + ")")
.call(xAxis)
.append("text")
.attr("class", "label")
.attr("x", width)
.attr("y", 35)
.style("text-anchor", "end")
.text("Time");
svg.append("g")
.attr("class", "y axis")
.call(yAxis)
.append("text")
.attr("class", "label")
.attr("transform", "rotate(-90)")
.attr("y", -60)
.attr("dy", ".71em")
.style("text-anchor", "end")
.text("Root-to-tip") ;
svg.selectAll(".dot")
.data(plot_data)
.enter().append("circle")
.attr("class", "dot")
.attr("r", function (d) {return 2*rescaled_size(tree.node_bubble_size(d));})
.attr("cx", function(d) { return x(d.numeric_date); })
.attr("cy", function(d) {
return y(d.rtt); })
.style("fill", function(d,i) { return "#000000"; });
function linear_fit (data) {
var ss = linear_data.reduce (function (p,c) {return c[2] + p}, 0), // sample count
sx = linear_data.reduce (function (p,c) {return c[2]*c[0] + p}, 0), // sum X
sy = linear_data.reduce (function (p,c) {return c[2]*c[1] + p}, 0) // sum Y
sxoss = sx/ss,
syoss = sy/ss;
var fitB = 0,
st2 = 0,
vary = 0;
data.forEach (function (point) {
var t = point[0] - sxoss;
st2 += point[2] * t * t;
fitB += point[2] * t * point[1];
vary += point[2] * (point[1]-syoss)*(point[1]-syoss);
});
fitB /= st2;
a = (sy - sx * fitB) / ss;
var varres = 0;
data.forEach (function (point) {
var t = point[1] - a - fitB * point[0];
varres += point[2] * t * t;
});
var normvarres = Math.sqrt (varres / (ss - 2));
return {'intercept' : a,
'slope' : fitB,
'r2': 1 - varres / vary,
'var (intercept)' : Math.sqrt ((1+sx*sx/(ss*st2))/ss),
'var (slope)' : Math.sqrt (1/st2)
};
};
var fit_with_counts = linear_fit (linear_data);
//console.log (fit_with_counts["R"]);
var label_format = d3.format (".2r");
function format_line (i, s) {
return label_format (i) + (s >= 0 ? '+' : '') + label_format (s) + '*T';
}
var positive_slope = 0;
for (s = 0; s < 1000; s += 1) {
fit_without_counts = (linear_fit (linear_data.map (function (d) {return [d[0], d[1], Math.floor (d[2]*(0.05 + 9.95*Math.random (0,1)))];})));
if (fit_without_counts ["slope"] > 0) {
positive_slope ++;
}
svg.append ("line")
.attr ("x1", x (x.domain()[0]))
.attr ("y1", y (x.domain()[0]*fit_without_counts['slope'] + fit_without_counts ['intercept']))
.attr ("x2", x (x.domain()[1]))
.attr ("y2", y (x.domain()[1]*fit_without_counts['slope'] + fit_without_counts ['intercept']))
.attr ("class", "fit fit-no-counts");
}
svg.append ("text").attr ("x", x (x.domain()[0])).attr ( y (y.domain [1])).text (d3.format(".2p")(positive_slope/s) + " positive slope");
svg.append ("line")
.attr ("x1", x (x.domain()[0]))
.attr ("y1", y (x.domain()[0]*fit_with_counts['slope'] + fit_with_counts ['intercept']))
.attr ("x2", x (x.domain()[1]))
.attr ("y2", y (x.domain()[1]*fit_with_counts['slope'] + fit_with_counts ['intercept']))
.attr ("class", "fit fit-counts");
svg.append ("text").attr ("x", x (x.domain()[1]))
.attr ("y", y (x.domain()[1]*fit_with_counts['slope'] + fit_with_counts ['intercept']))
.text (format_line (fit_with_counts['intercept'],fit_with_counts['slope']))
.attr ("class", "fit-label")
.attr ("dx", "2em")
.attr ("dy", "-.25 em");
}
$("#validate_newick").on ("click", function (e) {
var res = d3.layout.newick_parser ( $('textarea[id$="nwk_spec"]').val(), true);
if (res["error"] || ! res["json"]) {
var warning_div = d3.select ("#newick_body").selectAll ("div .alert-danger").data ([res["error"]])
warning_div.enter ().append ("div");
warning_div.html (function (d) {return d;}).attr ("class", "alert-danger");
} else {
drawATree ($('textarea[id$="nwk_spec"]').val());
$('#newick_modal').modal('hide');
}
});
$("[data-tree]").each (function () {
$(this).text ($(this).data("tag"));
});
$("[data-tree]").on ("click", function (e) {
loadTreeFromURL ($(this).data("tree"));
$("#menu-title").text ($(this).data("tag"));
});
$("[data-tree='tm1679-gag.tre']").click();
</script>
</body>
</html>
Raw
js1774-gag.tre
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Raw
js1774-pol-1.tre
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Raw
js1774-pol-2.tre
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Raw
sm1727-gag.tre
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Raw
sm1727-pol-1.tre
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Raw
sm1727-pol-2.tre
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Raw
tm1679-gag.tre
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Raw
tm1679-pol-1.tre
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Raw
tm1679-pol-2.tre
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