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* adding left-offset option
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* adding get and set partition methods
* adding get_node_by_name
* adding assign_attributes function
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@stevenweaver
stevenweaver committed Apr 4, 2016
1 parent da97602 commit 53c4e38
Showing 1 changed file with 45 additions and 13 deletions.
58 changes: 45 additions & 13 deletions phylotree.js
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Original file line number Diff line number Diff line change
Expand Up @@ -46,11 +46,13 @@ d3.layout.phylotree = function(container) {
'branches': 'step',
'scaling': true,
'bootstrap': false,
'color-fill': true,
'internal-names': false,
'selectable': true,
'collapsible': true,
'left-right-spacing': 'fixed-step', //'fit-to-size',
'top-bottom-spacing': 'fixed-step',
'left-offset': 0,
'show-scale': 'top',
// currently not implemented to support any other positioning
'draw-size-bubbles': false,
Expand Down Expand Up @@ -87,6 +89,7 @@ d3.layout.phylotree = function(container) {

nodes = [],
links = [],
partitions = [],
x_coord = function(d) {
return d.y
},
Expand Down Expand Up @@ -130,7 +133,7 @@ d3.layout.phylotree = function(container) {
right_most_leaf = 0,
label_width = 0,
radial_center = 0,
radius = 0,
radius = 1,
radius_pad_for_bubbles = 0,
radial_mapper = function(r, a) {
return {
Expand Down Expand Up @@ -243,9 +246,11 @@ d3.layout.phylotree = function(container) {


if (is_leaf) {

var _node_span = node_span(a_node) / rescale_node_span;

x = a_node.x = x + separation(last_node, a_node) + (last_span + _node_span) * 0.5;

_extents[1][1] = Math.max(_extents[1][1], a_node.y);
_extents[1][0] = Math.min(_extents[1][0], a_node.y - _node_span * 0.5);

Expand All @@ -254,9 +259,12 @@ d3.layout.phylotree = function(container) {
} else {
_extents[0][1] = Math.max(_extents[0][1], x + _node_span * 0.5 + separation(last_node, a_node));
}

last_node = a_node;
last_span = _node_span;

} else {

var count_undefined = 0;
if (d3_phylotree_is_node_collapsed(a_node) && !is_under_collapsed_parent) {

Expand Down Expand Up @@ -333,7 +341,6 @@ d3.layout.phylotree = function(container) {

shown_font_size = Math.min(font_size, scales[0]);


function do_lr() {

if (phylotree.radial() && at_least_one_dimension_fixed) {
Expand All @@ -342,19 +349,20 @@ d3.layout.phylotree = function(container) {

if (options['left-right-spacing'] == 'fixed-step') {
size[1] = max_depth * fixed_width[1];
scales[1] = (size[1] - offsets[1]) / _extents[1][1];
scales[1] = (size[1] - offsets[1] - options["left-offset"]) / _extents[1][1];
label_width = phylotree._label_width(shown_font_size);
} else {
label_width = phylotree._label_width(shown_font_size);
at_least_one_dimension_fixed = true;

var available_width = size[1] - offsets[1];
var available_width = size[1] - offsets[1] - options["left-offset"];
if (available_width * 0.5 < label_width) {
shown_font_size *= available_width * 0.5 / label_width;
label_width = available_width * 0.5;
}

scales[1] = (size[1] - offsets[1] - label_width) / _extents[1][1];
scales[1] = (size[1] - offsets[1] - options["left-offset"] - label_width) / _extents[1][1];

}
}

Expand Down Expand Up @@ -495,7 +503,6 @@ d3.layout.phylotree = function(container) {
d.x *= scales[0];
d.y *= scales[1];


if (d3_phylotree_is_leafnode(d)) {
right_most_leaf = Math.max(right_most_leaf, d.y + phylotree.node_bubble_size(d));
}
Expand Down Expand Up @@ -536,7 +543,7 @@ d3.layout.phylotree = function(container) {

} else {
domain_limit = _extents[1][1];
range_limit = (size[1] - offsets[1]);
range_limit = (size[1] - offsets[1] - options["left-offset"]);
}


Expand Down Expand Up @@ -617,7 +624,7 @@ d3.layout.phylotree = function(container) {
}

phylotree.pad_width = function() {
return offsets[1] + label_width;
return offsets[1] + options["left-offset"] + label_width;
}

phylotree.descendants = function(n) {
Expand Down Expand Up @@ -806,7 +813,7 @@ d3.layout.phylotree = function(container) {

phylotree.style_edges = function(attr) {
if (!arguments.length) return edge_styler;
edge_styler = attr;
edge_styler = attr.bind(this);
return phylotree;
};

Expand Down Expand Up @@ -1599,7 +1606,7 @@ d3.layout.phylotree = function(container) {
.attr("class", css_classes["tree-container"]);

enclosure.attr("transform", function(d) {
return d3_phylotree_svg_translate([offsets[1], phylotree.pad_height()]);
return d3_phylotree_svg_translate([offsets[1] + options["left-offset"], phylotree.pad_height()]);
});

if (draw_scale_bar) {
Expand All @@ -1608,7 +1615,7 @@ d3.layout.phylotree = function(container) {
scale_bar.attr("class", css_classes["tree-scale-bar"])
.style("font-size", "" + scale_bar_font_size)
.attr("transform", function(d) {
return d3_phylotree_svg_translate([offsets[1], phylotree.pad_height() - 10]);
return d3_phylotree_svg_translate([offsets[1] + options["left-offset"], phylotree.pad_height() - 10]);
})
.call(draw_scale_bar);
scale_bar.selectAll("text")
Expand Down Expand Up @@ -1765,7 +1772,7 @@ d3.layout.phylotree = function(container) {
.attr("class", css_classes["tree-selection-brush"]);

var brush_object = d3.svg.brush()
.x(d3.scale.identity().domain([0, sizes[0] - offsets[1]]))
.x(d3.scale.identity().domain([0, sizes[0] - offsets[1] - options["left-offset"]]))
.y(d3.scale.identity().domain([0, sizes[1] - phylotree.pad_height()]))
.on("brush", function() {
var extent = d3.event.target.extent(),
Expand Down Expand Up @@ -1804,6 +1811,8 @@ d3.layout.phylotree = function(container) {
}

phylotree.refresh = function() {
var self = this;

var enclosure = svg.selectAll("." + css_classes["tree-container"]);

var edges = enclosure.selectAll(d3_phylotree_edge_css_selectors(css_classes));
Expand Down Expand Up @@ -1884,6 +1893,7 @@ d3.layout.phylotree = function(container) {
}

phylotree.draw_edge = function(container, edge, transition) {

container = d3.select(container);

container.attr("class", phylotree.reclass_edge)
Expand All @@ -1893,7 +1903,6 @@ d3.layout.phylotree = function(container) {

var new_branch_path = draw_branch([edge.source, edge.target]);


if (transition) {
if (container.datum().existing_path) {
container.attr("d", function(d) {
Expand Down Expand Up @@ -2062,6 +2071,29 @@ d3.layout.phylotree = function(container) {
return nodes;
}

phylotree.get_node_by_name = function(name) {
return _.findWhere(nodes, {name : name});
}


phylotree.assign_attributes = function(attributes) {
//return nodes;
// add annotations to each matching node
_.each(nodes, function(d) {
if(_.indexOf(_.keys(attributes), d.name) >= 0) {
d["annotations"] = attributes[d.name];
}
});

}

phylotree.set_partitions = function(partitions) {
this.partitions = partitions;
}

phylotree.get_partitions = function(attributes) {
return this.partitions;
}

d3.rebind(phylotree, d3_hierarchy, "sort", "children", "value");

Expand Down

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