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README.md

Coloring clades

This is an example of using phylotree.js using css.

The Newick string is loaded from a file using an asynchronous d3.text call.

Raw
index.html
<!DOCTYPE html>
<html lang = 'en'>
<head>
<meta charset="utf-8">
<!-- Latest compiled and minified CSS -->
<script src="http://code.jquery.com/jquery.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script>
<link rel="stylesheet" href="http://netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap.min.css">
<link href="//netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
<!-- Optional theme -->
<link rel="stylesheet" href="http://netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap-theme.min.css">
<!-- Latest compiled and minified JavaScript -->
<script src="http://netdna.bootstrapcdn.com/bootstrap/3.0.0/js/bootstrap.min.js"></script>
<!-- <meta name="viewport" content="width=device-width, initial-scale=1.0">-->
<script src="http://d3js.org/d3.v3.min.js"></script>
<script src="phylotree.js"></script>
<link href="phylotree.css" rel="stylesheet">
<style>
.fa-rotate-45 {
-webkit-transform: rotate(45deg);
-moz-transform: rotate(45deg);
-ms-transform: rotate(45deg);
-o-transform: rotate(45deg);
transform: rotate(45deg);
}
.fa-rotate-135 {
-webkit-transform: rotate(135deg);
-moz-transform: rotate(135deg);
-ms-transform: rotate(135deg);
-o-transform: rotate(135deg);
transform: rotate(135deg);
}
.clade {
fill :white;
stroke :white;
}
</style>
</head>
<body style = 'padding-top: 70px;'>
<!--
###############################################################################################################################
-->
<nav class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container-fluid">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">phylotree.js</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Newick <b class="caret"></b></a>
<ul class="dropdown-menu">
<li><a href="#" data-toggle="modal" data-target="#newick_modal">Input Text</a></li>
<li><a href="#"><input type="file" id="newick_file"/></a></li>
<li class="divider"></li>
<li><a href="#" data-toggle="modal" data-target="#newick_export_modal">Export</a></li>
</ul>
</li>
<!--<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Display options <b class="caret"></b></a>
<ul class="dropdown-menu">
<li><a href="#" id = 'display_dengrogram'>Dendrogram</a></li>
<li><a href="#" id = 'display_tree'>Tree</a></li>
<li class="divider"></li>
<li><a href="#">Horizontal</a></li>
<li><a href="#">Vertical</a></li>
</ul>
</li>-->
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Examples <b class="caret"></b></a>
<ul class="dropdown-menu">
<li><a href="#" id = "example_hiv_scaled" >HIV-1 RT</a></li>
<li><a href="#" id = "example_influenza_color">Unscaled IAV HA colored by host</a></li>
<li><a href="#" id = "example_NGS" >NGS copy diversity</a></li>
<li><a href="#" id = "example_GVZ" >Compare NGS consensus</a></li>
<li><a href="#" id = "example_hiv_compartments" >HIV-1 env multiple timepoints and compartments</a></li>
</ul>
</li>
</ul>
<div class="form-group navbar-form navbar-right">
<input type="text" id = 'branch_filter' class="form-control" placeholder="Filter branches on">
</div>
<div class="row">
<div class="col-md-5 navbar-right ">
<div class="navbar-form " role="search">
<div class="input-group">
<span class="input-group-btn">
<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
Tag <span class="caret"></span>
</button>
<ul class="dropdown-menu" id = "selection_name_dropdown">
<li id = "selection_new"><a href="#">New selection set</a></li>
<li id = "selection_delete" class = "disabled"><a href="#">Delete selection set</a></li>
<li id = "selection_rename"><a href="#">Rename selection set</a></li>
<li class="divider"></li>
</ul>
</span>
<input type="text" class="form-control" value = "Foreground" id = "selection_name_box" disabled>
<span class="input-group-btn" id = "save_selection_name" style = "display: none" >
<button type="button" class="btn btn-default" id = "cancel_selection_button" >
Cancel
</button>
<button type="button" class="btn btn-default" id = "save_selection_button">
Save
</button>
</span>
<span class="input-group-btn">
<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection <span class="caret"></span></button>
<ul class="dropdown-menu">
<li><a href="#" id = "filter_add">Add filtered nodes to selection</a></li>
<li><a href="#" id = "filter_remove">Remove filtered nodes from selection</a></li>
<li class="divider"></li>
<li><a href="#" id = "select_all">Select all</a></li>
<li><a href="#" id = "select_all_internal">Select all internal nodes</a></li>
<li><a href="#" id = "select_all_leaves">Select all leaf nodes</a></li>
<li><a href="#" id = "clear_internal">Clear all internal nodes</a></li>
<li><a href="#" id = "clear_leaves">Clear all leaves</a></li>
<li><a href="#" id = "select_none">Clear selection</a></li>
<li class="divider"></li>
<li><a href="#" id = "mp_label">Label internal nodes using maximum parsimony</a></li>
<li><a href="#" id = "and_label">Label internal nodes using conjunction (AND) </a></li>
<li><a href="#" id = "or_label">Label internal nodes using disjunction (OR) </a></li>
</ul>
</span>
</div>
</div>
</div>
</div>
</div><!-- /.navbar-collapse -->
</div><!-- /.container-fluid -->
</nav>
<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 -->
<div class="modal" id = 'newick_export_modal'>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-body" id = 'newick_body'>
<textarea id = 'nwk_export_spec' autofocus = true placeholder = "" style = 'width: 100%; height: 100%' rows = 20></textarea>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
</div>
</div><!-- /.modal-content -->
</div><!-- /.modal-dialog -->
</div><!-- /.modal -->
<div class = 'container' id = "main_display">
<div class = 'row'>
<div class = 'col-md-12'>
<div class="btn-toolbar" role="toolbar">
<div class="btn-group">
<button type="button" class="btn btn-default btn-sm" data-direction = 'vertical' data-amount = '1' title = "Expand vertical spacing">
<i class="fa fa-arrows-v" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" data-direction = 'vertical' data-amount = '-1' title = "Compress vertical spacing">
<i class="fa fa-compress fa-rotate-135" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" data-direction = 'horizontal' data-amount = '1' title = "Expand horizonal spacing">
<i class="fa fa-arrows-h" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" data-direction = 'horizontal' data-amount = '-1' title = "Compress horizonal spacing">
<i class="fa fa-compress fa-rotate-45" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" id = "sort_ascending" title = "Sort deepest clades to the bototm">
<i class="fa fa-sort-amount-asc" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" id = "sort_descending" title = "Sort deepsest clades to the top">
<i class="fa fa-sort-amount-desc" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" id = "sort_original" title = "Restore original order">
<i class="fa fa-sort" ></i>
</button>
</div>
<div class="btn-group" data-toggle="buttons">
<label class="btn btn-default active btn-sm">
<input type="radio" name="options" class = "phylotree-layout-mode" data-mode = "linear" autocomplete="off" checked title = "Layout left-to-right"> Linear
</label>
<label class="btn btn-default btn-sm">
<input type="radio" name="options" class = "phylotree-layout-mode" data-mode = "radial" autocomplete="off" title = "Layout radially"> Radial
</label>
</div>
<div class="btn-group" data-toggle="buttons">
<label class="btn btn-default active btn-sm">
<input type="radio" class = "phylotree-align-toggler" data-align = "left" name="options-align" autocomplete="off" checked title = "Align tips labels to branches">
<i class="fa fa-align-left" ></i>
</input>
</label>
<label class="btn btn-default btn-sm">
<input type="radio" class = "phylotree-align-toggler" data-align = "right" name="options-align" autocomplete="off" title = "Align tips labels to the edge of the plot">
<i class="fa fa-align-right" ></i>
</input>
</label>
</div>
<label class = "pull-right">Selected <span class="badge" id = "selected_branch_counter">0</span> and filtered <span class="badge" id = "selected_filtered_counter">0</span> branches</label>
</div>
</div>
</div>
<div class = 'row'>
<div class = 'col-md-12'>
<div id = 'tree_container' class = 'tree-widget'>
</div>
</div>
</div>
</div>
<!--
###############################################################################################################################
-->
<script>
$('#newick_export_modal').on('show.bs.modal', function (e) {
$('textarea[id$="nwk_export_spec"]').val(
tree.get_newick (
function (node) {
var tags = [];
selection_set.forEach (function (d) { if (node[d]) {tags.push(d)}; });
if (tags.length) {
return "{" + tags.join (",") + "}";
}
return "";
}
)
);
})
$("#newick_file").on ("change", function (e) {
var files = e.target.files; // FileList object
if (files.length == 1) {
var f = files[0];
var reader = new FileReader();
reader.onload = (function(theFile) {
return function(e) {
var res = d3_phylotree_newick_parser (e.target.result);
if (res["json"]) {
if (!("children" in res["json"])) {
res["error"] = "Empty tree";
}
}
var warning_div = d3.select ("#main_display").insert ("div", ":first-child");
if (res["error"]) {
warning_div.attr ("class", "alert alert-danger alert-dismissable")
.html ("<strong>Newick parser error for file " + f.name +": </strong> In file " + res["error"]);
} else {
default_tree_settings ();
tree (res).svg (svg).layout();
warning_div.attr ("class", "alert alert-success alert-dismissable")
.html ("Loaded a tree from file <strong>" + f.name +": </strong>");
}
warning_div.append ("button")
.attr ("type", "button")
.attr ("class", "close")
.attr ("data-dismiss", "alert")
.attr ("aria-hidden", "true")
.html ("&times;");
};
})(f);
reader.readAsText(f);
}
});
$("#display_tree").on ("click", function (e) {
tree.options ({'branches' : 'straight'}, true);
});
$("#mp_label").on ("click", function (e) {
tree.max_parsimony (true);
});
$ ("[data-direction]").on ("click", function (e) {
var which_function = $(this).data ("direction") == 'vertical' ? tree.spacing_x : tree.spacing_y;
which_function (which_function () + (+ $(this).data ("amount"))).update();
});
$(".phylotree-layout-mode").on ("change", function (e) {
if ($(this).is(':checked')) {
if (tree.radial () != ($(this).data ("mode") == "radial")) {
tree.radial (!tree.radial ()).placenodes().update ();
}
}
});
$(".phylotree-align-toggler").on ("change", function (e) {
if ($(this).is(':checked')) {
if (tree.align_tips ($(this).data ("align") == "right")) {
tree.placenodes().update ();
}
}
});
function sort_nodes (asc) {
tree.traverse_and_compute (function (n) {
var d = 1;
if (n.children && n.children.length) {
d += d3.max (n.children, function (d) { return d["count_depth"];});
}
n["count_depth"] = d;
});
tree.resort_children (function (a,b) {
return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1);
});
}
$("#sort_original").on ("click", function (e) {
tree.resort_children (function (a,b) {
return a["original_child_order"] - b["original_child_order"];
});
});
$("#sort_ascending").on ("click", function (e) {
sort_nodes (true);
});
$("#sort_descending").on ("click", function (e) {
sort_nodes (false);
});
$("#and_label").on ("click", function (e) {
tree.internal_label (function (d) { return d.reduce (function (prev, curr) { return curr[current_selection_name] && prev; }, true)}, true);
});
$("#or_label").on ("click", function (e) {
tree.internal_label (function (d) { return d.reduce (function (prev, curr) { return curr[current_selection_name] || prev; }, false)}, true);
});
$("#filter_add").on ("click", function (e) {
tree.modify_selection (function (d) { return d.tag || d[current_selection_name];}, current_selection_name, false, true)
.modify_selection (function (d) { return false; }, "tag", false, false);
});
$("#filter_remove").on ("click", function (e) {
tree.modify_selection (function (d) { return !d.tag;});
});
$("#select_all").on ("click", function (e) {
tree.modify_selection (function (d) { return true;});
});
$("#select_all_internal").on ("click", function (e) {
tree.modify_selection (function (d) { return !d3_phylotree_is_leafnode (d.target);});
});
$("#select_all_leaves").on ("click", function (e) {
tree.modify_selection (function (d) { return d3_phylotree_is_leafnode (d.target);});
});
$("#select_none").on ("click", function (e) {
tree.modify_selection (function (d) { return false;});
});
$("#clear_internal").on ("click", function (e) {
tree.modify_selection (function (d) { return d3_phylotree_is_leafnode (d.target) ? d.target[current_selection_name] : false;});
});
$("#clear_leaves").on ("click", function (e) {
tree.modify_selection (function (d) { return !d3_phylotree_is_leafnode (d.target) ? d.target[current_selection_name] : false;});
});
$("#display_dengrogram").on ("click", function (e) {
tree.options ({'branches' : 'step'}, true);
});
// phylotree.modify_selection = function (callback, attr, place, skip_refresh, mode) {
$("#branch_filter").on ("input propertychange", function (e) {
var filter_value = $(this).val();
var rx = new RegExp (filter_value,"i");
tree.modify_selection (function (n) {
return filter_value.length && (tree.branch_name () (n.target).search (rx)) != -1;
},"tag");
});
$("#validate_newick").on ("click", function (e) {
var res = d3_phylotree_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 {
default_tree_settings ();
tree (res).svg (svg).layout();
$('#newick_modal').modal('hide');
}
});
function default_tree_settings () {
tree.branch_length (null);
tree.branch_name (null);
tree.node_span ('equal');
tree.options ({'draw-size-bubbles' : false}, false);
//tree.radial (true);
tree.style_nodes (node_colorizer);
tree.style_edges (edge_colorizer);
tree.selection_label (current_selection_name);
}
$("#example_hiv_scaled").on ("click", function (e) {
var hiv_tree = 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var res = d3_phylotree_newick_parser ( hiv_tree );
default_tree_settings ();
tree (res).svg (svg).layout();
});
function update_controls () {
$("[data-mode='" + (tree.radial() ? 'radial' : 'linear') + "']").click();
$("[data-align='" + (tree.align_tips () ? 'right' : 'left') + "']").click();
}
$("#example_hiv_compartments").on ("click", function (e) {
var hiv_tree = "((((NM487|20020117|CSF|1|env|21|1.05:0.00293,(NM487|20020117|CSF|1|env|0|22.65:0.00055,((NM487|20020128|CSF|2|env|3074|1.36:0.0,NM487|20020128|CSF|1|env|3057|1.24:0.0):0.00055,NM487|20020103|PBMC|1|env|81|1.01:0.00055)0.896:0.00055)0.840:0.00409)0.656:0.00587,NM487|20020117|CSF|1|env|13|0.95:0.00300)0.255:0.00053,NM487|20020117|CSF|1|env|4|1.10:0.00300)0.331:0.00055,NM487|20020128|CSF-PELLET|1|env|0|37.88:0.00055,((NM487|20020128|CSF|2|env|0|10.49:0.0,NM487|20020128|CSF|1|env|0|10.60:0.0):0.00055,((((NM487|20020128|CSF|2|env|111|1.28:0.0,NM487|20020128|CSF|1|env|111|1.27:0.0):0.00829,((NM487|20020128|CSF|2|env|41|4.05:0.0,NM487|20020128|CSF|1|env|41|4.15:0.0):0.00054,(NM487|20020128|CSF-PELLET|1|env|40|4.21:0.0,NM487|20020117|CSF|1|env|5|1.20:0.0):0.00055)0.978:0.00050)0.890:0.00303,(((NM487|20020128|CSF|2|env|54|1.22:0.0,NM487|20020128|CSF|1|env|54|1.21:0.0):0.00055,NM487|20020117|CSF|1|env|19|2.76:0.00055)0.904:0.00278,(NM487|20020103|PBMC|1|env|26|2.32:0.00303,((NM487|20020128|CSF|1|env|59|0.93:0.00055,(((NM487|20020128|BP|1|env|40|2.31:0.00055,NM487|20020128|BP|1|env|20|1.72:0.00279)0.993:0.01716,NM487|20020128|BP|1|env|27|0.56:0.00243)0.702:0.01285,NM487|20020128|CSF-PELLET|1|env|56|0.78:0.00548)0.979:0.00051)0.315:0.00053,(NM487|20020117|CSF|1|env|20|1.05:0.00303,((NM487|20020117|BP|1|env|59|0.45:0.0,NM487|20020117|CSF|1|env|6|15.58:0.0):0.00055,(NM487|20020128|CSF|2|env|59|0.87:0.00055,(((NM487|20020128|CSF|2|env|82|1.75:0.0,NM487|20020128|CSF|1|env|82|1.80:0.0):0.00055,(((NM487|20020128|BP|1|env|2749|0.61:0.00055,NM487|20020117|BP|1|env|8|1.02:0.00301)0.851:0.00279,(NM487|20020128|BP|1|env|2790|0.94:0.00281,(NM487|20020128|CSF-PELLET|1|env|66|0.87:0.00055,(((NM487|20020103|PBMC|1|env|55|1.33:0.00055,NM487|20020128|CSF-PELLET|1|env|62|0.82:0.00055)0.861:0.00282,(((NM487|20020128|PBMC|1|env|8|8.33:0.00349,((NM487|20020128|PBMC|1|env|31|1.70:0.02485,NM487|20020128|PBMC|1|env|34|0.78:0.00054)0.940:0.01527,NM487|20020128|PBMC|1|env|33|0.79:0.03194)0.754:0.00402)0.941:0.02781,((NM487|20020128|PBMC|1|env|92|1.19:0.00316,NM487|20020128|PBMC|1|env|43|1.00:0.00303)0.935:0.01805,NM487|20020128|PBMC|1|env|10|6.24:0.01423)0.878:0.02383)0.999:0.07655,(NM487|20020128|PBMC|1|env|38|0.91:0.01340,(NM487|20020128|PBMC|1|env|9|4.34:0.00055,NM487|20020128|PBMC|1|env|0|0.70:0.01863)0.883:0.01055)0.984:0.04877)1.000:0.09435)1.000:0.00053,((((NM487|20020103|PBMC|1|env|23|1.64:0.01157,(((NM487|20020128|CSF-PELLET|1|env|37|0.75:0.0,NM487|20020117|BP|1|env|21|0.65:0.0):0.00908,((NM487|20020103|PBMC|1|env|99|0.66:0.00054,((((NM487|20020128|CSF-PELLET|1|env|12|1.09:0.0,NM487|20020117|BP|1|env|9|0.54:0.0):0.00055,(NM487|20020128|BP|1|env|2767|1.72:0.00055,NM487|20020128|BP|1|env|28|1.44:0.00866)0.913:0.00055)0.965:0.01080,NM487|20020117|BP|1|env|24|0.68:0.00055)0.124:0.00054,(NM487|20020128|CSF-PELLET|1|env|38|1.33:0.0,NM487|20020117|BP|1|env|18|3.46:0.0,NM487|20020117|CSF|1|env|15|1.10:0.0):0.00302)0.828:0.00355)0.833:0.00354,NM487|20020103|PBMC|1|env|106|0.98:0.00055)0.854:0.00353)0.115:0.00053,NM487|20020103|PBMC|1|env|2|1.62:0.00055)0.829:0.00354)0.948:0.00054,NM487|20020103|PBMC|1|env|255|0.57:0.00055)0.919:0.00055,((((NM487|20020128|CSF|2|env|62|2.60:0.0,NM487|20020128|CSF|1|env|62|2.64:0.0):0.00055,((NM487|20020128|CSF|2|env|36|1.14:0.0,NM487|20020128|CSF|1|env|36|1.13:0.0):0.00221,(NM487|20020117|BP|1|env|10|4.48:0.0,NM487|20020117|CSF|1|env|1|2.71:0.0):0.00055)0.321:0.00059)0.635:0.01578,(NM487|20020117|BP|1|env|97|0.45:0.00604,NM487|20020117|BP|1|env|13|0.40:0.00055)0.762:0.00300)0.232:0.00055,((NM487|20020117|BP|1|env|14|0.43:0.00301,(NM487|20020128|BP|1|env|2752|3.14:0.00054,NM487|20020128|CSF-PELLET|1|env|1|8.27:0.00055)0.699:0.00069)0.622:0.00158,NM487|20020128|BP|1|env|13|2.81:0.00055)0.999:0.00051)0.960:0.01011)0.831:0.00264,(NM487|20020103|PBMC|1|env|152|0.55:0.01500,NM487|20020103|PBMC|1|env|4|0.87:0.01185)0.903:0.00055)0.859:0.00265)0.827:0.00263)0.825:0.00263)1.000:0.00054)0.801:0.00298,NM487|20020128|BP|1|env|2773|0.76:0.00288)0.988:0.01722)0.297:0.00051,NM487|20020128|CSF-PELLET|1|env|15|2.48:0.00055)0.260:0.00055)0.367:0.00050)0.444:0.00051)0.489:0.01342)0.749:0.00341)0.937:0.00055)0.845:0.00055)0.648:0.00055,(NM487|20020128|CSF|2|env|33|16.42:0.0,NM487|20020128|CSF|1|env|33|16.53:0.0):0.00055)0.874:0.00051)0.231:0.00055)";
default_tree_settings ();
tree.radial (true);
tree.align_tips (true);
tree.branch_name (function (data) {
if (data.children) {
return "";
} else {
bits = data.name.split ('|');
if (bits.length >= 6) {
return bits[0] + " [" + bits[1] + "] " + bits[2];
}
return data.name;
}
});
tree (d3_phylotree_newick_parser (hiv_tree)).svg (svg).layout();
update_controls ();
});
$("#example_influenza_color").on ("click", function (e) {
var flu_tree = 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002_H5N1_segment_4:0.00549839256281252,(gi_115502990_gb_DQ997377_1_Influenza_A_virus_A_chicken_Jilin_hf_2002_H5N1_segment_4:0.003730202066910738,(gi_115502941_gb_DQ997156_1_Influenza_A_virus_A_chicken_Hubei_wo_2003_H5N1_segment_4:0.01412399896869351,((gi_85062564_gb_DQ343150_1_Influenza_A_virus_A_chicken_Hebei_326_2005_H5N1_hemagglutinin_HA_gene:0.0119832032416233,gi_117414797_gb_DQ914814_1_Influenza_A_virus_A_chicken_Shanxi_2_2006_H5N1_segment_4:0.02646581670056432):0.01769230714106282,(gi_116271242_gb_DQ992802_1_Influenza_A_virus_A_duck_Yunnan_5236_2005_H5N1_hemagglutinin_HA_gene:0.009792926891152985,gi_116271226_gb_DQ992794_1_Influenza_A_virus_A_goose_Yunnan_3315_2005_H5N1_hemagglutinin_HA_gene:0.005533019462053305):0.005744816263230659):0):0.007231174873218021):0.006995706222144872):0.001737446897022598):0.002021056990540436,(((gi_84797149_gb_DQ320883_1_Influenza_A_virus_A_duck_Guangxi_1311_2004_H5N1_hemagglutinin_HA_gene:0,gi_84797161_gb_DQ320889_1_Influenza_A_virus_A_goose_Guangxi_2112_2004_H5N1_hemagglutinin_HA_gene:0):0.001754122782637976,gi_84797157_gb_DQ320887_1_Influenza_A_virus_A_duck_Guangxi_1793_2004_H5N1_hemagglutinin_HA_gene:0):0.009191254905631475,gi_71000185_dbj_AB212280_1_Influenza_A_virus_A_duck_Yokohama_aq10_2003_H5N1_HA_gene_for_hemagglutinin:0.007412816692354494):0.003236971178251705):0):0,gi_115397012_gb_DQ997308_1_Influenza_A_virus_A_chicken_Jilin_hh_2002_H5N1_hemagglutinin_HA_gene:0.001753119532114087):0.001816732100401747,(gi_101918580_dbj_AB259712_1_Influenza_A_virus_A_duck_Hokkaido_Vac_1_04_H5N1_genomic_RNA:0.005232751641785671,gi_109452300_dbj_AB263192_1_Influenza_A_virus_A_R_duck_Mongolia_54_01_duck_Mongolia_47_01_H5N1_genomic_RNA:0):0.07044093106693458):0.001723190782503228,gi_115502957_gb_DQ997268_1_Influenza_A_virus_A_chicken_Jilin_ha_2003_H5N1_segment_4:0.008922628548613474):0.00170676096400408,(gi_19697757_gb_AY059474_1_Influenza_A_virus_A_Goose_Hong_Kong_ww26_2000_H5N1_segment_4_hemagglutinin_HA_gene:0.001713731003501752,gi_19697759_gb_AY059475_1_Influenza_A_virus_A_Goose_Hong_Kong_ww28_2000_H5N1_segment_4_hemagglutinin_HA_gene:0):0.003450010292730959):0,((((gi_21359659_gb_AF468837_1_Influenza_A_virus_A_Duck_Anyang_AVL_1_2001_H5N1_hemagglutinin_H5_H5_gene:0.003500645154619918,gi_115527004_gb_DQ997522_1_Influenza_A_virus_A_goose_Guangdong_xb_2001_H5N1_segment_4:0.006873622954156017):0.001712727752977863,gi_85062568_gb_DQ343152_1_Influenza_A_virus_A_chicken_Hebei_108_02_H5N1_hemagglutinin_HA_gene:0.01228531746654179):0,gi_58374179_gb_AY854190_1_Influenza_A_virus_A_duck_Shandong_093_2004_H5N1_segment_4:0.005238169550378956):0.003443369809696002,gi_116583103_gb_DQ997538_1_Influenza_A_virus_A_chicken_Jilin_xv_2002_H5N1_hemagglutinin_HA_gene:0):0.003479506662947322):0.00181199504389235,(((gi_9863931_gb_AF216737_1_AF216737_Influenza_A_virus_A_Environment_Hong_Kong_437_10_99_H5N1_hemagglutinin_5_gene:0.001725835220679303,gi_9863913_gb_AF216729_1_AF216729_Influenza_A_virus_A_Environment_Hong_Kong_437_8_99_H5N1_hemagglutinin_5_gene:0.003478758783969347):0,gi_9863876_gb_AF216713_1_AF216713_Influenza_A_virus_A_Environment_Hong_Kong_437_4_99_H5N1_hemagglutinin_5_gene:0.001726021381335435):0,gi_9863895_gb_AF216721_1_AF216721_Influenza_A_virus_A_Environment_Hong_Kong_437_6_99_H5N1_hemagglutinin_5_gene:0.001725835220679303):0.007059043784511681):0.003388649089806319,gi_115503009_gb_DQ997547_1_Influenza_A_virus_A_chicken_Jilin_xw_2003_H5N1_segment_4:0):0.001721598007336999,gi_115382830_gb_DQ997133_1_Influenza_A_virus_A_chicken_Hubei_wl_1997_H5N1_segment_4:0.00521837847365329):0.003474838797059389):0,(((gi_4240437_gb_AF082035_1_Influenza_A_virus_A_Chicken_Hong_Kong_786_97_H5N1_hemagglutinin_H5_mRNA:0,gi_4240435_gb_AF082034_1_Influenza_A_virus_A_Chicken_Hong_Kong_728_97_H5N1_hemagglutinin_H5_mRNA:0.001733707092688165):0,((gi_3068720_gb_AF057291_1_AF057291_Influenza_A_virus_A_chicken_Hong_Kong_258_97_H5N1_hemagglutinin_mRNA:0.001733707092688165,(gi_86753755_gb_DQ366306_1_Influenza_A_virus_A_duck_Vietnam_1_2005_H5N1_hemagglutinin_mRNA:0.01506376995644411,gi_86753759_gb_DQ366322_1_Influenza_A_virus_A_duck_Vietnam_8_05_H5N1_hemagglutinin_mRNA:0.03873457055623361):0.009942760047882547):0,gi_86753757_gb_DQ366314_1_Influenza_A_virus_A_goose_Vietnam_3_05_H5N1_hemagglutinin_mRNA:0.001735713593735941):0.00173131949665679):0.001874828124024311,(gi_6048756_gb_AF098543_1_AF098543_Influenza_A_virus_A_Duck_Hong_Kong_p46_97_H5N1_hemagglutinin_gene:0,gi_6048760_gb_AF098545_1_AF098545_Influenza_A_virus_A_Goose_Hong_Kong_w355_97_H5N1_hemagglutinin_gene:0.00173842554186335):0.00159343086596657):0.01069237564731552):0.005156783435137814):0.)";
var res = d3_phylotree_newick_parser ( flu_tree );
default_tree_settings ();
tree.branch_length (function (n) {return undefined;});
var year_re = new RegExp ("_virus_A_([^_]+)"),
color_scale = d3.scale.category20();
tree.branch_name (function (d) {
var n = d.name.split ('_');
if (n.length > 13) {
return [n[9],n[10],n[12]].join (" ");
}
return n.join ("_");
});
tree.style_nodes (function (element, data) {
var m = (tree.branch_name () (data)).split (" ");
if (m.length > 1) {
element.style ("fill", color_scale(m[0]));
}
node_colorizer (element, data);
});
tree.style_edges (function (element, data) {
var m = (tree.branch_name () (data.target)).split (" ");
if (m.length > 1) {
element.style ("stroke", color_scale(m[0]));
}
edge_colorizer (element, data);
});
tree (res).svg (svg).layout();
});
$("#example_NGS").on ("click", function (e) {
var NGS = "((((((((((((((cluster_0_845:0.004893613603717699,cluster_1_109:0.004840816381616456)Node13:0,cluster_3_38:0.004857835778111792)Node12:0,(cluster_6_632:0,cluster_8_53:0)Node17:0)Node11:0,cluster_21_36:0.004879782649604827)Node10:0,cluster_72_37:0.004811683649331113)Node9:0,cluster_130_63:0.004864609127112797)Node8:0,cluster_144_67:0.004856896737854473)Node7:0,cluster_164_38:0.009738706927375622)Node6:0,cluster_201_67:0.004912342010654071)Node5:0,cluster_229_35:0.004811683644837275)Node4:0,cluster_230_36:0.004893613604419758)Node3:0,cluster_295_43:0.004811683649588835)Node2:0,cluster_306_33:0.004888242085157596)Node1:0,cluster_397_62:0.004938437463580042,cluster_524_39:0.0049142477452619)";
var res = d3_phylotree_newick_parser ( NGS );
var re = new RegExp("_([0-9]+)$"),
l10 = Math.log (10);
default_tree_settings ();
tree.node_span (function (a) { var m = re.exec (a.name); try {return Math.sqrt(parseFloat (m[1]))} catch (e) {} return null;});
tree.options ({'draw-size-bubbles' : true}, false);
tree (res).svg (svg).layout();
});
$("#example_GVZ").on ("click", function (e) {
default_tree_settings ();
function GVZ_colorizer (element, data) {
element.style ('stroke-width', 4)
.style ('stroke-linejoin', 'round')
.style ('stroke-linecap', 'round');
}
var GVZ = "(((A300_20090507_rt_PGM:0.00763,((A300_20090507_rt_miSeqR2:0.0,A300_20090507_rt_miSeqR1:0.0):0.00055,A300:0.00055)0.979:0.00055)1.000:0.03978,(A202_20081001_rt_PGM:0.00582,((A202_20081001_rt_miSeqR2:0.0,A202_20081001_rt_miSeqR1:0.0):0.00055,A202:0.00055)0.988:0.00054)0.984:0.01883)0.868:0.00764,((A158_20080617_rt_miSeqR2:0.0,A158_20080617_rt_miSeqR1:0.0,A158_20080617_rt_PGM:0.0,A158:0.0):0.03547,(((A207_20081020_rt_miSeqR2:0.0,A207_20081020_rt_miSeqR1:0.0,A207:0.0):0.00055,A207_20081020_rt_PGM:0.00055)1.000:0.03874,(A124:0.00055,((A124_20080207_rt_miSeqR2:0.0,A124_20080207_rt_miSeqR1:0.0):0.00055,A124_20080207_rt_PGM:0.00383)0.910:0.00054)0.980:0.01829)0.025:0.00507)0.737:0.00225,((((A326_20090902_rt_miSeqR2:0.0,A326_20090902_rt_miSeqR1:0.0,A326_20090902_rt_PGM:0.0):0.03017,((A364_20100120_rt_PGM:0.00585,((A364_20100120_rt_miSeqR2:0.0,A364_20100120_rt_miSeqR1:0.0):0.00055,A364:0.00055)0.829:0.00357)0.996:0.02199,(((A297_20090526_rt_miSeqR2:0.0,A297_20090526_rt_miSeqR1:0.0,A297:0.0):0.00055,A297_20090526_rt_PGM:0.00189)1.000:0.04029,((A313:0.00055,((A313_20090715_rt_miSeqR2:0.0,A313_20090715_rt_miSeqR1:0.0):0.00053,A313_20090715_rt_PGM:0.00577)0.891:0.00055)1.000:0.04241,(A318:0.00055,((A318_20090728_rt_miSeqR2:0.0,A318_20090728_rt_miSeqR1:0.0):0.00053,A318_20090728_rt_PGM:0.00582)0.884:0.00055)0.999:0.03273)0.917:0.01184)0.658:0.00196)0.923:0.00824)0.525:0.00054,((((A144_20080513_rt_miSeqR2:0.0,A144_20080513_rt_miSeqR1:0.0,A144:0.0):0.00055,A144_20080513_rt_PGM:0.00188)0.998:0.02715,(A157:0.00055,((A157_20080617_rt_miSeqR2:0.0,A157_20080617_rt_miSeqR1:0.0):0.00055,A157_20080617_rt_PGM:0.00194)0.825:0.00053)1.000:0.03065)0.912:0.01106,(((A137_20080318_rt_miSeqR2:0.0,A137_20080318_rt_miSeqR1:0.0,A137:0.0):0.00054,A137_20080318_rt_PGM:0.00575)1.000:0.05302,((A302_20090604_rt_miSeqR2:0.0,A302_20090604_rt_miSeqR1:0.0,A302:0.0):0.00054,A302_20090604_rt_PGM:0.00574)1.000:0.03598)0.745:0.00848)0.465:0.00054)0.785:0.00274,((A312_20090702_rt_miSeqR2:0.0,A312_20090702_rt_miSeqR1:0.0,A312:0.0):0.00055,A312_20090702_rt_PGM:0.00571)0.999:0.02550)0.884:0.00629)";
var res = d3_phylotree_newick_parser ( GVZ );
var colorizer = d3.scale.category10 ();
tree.branch_name (function (d) {
var n = d.name.split ('_');
if (n.length > 1) {
return n[0] + "(" + n[n.length-1] + ")";
}
return n + " (Sanger)";
});
tree.node_span ('equal');
tree.options ({'draw-size-bubbles' : false}, false);
tree.font_size (14);
tree.scale_bar_font_size (12);
tree.node_circle_size (4);
tree.spacing_x (16, true);
tree.style_edges (GVZ_colorizer);
tree.options ({'draw-size-bubbles' : false}, false);
tree (res).svg (svg).layout();
});
function node_colorizer (element, data) {
try{
var count_class = 0;
selection_set.forEach (function (d,i) { if (data[d]) {count_class ++; element.style ("fill", color_scheme(i), i == current_selection_id ? "important" : null);}});
if (count_class > 1) {
} else {
if (count_class == 0) {
element.style ("fill", null);
}
}
}
catch (e) {
}
}
function edge_colorizer (element, data) {
//console.log (data[current_selection_name]);
try {
var count_class = 0;
selection_set.forEach (function (d,i) { if (data[d]) {count_class ++; element.style ("stroke", color_scheme(i), i == current_selection_id ? "important" : null);}});
if (count_class > 1) {
element.classed ("branch-multiple", true);
} else
if (count_class == 0) {
element.style ("stroke", null)
.classed ("branch-multiple", false);
}
}
catch (e) {
}
}
var valid_id = new RegExp ("^[\\w]+$");
$("#selection_name_box").on ("input propertychange", function (e) {
var name = $(this).val();
var accept_name = (selection_set.indexOf (name) < 0) &&
valid_id.exec (name) ;
d3.select ("#save_selection_button").classed ("disabled", accept_name ? null : true );
});
$("#selection_rename > a").on ("click", function (e) {
d3.select ("#save_selection_button")
.classed ("disabled",true)
.on ("click", function (e) { // save selection handler
var old_selection_name = current_selection_name;
selection_set[current_selection_id] = current_selection_name = $("#selection_name_box").val();
if (old_selection_name != current_selection_name) {
tree.update_key_name (old_selection_name, current_selection_name);
update_selection_names (current_selection_id);
}
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['save', this]}));
});
d3.select ("#cancel_selection_button")
.classed ("disabled",false)
.on ("click", function (e) { // save selection handler
$("#selection_name_box").val(current_selection_name);
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['cancel', this]}));
});
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['rename', this]}));
e.preventDefault ();
});
$("#selection_delete > a").on ("click", function (e) {
tree.update_key_name (selection_set[current_selection_id], null)
selection_set.splice (current_selection_id, 1);
if (current_selection_id > 0) {
current_selection_id --;
}
current_selection_name = selection_set[current_selection_id];
update_selection_names (current_selection_id)
$("#selection_name_box").val(current_selection_name)
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['save', this]}));
e.preventDefault ();
});
$("#selection_new > a").on ("click", function (e) {
d3.select ("#save_selection_button")
.classed ("disabled",true)
.on ("click", function (e) { // save selection handler
current_selection_name = $("#selection_name_box").val();
current_selection_id = selection_set.length;
selection_set.push (current_selection_name);
update_selection_names (current_selection_id);
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['save', this]}));
});
d3.select ("#cancel_selection_button")
.classed ("disabled",false)
.on ("click", function (e) { // save selection handler
$("#selection_name_box").val(current_selection_name);
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['cancel', this]}));
});
send_click_event_to_menu_objects (new CustomEvent (selection_menu_element_action,
{'detail' : ['new', this]}));
e.preventDefault ();
});
function send_click_event_to_menu_objects (e) {
$("#selection_new, #selection_delete, #selection_rename, #save_selection_name, #selection_name_box, #selection_name_dropdown").get().forEach (
function (d) {
d.dispatchEvent (e);
}
);
}
function update_selection_names (id, skip_rebuild) {
skip_rebuild = skip_rebuild || false;
id = id || 0;
current_selection_name = selection_set[id];
current_selection_id = id;
if (!skip_rebuild) {
d3.selectAll (".selection_set").remove();
d3.select ("#selection_name_dropdown")
.selectAll (".selection_set")
.data (selection_set)
.enter()
.append ("li")
.attr ("class", "selection_set")
.append ("a")
.attr ("href", "#")
.text (function (d) { return d;})
.style ("color", function (d,i) {return color_scheme(i);})
.on ("click", function (d,i) {update_selection_names (i,true);});
}
d3.select ("#selection_name_box")
.style ("color", color_scheme(id))
.property ("value", current_selection_name);
tree.selection_label (selection_set[id]);
}
var width = 800, //$(container_id).width(),
height = 600, //$(container_id).height()
selection_set = ['Foreground'],
current_selection_name = $("#selection_name_box").val(),
current_selection_id = 0,
max_selections = 10;
color_scheme = d3.scale.category10(),
selection_menu_element_action = "phylotree_menu_element_action";
var tree = d3.layout.phylotree("body")
.size([height, width])
.separation (function (a,b) {return 0;})
.count_handler (function (count) {
$("#selected_branch_counter").text (function (d) {return count[current_selection_name];});
$("#selected_filtered_counter").text (count.tag);
}
);
//.node_span (function (a) {if (a.children && a.children.length) return 1; return isNaN (parseFloat (a["attribute"]) * 100) ? 1 : parseFloat (a["attribute"]) * 100; });
var test_string = "(((EELA:0.150276,CONGERA:0.213019):0.230956,(EELB:0.263487,CONGERB:0.202633):0.246917):0.094785,((CAVEFISH:0.451027,(GOLDFISH:0.340495,ZEBRAFISH:0.390163):0.220565):0.067778,((((((NSAM:0.008113,NARG:0.014065):0.052991,SPUN:0.061003,(SMIC:0.027806,SDIA:0.015298,SXAN:0.046873):0.046977):0.009822,(NAUR:0.081298,(SSPI:0.023876,STIE:0.013652):0.058179):0.091775):0.073346,(MVIO:0.012271,MBER:0.039798):0.178835):0.147992,((BFNKILLIFISH:0.317455,(ONIL:0.029217,XCAU:0.084388):0.201166):0.055908,THORNYHEAD:0.252481):0.061905):0.157214,LAMPFISH:0.717196,((SCABBARDA:0.189684,SCABBARDB:0.362015):0.282263,((VIPERFISH:0.318217,BLACKDRAGON:0.109912):0.123642,LOOSEJAW:0.397100):0.287152):0.140663):0.206729):0.222485,(COELACANTH:0.558103,((CLAWEDFROG:0.441842,SALAMANDER:0.299607):0.135307,((CHAMELEON:0.771665,((PIGEON:0.150909,CHICKEN:0.172733):0.082163,ZEBRAFINCH:0.099172):0.272338):0.014055,((BOVINE:0.167569,DOLPHIN:0.157450):0.104783,ELEPHANT:0.166557):0.367205):0.050892):0.114731):0.295021)";
var container_id = '#tree_container';
//var test_string = "(a : 0.1, (b : 0.11, (c : 0.12, d : 0.13) : 0.14) : 0.15)";
//window.setInterval (function () {});
var svg = d3.select(container_id).append("svg")
.attr("width", width)
.attr("height", height);
function selection_handler_name_box (e) {
var name_box = d3.select (this);
switch (e.detail[0]) {
case 'save':
case 'cancel':
name_box.property ("disabled", true)
.style ("color", color_scheme(current_selection_id));
break;
case 'new':
name_box.property ("disabled", false)
.property ("value", "new_selection_name")
.style ("color", color_scheme(selection_set.length));
break;
case 'rename':
name_box.property ("disabled", false);
break;
}
}
function selection_handler_new (e) {
var element = d3.select (this);
$(this).data('tooltip', false);
switch (e.detail[0]) {
case 'save':
case 'cancel':
if (selection_set.length == max_selections) {
element.classed ("disabled", true);
$(this).tooltip ({'title' : 'Up to ' + max_selections + ' are allowed', 'placement' : 'left'});
} else {
element.classed ("disabled", null);
}
break;
default:
element.classed ("disabled", true);
break;
}
}
function selection_handler_rename (e) {
var element = d3.select (this);
element.classed ("disabled", (e.detail[0] == "save" || e.detail[0] == "cancel") ? null : true);
}
function selection_handler_save_selection_name (e) {
var element = d3.select (this);
element.style ("display", (e.detail[0] == "save" || e.detail[0] == "cancel") ? "none" : null);
}
function selection_handler_name_dropdown (e) {
var element = d3.select (this).selectAll (".selection_set");
element.classed ("disabled", (e.detail[0] == "save" || e.detail[0] == "cancel") ? null : true);
}
function selection_handler_delete (e) {
var element = d3.select (this);
$(this).tooltip('destroy');
switch (e.detail[0]) {
case 'save':
case 'cancel':
if (selection_set.length == 1) {
element.classed ("disabled", true);
$(this).tooltip ({'title' : 'At least one named selection set <br> is required;<br>it can be empty, however', 'placement' : 'bottom', 'html': true});
} else {
element.classed ("disabled", null);
}
break;
default:
element.classed ("disabled", true);
break;
}}
$( document ).ready( function () {
default_tree_settings();
tree(test_string).svg (svg).layout();
$("#selection_new").get(0).addEventListener(selection_menu_element_action,selection_handler_new,false);
$("#selection_rename").get(0).addEventListener(selection_menu_element_action,selection_handler_rename,false);
$("#selection_delete").get(0).addEventListener(selection_menu_element_action,selection_handler_delete,false);
$("#selection_delete").get(0).dispatchEvent (new CustomEvent (selection_menu_element_action,
{'detail' : ['cancel', null]}));
$("#selection_name_box").get(0).addEventListener(selection_menu_element_action,selection_handler_name_box,false);
$("#save_selection_name").get(0).addEventListener(selection_menu_element_action,selection_handler_save_selection_name,false);
$("#selection_name_dropdown").get(0).addEventListener(selection_menu_element_action,selection_handler_name_dropdown,false);
update_selection_names();
});
</script>
</body>
</html>
Raw
phylotree.css
.tree-selection-brush .extent {
fill-opacity: .05;
stroke: #fff;
shape-rendering: crispEdges;
}
.tree-scale-bar text {
font: sans-serif;
}
.tree-scale-bar line,
.tree-scale-bar path {
fill: none;
stroke: #000;
shape-rendering: crispEdges;
}
.node circle, .node ellipse, .node rect {
fill: steelblue;
stroke: black;
stroke-width: 0.5px;
}
.internal-node circle, .internal-node ellipse, .internal-node rect{
fill: #CCC;
stroke: black;
stroke-width: 0.5px;
}
.node {
font: 10px sans-serif;
}
.node-selected {
fill: #f00 !important;
}
.node-collapsed circle, .node-collapsed ellipse, .node-collapsed rect{
fill: black !important;
}
.node-tagged {
fill: #00f;
}
.branch {
fill: none;
stroke: #999;
stroke-width: 2px;
}
.clade {
fill: #1f77b4;
stroke: #444;
stroke-width: 2px;
opacity: 0.5;
}
.branch-selected {
stroke: #f00 !important;
stroke-width: 3px;
}
.branch-tagged {
stroke: #00f;
stroke-dasharray: 10,5;
stroke-width: 2px;
}
.branch-tracer {
stroke: #bbb;
stroke-dasharray: 3,4;
stroke-width: 1px;
}
.branch-multiple {
stroke-dasharray: 5, 5, 1, 5;
stroke-width: 3px;
}
.branch:hover {
stroke-width: 10px;
}
.internal-node circle:hover, .internal-node ellipse:hover, .internal-node rect:hover {
fill: black;
stroke: #CCC;
}
.tree-widget {
}
Raw
phylotree.js
(function() {
var d3_layout_phylotree_event_id = "d3.layout.phylotree.event",
d3_layout_phylotree_context_menu_id = "d3_layout_phylotree_context_menu";
d3.layout.phylotree = function(container) {
var item_selected = d3_phylotree_item_selected,
node_visible = d3_phylotree_node_visible,
node_notshown = d3_phylotree_node_notshown,
edge_visible = d3_phylotree_edge_visible,
item_tagged = d3_phylotree_item_tagged,
resize_svg = d3_phylotree_resize_svg,
is_leafnode = d3_phylotree_is_leafnode,
has_hidden_nodes = d3_phylotree_has_hidden_nodes,
is_node_collapsed = d3_phylotree_is_node_collapsed,
node_css_selectors = d3_phylotree_node_css_selectors,
edge_css_selectors = d3_phylotree_edge_css_selectors,
clade_css_selectors = d3_phylotree_clade_css_selectors,
newick_parser = d3_phylotree_newick_parser,
rootpath = d3_phylotree_rootpath,
rescale = d3_phylotree_rescale,
trigger_refresh = d3_phylotree_trigger_refresh,
trigger_count_update = d3_phylotree_trigger_count_update,
event_listener = d3_phylotree_event_listener,
add_event_listener = d3_phylotree_add_event_listener,
svg_translate = d3_phylotree_svg_translate,
svg_rotate = d3_phylotree_svg_rotate;
var self = {},
d3_hierarchy = d3.layout.hierarchy().sort(null).value(null),
size = [1, 1],
phylo_attr = [1, 1],
newick_string = null,
separation = function(_node, _previos) {
return 0;
},
node_span = function(_node) {
return 1;
},
relative_node_span = function(_node) {
return node_span(_node) / rescale_node_span;
},
def_branch_length_accessor = function(_node) {
if ("attribute" in _node && _node["attribute"] && _node["attribute"].length) {
var bl = parseFloat(_node["attribute"]);
if (!isNaN(bl)) {
return Math.max(0, bl);
}
}
//console.log ("No branch length for ", _node.name);
return undefined;
},
branch_length_accessor = def_branch_length_accessor,
def_node_label = function(_node) {
if (options['internal-names'] || d3_phylotree_is_leafnode(_node)) {
return _node.name || "";
}
return "";
},
node_label = def_node_label,
length_attribute = null,
scale_attribute = "y_scaled",
needs_redraw = true,
svg = null,
options = {
'layout': 'left-to-right',
'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,
'binary-selectable': false,
'is-radial': false,
'attribute-list': [],
'max-radius': 768,
'annular-limit': 0.38196601125010515,
'compression': 0.2,
'align-tips': false,
'maximim-per-node-spacing': 100,
'minimum-per-node-spacing': 2,
'maximim-per-level-spacing': 100,
'minimum-per-level-spacing': 10,
'node_circle_size': d3.functor(3),
'transitions': null
},
css_classes = {
'tree-container': 'phylotree-container',
'tree-scale-bar': 'tree-scale-bar',
'node': 'node',
'internal-node': 'internal-node',
'tagged-node': 'node-tagged',
'selected-node': 'node-selected',
'collapsed-node': 'node-collapsed',
'branch': 'branch',
'selected-branch': 'branch-selected',
'tagged-branch': 'branch-tagged',
'tree-selection-brush': 'tree-selection-brush',
'branch-tracer': 'branch-tracer',
'clade': 'clade',
},
nodes = [],
links = [],
partitions = [],
x_coord = function(d) {
return d.y;
},
y_coord = function(d) {
return d.x;
},
scales = [1, 1],
fixed_width = [15, 20],
font_size = 12,
scale_bar_font_size = 12,
offsets = [0, font_size],
draw_line = d3.svg.line()
.x(function(d) {
return x_coord(d);
})
.y(function(d) {
return y_coord(d);
})
.interpolate("step-before"),
draw_arc = function(points) {
var start = radial_mapper(points[0].radius, points[0].angle),
end = radial_mapper(points[0].radius, points[1].angle);
return "M " + x_coord(start) + "," + y_coord(start) + " A " + points[0].radius + "," + points[0].radius +
" 0,0, " + (points[1].angle > points[0].angle ? 1 : 0) + " " + x_coord(end) + "," + y_coord(end) +
" L " + x_coord(points[1]) + "," + y_coord(points[1]);
};
draw_branch = draw_line,
draw_scale_bar = null,
rescale_node_span = 1,
count_listener_handler = undefined,
node_styler = undefined,
edge_styler = undefined,
shown_font_size = font_size,
selection_attribute_name = 'selected',
popover_displayed = null,
right_most_leaf = 0,
label_width = 0,
radial_center = 0,
radius = 1,
radius_pad_for_bubbles = 0,
radial_mapper = function(r, a) {
return {
'x': radial_center + r * Math.sin(a),
'y': radial_center + r * Math.cos(a)
};
},
cartesian_mapper = function(x, y) {
return polar_to_cartesian(x - radial_center, y - radial_center);
},
cartesian_to_polar = function(node, radius, radial_root_offset) {
node.x *= scales[0];
node.y *= scales[1];
node.radius = radius * (node.y / size[1] + radial_root_offset);
if (!node.angle) {
node.angle = 2 * Math.PI * node.x * scales[0] / size[0];
}
var radial = radial_mapper(node.radius, node.angle);
node.x = radial.x;
node.y = radial.y;
return node;
},
polar_to_cartesian = function(x, y) {
r = Math.sqrt(Math.pow(x, 2) + Math.pow(y, 2));
a = Math.atan2(y, x);
return [r, a];
};
self.container = container || "body";
/*--------------------------------------------------------------------------------------*/
phylotree.placenodes = function() {
var x = 0.0,
_extents = [
[0, 0],
[0, 0]
],
last_node = null,
last_span = 0,
save_x = x,
save_span = last_span * 0.5;
var do_scaling = options["scaling"],
undef_BL = false,
is_under_collapsed_parent = false,
max_depth = 1,
leaf_counter = 0;
function process_internal_node(a_node) {
var count_undefined = 0;
a_node.x = a_node.children.map(tree_layout).reduce(function(a, b) {
if (typeof b == "number") return a + b;
count_undefined += 1;
return a;
}, 0.0);
if (count_undefined == a_node.children.length) {
a_node.notshown = true;
a_node.x = undefined;
return;
} else {
a_node.x /= (a_node.children.length - count_undefined);
}
}
function tree_layout(a_node) {
if (d3_phylotree_node_notshown(a_node)) {
return undefined;
}
var is_leaf = d3_phylotree_is_leafnode(a_node);
a_node.text_angle = null;
a_node.text_align = null;
a_node.radius = null;
a_node.angle = null;
if (a_node['parent']) {
if (do_scaling) {
if (undef_BL) {
return 0;
}
a_node.y = branch_length_accessor(a_node);
if (typeof a_node.y === 'undefined') {
undef_BL = true;
return 0;
}
a_node.y += a_node.parent.y;
} else {
a_node.y = is_leaf ? max_depth : a_node.depth;
}
} else {
x = 0.0;
_extents = [
[0, 0],
[0, 0]
];
last_node = null;
last_span = 0;
a_node.y = 0.0;
}
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);
if (is_under_collapsed_parent) {
_extents[0][1] = Math.max(_extents[0][1], (save_x + (a_node.x - save_x) * options['compression'] + save_span) + (_node_span * 0.5 + separation(last_node, a_node)) * options['compression']);
} 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) {
save_x = x;
save_span = last_span * 0.5;
is_under_collapsed_parent = true;
process_internal_node(a_node);
is_under_collapsed_parent = false;
if (typeof a_node.x === "number") {
a_node.x = save_x + (a_node.x - save_x) * options['compression'] + save_span;
a_node.collapsed = [
[a_node.x, a_node.y]
];
var map_me = function(n) {
n.hidden = true;
if (d3_phylotree_is_leafnode(n)) {
x = n.x = save_x + (n.x - save_x) * options['compression'] + save_span;
a_node.collapsed.push([n.x, n.y]);
} else {
n.children.map(map_me);
}
};
x = save_x;
map_me(a_node);
a_node.collapsed.splice(1, 0, [save_x, a_node.y]);
a_node.collapsed.push([x, a_node.y]);
a_node.collapsed.push([a_node.x, a_node.y]);
a_node.hidden = false;
}
} else {
process_internal_node(a_node);
}
}
return a_node.x;
}
rescale_node_span = nodes.map(function(d) {
return node_span(d);
}).reduce(function(p, c) {
return Math.min(c, p || 1e200);
}, null) || 1;
nodes[0].x = tree_layout(nodes[0], do_scaling);
max_depth = d3.max(nodes, (function(n) {
return n.depth;
}));
if (do_scaling && undef_BL) {
do_scaling = false;
nodes[0].x = tree_layout(nodes[0]);
}
var at_least_one_dimension_fixed = false;
draw_scale_bar = options['show-scale'] && do_scaling;
// this is a hack so that phylotree.pad_height would return ruler spacing
if (options['top-bottom-spacing'] == 'fixed-step') {
offsets[1] = Math.max(font_size, -_extents[1][0] * fixed_width[0]);
size[0] = _extents[0][1] * fixed_width[0];
scales[0] = fixed_width[0];
} else {
scales[0] = (size[0] - phylotree.pad_height()) / _extents[0][1];
at_least_one_dimension_fixed = true;
}
shown_font_size = Math.min(font_size, scales[0]);
function do_lr() {
if (phylotree.radial() && at_least_one_dimension_fixed) {
offsets[1] = 0;
}
if (options['left-right-spacing'] == 'fixed-step') {
size[1] = max_depth * fixed_width[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] - 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] - options["left-offset"] - label_width) / _extents[1][1];
}
}
if (phylotree.radial()) { // map the nodes to polar coordinates
draw_branch = draw_arc;
var last_child_angle = null,
last_circ_position = null,
last_child_radius = null,
min_radius = 0,
zero_length = null,
effective_span = _extents[0][1] * scales[0];
var compute_distance = function(r1, r2, a1, a2, annular_shift) {
annular_shift = annular_shift || 0;
return Math.sqrt((r2 - r1) * (r2 - r1) + 2 * (r1 + annular_shift) * (r2 + annular_shift) * (1 - Math.cos(a1 - a2)));
};
var max_r = 0;
nodes.forEach(function(d) {
var my_circ_position = d.x * scales[0];
d.angle = 2 * Math.PI * my_circ_position / effective_span;
d.text_angle = (d.angle - Math.PI / 2);
d.text_angle = d.text_angle > 0 && d.text_angle < Math.PI;
d.text_align = d.text_angle ? "end" : "start";
d.text_angle = (d.text_angle ? 180 : 0) + d.angle * 180 / Math.PI;
d.radius = d.y * scales[1] / size[1];
max_r = Math.max (max_r, d.radius);
});
do_lr();
var annular_shift = 0,
do_tip_offset = phylotree.align_tips() && !options['draw-size-bubbles'];
nodes.forEach(function(d) {
if (!d.children) {
var my_circ_position = d.x * scales[0];
if (last_child_angle !== null) {
var required_spacing = my_circ_position - last_circ_position,
radial_dist = compute_distance(d.radius, last_child_radius, d.angle, last_child_angle, annular_shift);
var local_mr = radial_dist > 0 ? required_spacing / radial_dist : 10 * options['max-radius'];
if (local_mr > options['max-radius']) { // adjust the annular shift
var dd = required_spacing / options['max-radius'],
b = d.radius + last_child_radius,
c = d.radius * last_child_radius - (dd * dd - (last_child_radius - d.radius) * (last_child_radius - d.radius)) / 2 / (1 - Math.cos(last_child_angle - d.angle)),
st = Math.sqrt(b * b - 4 * c);
annular_shift = Math.min(options['annular-limit'] * max_r, (-b + st) / 2);
min_radius = options['max-radius'];
} else {
min_radius = local_mr;
}
}
last_child_angle = d.angle;
last_circ_position = my_circ_position;
last_child_radius = d.radius;
}
});
radius = Math.min(options['max-radius'], Math.max(effective_span / 2 / Math.PI, min_radius));
if (annular_shift) {
var scaler = 1;
nodes.forEach(function(d) {
d.radius = d.y*scales[1]/size[1] + annular_shift;
scaler = Math.max (scaler, d.radius);
});
if (scaler > 1) {
scales[0] /= scaler;
scales[1] /= scaler;
annular_shift /= scaler;
}
}
if (at_least_one_dimension_fixed) {
radius = Math.min(radius, (Math.min(effective_span, _extents[1][1] * scales[1]) - label_width) * 0.5 - radius * annular_shift);
}
radial_center = radius_pad_for_bubbles = radius;
nodes.forEach(function(d) {
cartesian_to_polar(d, radius, annular_shift);
if (options['draw-size-bubbles']) {
radius_pad_for_bubbles = Math.max(radius_pad_for_bubbles, d.radius + phylotree.node_bubble_size(d));
} else {
radius_pad_for_bubbles = Math.max(radius_pad_for_bubbles, d.radius);
}
if (d.collapsed) {
d.collapsed = d.collapsed.map(function(p) {
var z = {};
z.x = p[0];
z.y = p[1];
z = cartesian_to_polar(z, radius, annular_shift);
return [z.x, z.y];
});
var last_point = d.collapsed[1];
d.collapsed = d.collapsed.filter(function(p, i) {
if (i < 3 || i > d.collapsed.length - 4) return true;
if (Math.sqrt(Math.pow(p[0] - last_point[0], 2) + Math.pow(p[1] - last_point[1], 2)) > 3) {
last_point = p;
return true;
}
return false;
});
}
});
size[0] = radial_center + radius;
size[1] = radial_center + radius;
} else {
do_lr();
draw_branch = draw_line;
right_most_leaf = 0;
nodes.forEach(function(d) {
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));
}
if (d.collapsed) {
d.collapsed.map(function(p) {
return [p[0] *= scales[0], p[1] *= scales[1]];
});
var last_x = d.collapsed[1][0];
d.collapsed = d.collapsed.filter(function(p, i) {
if (i < 3 || i > d.collapsed.length - 4) return true;
if (p[0] - last_x > 3) {
last_x = p[0];
return true;
}
return false;
});
}
});
}
if (draw_scale_bar) {
var domain_limit,
range_limit;
if (phylotree.radial()) {
range_limit = Math.min(radius / 5, 50);
domain_limit = Math.pow(10, Math.ceil(Math.log(_extents[1][1] * range_limit / radius) / Math.log(10)));
range_limit = domain_limit * (radius / _extents[1][1]);
if (range_limit < 30) {
var stretch = Math.ceil(30 / range_limit);
//console.log (stretch, domain_limit, radius, _extents[1][1], range_limit, domain_limit);
range_limit *= stretch;
domain_limit *= stretch;
}
} else {
domain_limit = _extents[1][1];
range_limit = (size[1] - offsets[1] - options["left-offset"]);
}
var scale = d3.scale.linear()
.domain([0, domain_limit])
.range([shown_font_size, shown_font_size + range_limit]),
scaleTickFormatter = d3.format(".2g");
draw_scale_bar = d3.svg.axis().scale(scale).orient("top")
.tickFormat(function(d) {
if (d === 0) {
return "";
}
return scaleTickFormatter(d);
});
if (phylotree.radial()) {
draw_scale_bar.tickValues([domain_limit]);
} else {
var my_ticks = scale.ticks();
my_ticks = my_ticks.length > 1 ? my_ticks[1] : my_ticks[0];
draw_scale_bar.ticks(Math.min(10, d3.round(range_limit / (shown_font_size * scaleTickFormatter(my_ticks).length * 0.8), 0)));
}
//_extentsconsole.log (scale.domain(), scale.range());
} else {
draw_scale_bar = null;
}
return phylotree;
};
function phylotree(nwk, bootstrap_values) {
d3_phylotree_add_event_listener();
var _node_data = (typeof nwk == "string") ? d3_phylotree_newick_parser(nwk, bootstrap_values) : nwk;
// this builds children and links;
if (!_node_data['json']) {
nodes = [];
} else {
newick_string = nwk;
nodes = d3_hierarchy.call(this, _node_data.json);
}
phylotree.placenodes();
links = phylotree.links(nodes);
return phylotree;
}
phylotree.size = function(attr) {
if (arguments.length) {
phylo_attr = attr;
}
if (options['top-bottom-spacing'] != 'fixed-step') {
size[0] = phylo_attr[0];
}
if (options['left-right-spacing'] != 'fixed-step') {
size[1] = phylo_attr[1];
}
if (!arguments.length) {
return size;
}
return phylotree;
};
phylotree.pad_height = function() {
if (draw_scale_bar) {
return scale_bar_font_size + 25;
}
return 0;
};
phylotree.pad_width = function() {
return offsets[1] + options["left-offset"] + label_width;
};
phylotree.descendants = function(n) {
var desc = [];
function recurse_d(nd) {
if (d3_phylotree_is_leafnode(nd)) {
desc.push(nd);
} else {
nd.children.forEach(recurse_nd);
}
}
recurse_d(n);
return desc;
};
phylotree.collapse_node = function(n) {
if (!d3_phylotree_is_node_collapsed(n)) {
n.collapsed = true;
}
};
phylotree.separation = function(attr) {
if (!arguments.length) return separation;
separation = attr;
return phylotree;
};
phylotree.selection_label = function(attr) {
if (!arguments.length) return selection_attribute_name;
selection_attribute_name = attr;
phylotree.sync_edge_labels();
return phylotree;
};
phylotree.handle_node_click = function(node) {
var menu_object = d3.select(self.container).select("#" + d3_layout_phylotree_context_menu_id);
if (menu_object.empty()) {
menu_object = d3.select(self.container).append("ul")
.attr("id", d3_layout_phylotree_context_menu_id)
.attr("class", "dropdown-menu")
.attr("role", "menu");
}
menu_object.selectAll("li").remove();
if (node) {
if (!d3_phylotree_is_leafnode(node)) {
if (options["collapsible"]) {
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text(d3_phylotree_is_node_collapsed(node) ? "Expand Subtree" : "Collapse Subtree")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.toggle_collapse(node).update();
});
menu_object.append("li").attr("class", "divider");
menu_object.append("li").attr("class", "dropdown-header").text("Toggle selection");
}
if (options["selectable"]) {
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("All descendant branches")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection(phylotree.select_all_descendants(node, true, true));
});
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("All terminal branches")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection(phylotree.select_all_descendants(node, true, false));
});
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("All internal branches")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection(phylotree.select_all_descendants(node, false, true));
});
}
}
if (node.parent) {
if (options["selectable"]) {
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("Incident branch")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection([node]);
});
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("Path to root")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection(phylotree.path_to_root(node));
});
menu_object.append("li").attr("class", "divider");
}
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("Reroot on this node")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.reroot(node).update();
});
menu_object.append("li").attr("class", "divider");
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("Hide this " + (d3_phylotree_is_leafnode(node) ? "node" : "subtree"))
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection([node], "notshown", true, true).update_has_hidden_nodes().update();
});
}
if (d3_phylotree_has_hidden_nodes(node)) {
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text("Show all descendant nodes")
.on("click", function(d) {
menu_object.style("display", "none");
phylotree.modify_selection(phylotree.select_all_descendants(node, true, true), "notshown", true, true, "false").update_has_hidden_nodes().update();
});
}
// now see if we need to add user defined menus
var has_user_elements = [];
if ("menu_items" in node && typeof node["menu_items"] === "object") {
node["menu_items"].forEach(function(d) {
if (d.length == 3) {
if (!d[2] || d[2](node)) {
has_user_elements.push([d[0], d[1]]);
}
}
});
}
if (has_user_elements.length) {
menu_object.append("li").attr("class", "divider");
has_user_elements.forEach(function(d) {
menu_object.append("li").append("a")
.attr("tabindex", "-1")
.text(d[0](node))
.on("click", d[1]);
});
}
var tree_container = $(self.container);
var coordinates = d3.mouse(tree_container[0]);
menu_object.style("position", "absolute")
.style("left", "" + (coordinates[0]) + "px")
.style("top", "" + (coordinates[1]) + "px")
.style("display", "block");
} else {
menu_object.style("display", "none");
}
};
phylotree.style_nodes = function(attr) {
if (!arguments.length) return node_styler;
node_styler = attr;
return phylotree;
};
phylotree.style_edges = function(attr) {
if (!arguments.length) return edge_styler;
edge_styler = attr.bind(this);
return phylotree;
};
phylotree.get_newick = function(annotator) {
function escape_string(nn) {
var need_escape = /[\s\[\]\,\)\(\:\'\"]/;
var enquote = need_escape.test(nn);
return enquote ? "'" + nn.replace("'", "''") + "'" : nn;
}
function node_display(n) {
if (!d3_phylotree_is_leafnode(n)) {
element_array.push("(");
n.children.forEach(function(d, i) {
if (i) {
element_array.push(",");
}
node_display(d);
});
element_array.push(")");
}
element_array.push(escape_string(node_label(n)));
element_array.push(annotator(n));
var bl = branch_length_accessor(n);
if (bl !== undefined) {
element_array.push(":" + bl);
}
}
var element_array = [];
annotator = annotator || "";
node_display(nodes[0]);
return element_array.join("");
};
phylotree.update_layout = function(new_json, do_hierarchy) {
if (do_hierarchy) {
nodes = d3_hierarchy.call(this, new_json);
nodes.forEach(function(d) {
d.id = null;
});
}
phylotree.placenodes();
links = phylotree.links(nodes);
phylotree.sync_edge_labels();
};
phylotree.sync_edge_labels = function() {
links.forEach(function(d) {
d[selection_attribute_name] = d.target[selection_attribute_name] || false;
d.tag = d.target.tag || false;
});
d3_phylotree_trigger_refresh(phylotree);
if (phylotree.count_handler()) {
var counts = {};
counts[selection_attribute_name] = links.reduce(function(p, c) {
return p + (c[selection_attribute_name] ? 1 : 0);
}, 0);
counts['tagged'] = links.reduce(function(p, c) {
return p + (d3_phylotree_item_tagged(c) ? 1 : 0);
}, 0);
d3_phylotree_trigger_count_update(phylotree,
counts, phylotree.count_handler());
}
};
phylotree.modify_selection = function(callback, attr, place, skip_refresh, mode) {
attr = attr || selection_attribute_name;
mode = mode || "toggle";
if (options["selectable"] && !options["binary-selectable"]) {
var do_refresh = false;
if (typeof callback === 'function') {
links.forEach(function(d) {
var select_me = callback(d);
d[attr] = d[attr] || false;
if (d[attr] != select_me) {
d[attr] = select_me;
do_refresh = true;
d.target[attr] = select_me;
}
});
} else {
callback.forEach(function(d) {
var new_value;
switch (mode) {
case 'true':
new_value = true;
break;
case 'false':
new_value = false;
break;
default:
new_value = !d[attr];
break;
}
if (d[attr] != new_value) {
d[attr] = new_value;
do_refresh = true;
}
});
links.forEach(function(d) {
d[attr] = d.target[attr];
});
}
if (do_refresh) {
if (!skip_refresh) {
d3_phylotree_trigger_refresh(phylotree);
}
if (phylotree.count_handler()) {
var counts = {};
counts[attr] = links.reduce(function(p, c) {
return p + (c[attr] ? 1 : 0);
}, 0);
d3_phylotree_trigger_count_update(phylotree,
counts,
phylotree.count_handler());
}
if (place) {
phylotree.placenodes();
}
}
} else if (options['binary-selectable']) {
if (typeof callback === 'function') {
links.forEach(function(d) {
var select_me = callback(d);
d[attr] = d[attr] || false;
if (d[attr] != select_me) {
d[attr] = select_me;
do_refresh = true;
d.target[attr] = select_me;
}
options['attribute-list'].forEach(function(type) {
if (type != attr && d[attr] === true) {
d[type] = false;
d.target[type] = false;
}
});
});
} else {
callback.forEach(function(d) {
var new_value;
new_value = !d[attr];
if (d[attr] != new_value) {
d[attr] = new_value;
do_refresh = true;
}
});
links.forEach(function(d) {
d[attr] = d.target[attr];
options['attribute-list'].forEach(function(type) {
if (type != attr && d[attr] !== true) {
d[type] = false;
d.target[type] = false;
}
});
});
}
if (do_refresh) {
if (!skip_refresh) {
d3_phylotree_trigger_refresh(phylotree);
}
if (phylotree.count_handler()) {
var counts = {};
counts[attr] = links.reduce(function(p, c) {
return p + (c[attr] ? 1 : 0);
}, 0);
d3_phylotree_trigger_count_update(phylotree,
counts,
phylotree.count_handler());
}
if (place) {
phylotree.placenodes();
}
}
}
return phylotree;
};
phylotree.trigger_refresh = function() {
trigger_refresh(phylotree);
};
phylotree.radial = function(attr) {
if (!arguments.length) return options['is-radial'];
options['is-radial'] = attr;
return phylotree;
};
phylotree.align_tips = function(attr) {
if (!arguments.length) return options['align-tips'];
options['align-tips'] = attr;
return phylotree;
};
phylotree.node_bubble_size = function(node) {
return options['draw-size-bubbles'] ? relative_node_span(node) * scales[0] * 0.5 : 0;
};
phylotree.shift_tip = function(d) {
if (options['is-radial']) {
return [(d.text_align == "end" ? -1 : 1) * (radius_pad_for_bubbles - d.radius), 0];
}
return [right_most_leaf - d.screen_x, 0];
};
phylotree.get_selection = function() {
return nodes.filter(function(d) {
return d[selection_attribute_name];
});
};
phylotree.count_handler = function(attr) {
if (!arguments.length) return count_listener_handler;
count_listener_handler = attr;
return phylotree;
};
phylotree.internal_label = function(callback, respect_existing) {
phylotree.clear_internal_nodes(respect_existing);
for (var i = nodes.length - 1; i >= 0; i--) {
var d = nodes[i];
if (!(d3_phylotree_is_leafnode(d) || d3_phylotree_item_selected(d, selection_attribute_name))) {
d[selection_attribute_name] = callback(d.children);
//console.log (d[selection_attribute_name]);
}
}
phylotree.modify_selection(function(d, callback) {
if (d3_phylotree_is_leafnode(d.target)) {
return d.target[selection_attribute_name];
}
return d.target[selection_attribute_name];
});
};
phylotree.max_parsimony = function(respect_existing) {
phylotree.clear_internal_nodes(respect_existing);
function populate_mp_matrix(d) {
d.mp = [
[0, 0], // score for parent selected / not selected
[false, false]
]; // selected or not
if (d3_phylotree_is_leafnode(d)) {
d.mp[1][0] = d.mp[1][1] = d[selection_attribute_name] || false;
d.mp[0][0] = d.mp[1][0] ? 1 : 0;
d.mp[0][1] = 1 - d.mp[0][0];
} else {
d.children.forEach(populate_mp_matrix);
var s0 = d.children.reduce(function(p, n) {
return n.mp[0][0] + p;
}, 0);
// cumulative children score if this node is 0
var s1 = d.children.reduce(function(p, n) {
return n.mp[0][1] + p;
}, 0);
// cumulative children score if this node is 1
// parent = 0
if (d[selection_attribute_name]) {
// respect selected
d.mp[0][0] = s1 + 1;
d.mp[1][0] = true;
d.mp[0][1] = s1;
d.mp[1][1] = true;
} else {
if (s0 < s1 + 1) {
d.mp[0][0] = s0;
d.mp[1][0] = false;
} else {
d.mp[0][0] = s1 + 1;
d.mp[1][0] = true;
}
// parent = 1
if (s1 < s0 + 1) {
d.mp[0][1] = s1;
d.mp[1][1] = true;
} else {
d.mp[0][1] = s0 + 1;
d.mp[1][1] = false;
}
}
}
}
populate_mp_matrix(nodes[0]);
nodes.forEach(function(d) {
if (d.parent) {
d.mp = d.mp[1][d.parent.mp ? 1 : 0];
} else {
d.mp = d.mp[1][d.mp[0][0] < d.mp[0][1] ? 0 : 1];
}
});
phylotree.modify_selection(function(d, callback) {
if (d3_phylotree_is_leafnode(d.target)) {
return d.target[selection_attribute_name];
}
return d.target.mp;
});
};
phylotree.node_span = function(attr) {
if (!arguments.length) return node_span;
if (typeof attr == "string" && attr == 'equal') {
node_span = function(d) {
return 1;
};
} else {
node_span = attr;
}
return phylotree;
};
/*phylotree.reroot = function (node) {
}*/
phylotree.resort_children = function(comparator) {
function sort_children(node) {
if (node.children) {
for (var k = 0; k < node.children.length; k++) {
sort_children(node.children[k]);
}
node.children.sort(comparator);
}
}
sort_children(nodes[0]);
phylotree.update_layout(nodes);
phylotree.update();
};
phylotree.graft_a_node = function(graft_at, new_child, new_parent, lengths) {
if (graft_at.parent) {
var node_index = nodes.indexOf(graft_at);
if (node_index >= 0) {
var parent_index = graft_at.parent.children.indexOf(graft_at);
var new_split = {
"name": new_parent,
"parent": graft_at.parent,
"attribute": lengths ? lengths[2] : null,
"original_child_order": graft_at["original_child_order"]
},
new_node = {
"name": new_child,
"parent": new_split,
"attribute": lengths ? lengths[1] : null,
"original_child_order": 2
};
new_split["children"] = [graft_at, new_node];
graft_at["parent"].children[parent_index] = new_split;
graft_at.parent = new_split;
graft_at["attribute"] = lengths ? lengths[0] : null;
graft_at["original_child_order"] = 1;
phylotree.update_layout(nodes[0], true);
}
}
return phylotree;
};
phylotree.delete_a_node = function(index) {
if (typeof index != "number") {
return phylotree.delete_a_node(nodes.indexOf(index));
}
if (index > 0 && index < nodes.length) {
var node = nodes[index];
if (node.parent) { // can only delete nodes that are not the root
var delete_me_idx = node.parent.children.indexOf(node);
//console.log (delete_me_idx, node, index);
if (delete_me_idx >= 0) {
nodes.splice(index, 1);
if (node.children) {
node.children.forEach(function(d) {
d['original_child_order'] = node.parent.children.length;
node.parent.children.push(d);
d.parent = node.parent;
});
}
if (node.parent.children.length > 2) {
node.parent.children.splice(delete_me_idx, 1);
} else {
if (node.parent.parent) {
node.parent.parent.children[node.parent.parent.children.indexOf(node.parent)] = node.parent.children[1 - delete_me_idx];
node.parent.children[1 - delete_me_idx].parent = node.parent.parent;
nodes.splice(nodes.indexOf(node.parent), 1);
} else {
nodes.splice(0, 1);
nodes[0].parent = null;
delete nodes[0]['attribute'];
delete nodes[0]['annotation'];
delete nodes[0]['original_child_order'];
nodes[0].name = 'root';
}
}
phylotree.update_layout(nodes[0], true);
}
}
}
return phylotree;
};
phylotree.traverse_and_compute = function(callback, traversal_type) {
traversal_type = traversal_type || "post-order";
function post_order(node) {
if (node.children) {
for (var k = 0; k < node.children.length; k++) {
post_order(node.children[k]);
}
}
callback(node);
}
if (traversal_type == 'post-order') {
traversal_type = post_order;
}
traversal_type(nodes[0]);
};
phylotree.reroot = function(node) {
if (node.parent) {
new_json = {
'name': 'new_root',
'__mapped_bl': undefined,
'children': [node]
};
nodes.forEach(function(n) {
n.__mapped_bl = branch_length_accessor(n);
});
phylotree.branch_length(function(n) {
return n.__mapped_bl;
});
var remove_me = node,
current_node = node.parent,
parent_length = current_node.__mapped_bl,
stashed_bl = _.noop();
if (current_node.parent) {
node.__mapped_bl = node.__mapped_bl === undefined ? undefined : node.__mapped_bl * 0.5;
stashed_bl = current_node.__mapped_bl;
current_node.__mapped_bl = node.__mapped_bl;
new_json.children.push(current_node);
while (current_node.parent) {
var remove_idx = current_node.children.indexOf(remove_me);
if (current_node.parent.parent) {
current_node.children.splice(remove_idx, 1, current_node.parent);
} else {
current_node.children.splice(remove_idx, 1);
}
var t = current_node.parent.__mapped_bl;
if (t !== undefined) {
current_node.parent.__mapped_bl = stashed_bl;
stashed_bl = t;
}
remove_me = current_node;
current_node = current_node.parent;
}
var remove_idx = current_node.children.indexOf(remove_me);
current_node.children.splice(remove_idx, 1);
} else {
var remove_idx = current_node.children.indexOf(remove_me);
current_node.children.splice(remove_idx, 1);
remove_me = new_json;
}
// current_node is now old root, and remove_me is the root child we came up
// the tree through
if (current_node.children.length == 1) {
if (stashed_bl) {
current_node.children[0].__mapped_bl += stashed_bl;
}
remove_me.children = remove_me.children.concat(current_node.children);
} else {
var new_node = {
"name": "__reroot_top_clade"
};
new_node.__mapped_bl = stashed_bl;
new_node.children = current_node.children.map(function(n) {
return n;
});
remove_me.children.push(new_node);
}
phylotree.update_layout(new_json, true);
}
return phylotree;
};
phylotree.update_key_name = function(old_key, new_key) {
nodes.forEach(function(n) {
if (old_key in n) {
if (new_key) {
n[new_key] = n[old_key];
}
delete n[old_key];
}
});
phylotree.sync_edge_labels();
};
phylotree.spacing_x = function(attr, skip_render) {
if (!arguments.length) return fixed_width[0];
if (fixed_width[0] != attr && attr >= options['minimum-per-node-spacing'] && attr <= options['maximim-per-node-spacing']) {
fixed_width[0] = attr;
if (!skip_render) {
phylotree.placenodes();
}
}
return phylotree;
};
phylotree.spacing_y = function(attr, skip_render) {
if (!arguments.length) return fixed_width[1];
if (fixed_width[1] != attr && attr >= options['minimum-per-level-spacing'] && attr <= options['maximim-per-level-spacing']) {
fixed_width[1] = attr;
if (!skip_render) {
phylotree.placenodes();
}
}
return phylotree;
};
phylotree.toggle_collapse = function(node) {
if (node.collapsed) {
node.collapsed = false;
var unhide = function (n) {
if (!d3_phylotree_is_leafnode(n)) {
if (!n.collapsed) {
n.children.forEach(unhide);
}
}
n.hidden = false;
};
unhide(node);
} else {
node.collapsed = true;
}
phylotree.placenodes();
return phylotree;
};
phylotree.update_has_hidden_nodes = function() {
for (k = nodes.length - 1; k >= 0; k -= 1) {
if (d3_phylotree_is_leafnode(nodes[k])) {
nodes[k].has_hidden_nodes = nodes[k].notshown;
} else {
nodes[k].has_hidden_nodes = nodes[k].children.reduce(function(p, c) {
return c.notshown || p;
}, false);
}
}
return phylotree;
};
phylotree.branch_length = function(attr) {
if (!arguments.length) return branch_length_accessor;
branch_length_accessor = attr ? attr : def_branch_length_accessor;
return phylotree;
};
phylotree.branch_name = function(attr) {
if (!arguments.length) return node_label;
node_label = attr ? attr : def_node_label;
return phylotree;
};
phylotree.length = function(attr) {
if (!arguments.length) return default_length_attribute;
if (default_length_attribute != attr) {
default_length_attribute = attr;
needs_redraw = true;
}
return phylotree;
};
phylotree._label_width = function(_font_size) {
_font_size = _font_size || shown_font_size;
var width = 0;
nodes.filter(d3_phylotree_node_visible).forEach(function(node) {
var node_width = node_label(node).length * _font_size * 0.6;
if (node.angle !== null) {
node_width *= Math.max(Math.abs(Math.cos(node.angle)), Math.abs(Math.sin(node.angle)));
}
width = Math.max(node_width, width);
});
return width;
};
phylotree.font_size = function(attr) {
if (!arguments.length) return font_size;
font_size = attr === undefined ? 12 : attr;
return phylotree;
};
phylotree.scale_bar_font_size = function(attr) {
if (!arguments.length) return scale_bar_font_size;
scale_bar_font_size = attr === undefined ? 12 : attr;
return phylotree;
};
phylotree.node_circle_size = function(attr, attr2) {
if (!arguments.length) return options['node_circle_size'];
options['node_circle_size'] = d3.functor(attr === undefined ? 3 : attr);
return phylotree;
};
phylotree.needs_redraw = function() {
return needs_redraw;
};
phylotree.svg = function(svg_element) {
if (!arguments.length) return svg_element;
if (svg !== svg_element) {
svg = svg_element;
svg.selectAll("*").remove();
svg_defs = svg.append("defs");
d3.select(self.container).on("click", function(d) {
phylotree.handle_node_click(null);
}, true);
}
return phylotree;
};
phylotree.css = function(opt) {
if (arguments.length === 0) return css_classes;
if (arguments.length > 2) {
var arg = {};
arg[opt[0]] = opt[1];
return phylotree.css(arg);
}
for (var key in css_classes) {
if (key in opt && opt[key] != css_classes[key]) {
css_classes[key] = opt[key];
}
}
return phylotree;
};
phylotree.options = function(opt, run_update) {
if (!arguments.length) return options;
var do_update = false;
for (var key in options) {
if (key in opt && opt[key] != options[key]) {
do_update = true;
options[key] = opt[key];
switch (key) {
case 'branches':
{
switch (opt[key]) {
case 'straight':
{
draw_branch.interpolate('linear');
break;
}
default:
{
draw_branch.interpolate('step-before');
break;
}
}
}
break;
}
}
}
if (run_update && do_update) {
phylotree.layout();
}
return phylotree;
};
phylotree.transitions = function(arg) {
if (arg !== undefined) {
return arg;
}
if (options['transitions'] !== null) {
return options['transitions'];
}
return nodes.length <= 300;
};
phylotree.update = function(transitions) {
if (!phylotree.svg)
return phylotree;
transitions = phylotree.transitions(transitions);
var node_id = 0;
var enclosure = svg.selectAll("." + css_classes["tree-container"]).data([0]);
enclosure.enter().append("g")
.attr("class", css_classes["tree-container"]);
enclosure.attr("transform", function(d) {
return d3_phylotree_svg_translate([offsets[1] + options["left-offset"], phylotree.pad_height()]);
});
if (draw_scale_bar) {
var scale_bar = svg.selectAll("." + css_classes["tree-scale-bar"]).data([0]);
scale_bar.enter().append("g");
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] + options["left-offset"], phylotree.pad_height() - 10]);
})
.call(draw_scale_bar);
scale_bar.selectAll("text")
.style("text-anchor", "end");
} else {
svg.selectAll("." + css_classes["tree-scale-bar"]).remove();
}
var drawn_links = enclosure.selectAll(d3_phylotree_edge_css_selectors(css_classes))
.data(links.filter(d3_phylotree_edge_visible), function(d) {
return d.target.id || (d.target.id = ++node_id);
});
if (transitions) {
drawn_links.exit().transition().remove();
} else {
drawn_links.exit().remove();
}
drawn_links.enter().insert("path", ":first-child");
drawn_links.each(function(d) {
phylotree.draw_edge(this, d, transitions);
});
var collapsed_clades = enclosure.selectAll(d3_phylotree_clade_css_selectors(css_classes))
.data(nodes.filter(d3_phylotree_is_node_collapsed), function(d) {
return d.id || (d.id = ++node_id);
});
var spline = function() {};
var spline_f = _.noop();
// Collapse radial differently
if (phylotree.radial()) {
// create interpolator
var interpolator = function(points) {
points.pop();
var center_node = points.shift();
var path_string = points.join("L");
var polar_coords = cartesian_mapper(center_node[0], center_node[1]);
var first_angle = cartesian_mapper(points[0][0], points[0][1])[1];
var last_angle = cartesian_mapper(points[points.length - 1][0], points[points.length - 1][1])[1];
var connecting_arc = "A " + polar_coords[0] + " " + polar_coords[0] + " " + (first_angle > last_angle ? 1 : 0) + " 0 0 " + points[0].join(',');
return path_string + connecting_arc;
};
spline = d3.svg.line()
.interpolate(interpolator)
.y(function(d) {
return d[0];
})
.x(function(d) {
return d[1];
});
spline_f = function(coord, i, d, init_0, init_1) {
if (i) {
return [d.screen_y + (coord[0] - init_0) / 50, d.screen_x + (coord[1] - init_1) / 50];
} else {
return [d.screen_y, d.screen_x];
}
};
} else {
spline = d3.svg.line()
.interpolate("basis")
.y(function(d) {
return d[0];
})
.x(function(d) {
return d[1];
});
spline_f = function(coord, i, d, init_0, init_1) {
if (i) {
return [d.screen_y + (coord[0] - init_0) / 50, d.screen_x + (coord[1] - init_1) / 50];
} else {
return [d.screen_y, d.screen_x];
}
};
}
var cce = collapsed_clades.exit().each(function(d) {
d.collapsed_clade = null;
}).remove();
if (transitions) {
collapsed_clades.enter().insert("path", ":first-child");
collapsed_clades.attr("class", css_classes["clade"])
.attr("d", function(d) {
if (d.collapsed_clade) {
return d.collapsed_clade;
}
var init_0 = d.collapsed[0][0];
var init_1 = d.collapsed[0][1];
return spline(d.collapsed.map(spline_f, d, init_0, init_1));
})
.transition()
.attr("d", function(d) {
return d.collapsed_clade = spline(d.collapsed);
});
} else {
collapsed_clades.enter().insert("path", ":first-child")
.attr("class", css_classes["clade"])
.attr("d", function(d) {
return spline(d.collapsed);
});
}
var drawn_nodes = enclosure.selectAll(d3_phylotree_node_css_selectors(css_classes))
.data(nodes.filter(d3_phylotree_node_visible), function(d) {
return d.id || (d.id = ++node_id);
});
var append_here = drawn_nodes.enter().append("g");
if (transitions) {
//drawn_nodes.exit().transition ().style ("opacity", "0").remove();
drawn_nodes.exit().transition().remove();
drawn_nodes = drawn_nodes.attr("transform", function(d) {
if(!_.isUndefined(d.screen_x) && !_.isUndefined(d.screen_y)) {
return "translate(" + d.screen_x + "," + d.screen_y + ")";
}
}).transition();
} else {
drawn_nodes.exit().remove();
}
drawn_nodes.attr("transform", function(d) {
d.screen_x = x_coord(d);
d.screen_y = y_coord(d);
return d3_phylotree_svg_translate([d.screen_x, d.screen_y]);
})
.attr("class", phylotree.reclass_node).each(function(d) {
phylotree.draw_node(this, d, transitions);
});
var sizes = d3_phylotree_resize_svg(phylotree, svg, transitions);
var brush = enclosure.selectAll("." + css_classes["tree-selection-brush"]).data([0]);
brush.enter().insert("g", ":first-child")
.attr("class", css_classes["tree-selection-brush"]);
var brush_object = d3.svg.brush()
.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(),
shown_links = links.filter(d3_phylotree_edge_visible),
selected_links = shown_links.filter(function(d, i) {
return d.source.screen_x >= extent[0][0] && d.source.screen_x <= extent[1][0] && d.source.screen_y >= extent[0][1] && d.source.screen_y <= extent[1][1] && d.target.screen_x >= extent[0][0] && d.target.screen_x <= extent[1][0] && d.target.screen_y >= extent[0][1] && d.target.screen_y <= extent[1][1];
}).map(function(d) {
return d.target;
});
phylotree.modify_selection(links.map(function(d) {
return d.target;
}), "tag", false, selected_links.length > 0, "false");
phylotree.modify_selection(selected_links, "tag", false, false, "true");
}).
on("brushend", function() {
brush.call(d3.event.target.clear());
});
brush.call(brush_object);
return phylotree;
};
phylotree.css_classes = function() {
return css_classes;
};
phylotree.layout = function(transitions) {
if (svg) {
svg.selectAll("." + css_classes["tree-container"] + ",." + css_classes["tree-scale-bar"] + ",." + css_classes["tree-selection-brush"]).remove();
return phylotree.update(transitions);
}
return phylotree;
};
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));
edges.attr("class", phylotree.reclass_edge);
if (edge_styler) {
edges.each(function(d) {
edge_styler(d3.select(this), d);
});
}
var nodes = enclosure.selectAll(d3_phylotree_node_css_selectors(css_classes));
nodes.attr("class", phylotree.reclass_node);
if (node_styler) {
nodes.each(function(d) {
node_styler(d3.select(this), d);
});
}
};
phylotree.reclass_edge = function(edge) {
var class_var = css_classes["branch"];
if (d3_phylotree_item_tagged(edge)) {
class_var += " " + css_classes["tagged-branch"];
}
if (d3_phylotree_item_selected(edge, selection_attribute_name)) {
class_var += " " + css_classes["selected-branch"];
}
return class_var;
};
phylotree.reclass_node = function(node) {
var class_var = css_classes[d3_phylotree_is_leafnode(node) ? "node" : "internal-node"];
if (d3_phylotree_item_tagged(node)) {
class_var += " " + css_classes["tagged-node"];
}
if (d3_phylotree_item_selected(node, selection_attribute_name)) {
class_var += " " + css_classes["selected-node"];
}
if (d3_phylotree_is_node_collapsed(node) || d3_phylotree_has_hidden_nodes(node)) {
class_var += " " + css_classes['collapsed-node'];
}
return class_var;
};
phylotree.select_all_descendants = function(node, terminal, internal) {
var selection = [];
function sel(d) {
if (d3_phylotree_is_leafnode(d)) {
if (terminal) {
if (d != node)
selection.push(d);
}
} else {
if (internal) {
if (d != node)
selection.push(d);
}
d.children.forEach(sel);
}
}
sel(node);
return selection;
};
phylotree.path_to_root = function(node) {
var selection = [];
while (node) {
selection.push(node);
node = node.parent;
}
return selection;
};
phylotree.draw_edge = function(container, edge, transition) {
container = d3.select(container);
container.attr("class", phylotree.reclass_edge)
.on("click", function(d) {
phylotree.modify_selection([d.target], selection_attribute_name);
});
var new_branch_path = draw_branch([edge.source, edge.target]);
if (transition) {
if (container.datum().existing_path) {
container.attr("d", function(d) {
return d.existing_path;
});
}
container.transition().attr("d", new_branch_path);
} else {
container.attr("d", new_branch_path);
}
edge.existing_path = new_branch_path;
var bl = branch_length_accessor(edge.target);
if (bl !== undefined) {
var haz_title = container.selectAll("title");
if (haz_title.empty()) {
haz_title = container.append("title");
}
haz_title.text("Length = " + bl);
} else {
container.selectAll("title").remove();
}
if (edge_styler) {
edge_styler(container, edge);
}
return phylotree;
};
phylotree.clear_internal_nodes = function(respect) {
if (!respect) {
nodes.forEach(function(d) {
if (!d3_phylotree_is_leafnode(d)) {
d[selection_attribute_name] = false;
}
});
}
};
phylotree.draw_node = function(container, node, transitions) {
container = d3.select(container);
if (d3_phylotree_is_leafnode(node)) {
var labels = container.selectAll("text").data([node]),
tracers = container.selectAll("line");
if (transitions) {
labels.enter().append("text").style("opacity", 0).transition().style("opacity", 1);
} else {
labels.enter().append("text");
}
labels.on("click", function(d, i) {
phylotree.handle_node_click(d);
})
.attr("dy", function(d) {
return shown_font_size * 0.33;
})
.text(function(d) {
return node_label(d);
}).style("font-size", function(d) {
return shown_font_size;
});
if (phylotree.radial()) {
(transitions ? labels.transition() : labels).attr("transform", function(d) {
return d3_phylotree_svg_rotate(d.text_angle) + d3_phylotree_svg_translate(phylotree.align_tips() ? phylotree.shift_tip(d) : null);
})
.attr("text-anchor", function(d) {
return d.text_align;
});
} else {
(transitions ? labels.transition() : labels).attr("text-anchor", "start")
.attr("transform", function(d) {
return d3_phylotree_svg_translate(phylotree.align_tips() ? phylotree.shift_tip(d) : null);
});
}
if (phylotree.align_tips()) {
tracers = tracers.data([node]);
if (transitions) {
tracers.enter().append("line").style("opacity", 0).transition().style("opacity", 1);
tracers.attr("x1", function(d) {
return (d.text_align == "end" ? -1 : 1) * phylotree.node_bubble_size(node);
}).attr("x2", 0).attr("y1", 0).attr("y2", 0);
tracers.transition().attr("x2", function(d) {
return phylotree.shift_tip(d)[0];
}).attr("transform", function(d) {
return d3_phylotree_svg_rotate(d.text_angle);
});
} else {
tracers.enter().append("line");
tracers.attr("x1", function(d) {
return (d.text_align == "end" ? -1 : 1) * phylotree.node_bubble_size(node);
}).attr("y2", 0).attr("y1", 0).transition().attr("x2", function(d) {
return phylotree.shift_tip(d)[0];
});
tracers.attr("transform", function(d) {
return d3_phylotree_svg_rotate(d.text_angle);
});
}
tracers.classed(css_classes['branch-tracer'], true);
} else {
tracers.remove();
}
if (options['draw-size-bubbles']) {
var shift = phylotree.node_bubble_size(node);
var circles = container.selectAll("circle").data([shift]);
circles.enter().append("circle");
if (transitions) {
circles = circles.transition();
}
circles.attr("r", function(d) {
return d;
});
if (shown_font_size >= 5) {
labels.attr("dx", function(d) {
return (d.text_align == "end" ? -1 : 1) * ((phylotree.align_tips() ? 0 : shift) + shown_font_size * 0.33);
});
}
} else {
if (shown_font_size >= 5) {
labels.attr("dx", function(d) {
return (d.text_align == "end" ? -1 : 1) * shown_font_size * 0.33;
});
}
}
} else {
var circles = container.selectAll("circle").data([node]),
radius = phylotree.node_circle_size()(node);
if (radius > 0) {
circles.enter().append("circle");
circles.attr("r", function(d) {
return Math.min(shown_font_size * 0.75, radius);
})
.on("click", function(d) {
phylotree.handle_node_click(d);
});
} else {
circles.remove();
}
}
if (node_styler) {
node_styler(container, node);
}
return node;
};
phylotree.get_nodes = function() {
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");
// Add an alias for nodes and links, for convenience.
phylotree.nodes = phylotree;
phylotree.links = d3.layout.cluster().links;
return phylotree;
};
//------------------------------------------------------------------------------
function d3_phylotree_item_selected(item, tag) {
return (item[tag] || false);
}
function d3_phylotree_node_visible(node) {
return !(node.hidden || node.notshown || false);
}
function d3_phylotree_node_notshown(node) {
return node.notshown;
}
function d3_phylotree_edge_visible(edge) {
return !(edge.target.hidden || edge.target.notshown || false);
}
function d3_phylotree_item_tagged(item) {
return (item.tag || false);
}
function d3_phylotree_resize_svg(tree, svg, tr) {
var sizes = tree.size();
if (tree.radial()) {
var pad_radius = tree.pad_width(),
vertical_offset = (tree.options()['top-bottom-spacing'] != 'fit-to-size' ? tree.pad_height() : 0);
sizes = [sizes[1] + 2 * pad_radius,
sizes[0] + 2 * pad_radius + vertical_offset
];
if (svg) {
svg.selectAll("." + tree.css_classes()['tree-container']).attr("transform", "translate (" + (pad_radius) + "," + (pad_radius + vertical_offset) + ")");
}
} else {
sizes = [sizes[1] + (tree.options()['left-right-spacing'] != 'fit-to-size' ? tree.pad_width() : 0),
sizes[0] + (tree.options()['top-bottom-spacing'] != 'fit-to-size' ? tree.pad_height() : 0)
];
}
if (svg) {
if (tr) {
svg = svg.transition(100);
}
svg.attr("height", sizes[1])
.attr("width", sizes[0]);
}
return sizes;
}
function d3_phylotree_is_leafnode(node) {
return !(node.children && node.children.length);
}
function d3_phylotree_has_hidden_nodes(node) {
return node.has_hidden_nodes || false;
}
function d3_phylotree_is_node_collapsed(node) {
return node.collapsed || false;
}
function d3_phylotree_node_css_selectors(css_classes) {
return [css_classes['node'], css_classes['internal-node'], css_classes['collapsed-node'], css_classes['tagged-node']]
.reduce(function(p, c, i, a) {
return p += "g." + c + ((i < a.length - 1) ? "," : "");
}, "");
}
function d3_phylotree_edge_css_selectors(css_classes) {
return [css_classes['branch'], css_classes['selected-branch'], css_classes['tagged-branch']]
.reduce(function(p, c, i, a) {
return p += "path." + c + ((i < a.length - 1) ? "," : "");
}, "");
}
function d3_phylotree_clade_css_selectors(css_classes) {
return [css_classes['clade']]
.reduce(function(p, c, i, a) {
return p += "path." + c + ((i < a.length - 1) ? "," : "");
}, "");
}
function d3_phylotree_newick_parser(nwk_str, bootstrap_values) {
var clade_stack = [];
function add_new_tree_level() {
var new_level = {
"name": null
};
var the_parent = clade_stack[clade_stack.length - 1];
if (!("children" in the_parent)) {
the_parent["children"] = [];
}
clade_stack.push(new_level);
the_parent["children"].push(clade_stack[clade_stack.length - 1]);
clade_stack[clade_stack.length - 1]["original_child_order"] = the_parent["children"].length;
}
function finish_node_definition() {
var this_node = clade_stack.pop();
if (bootstrap_values && 'children' in this_node) {
this_node["bootstrap_values"] = current_node_name;
} else {
this_node["name"] = current_node_name;
}
this_node["attribute"] = current_node_attribute;
this_node["annotation"] = current_node_annotation;
current_node_name = '';
current_node_attribute = '';
current_node_annotation = '';
}
function generate_error(location) {
return {
"json": null,
"error": "Unexpected '" + nwk_str[location] + "' in '" + nwk_str.substring(location - 20, location + 1) + "[ERROR HERE]" + nwk_str.substring(location + 1, location + 20) + "'"
};
}
var automaton_state = 0;
var current_node_name = '';
var current_node_attribute = '';
var current_node_annotation = '';
var quote_delimiter = null;
var name_quotes = {
"'": 1,
"\"": 1
};
var tree_json = {
"name": "root"
};
clade_stack.push(tree_json);
var space = /\s/;
for (var char_index = 0; char_index < nwk_str.length; char_index++) {
try {
var current_char = nwk_str[char_index];
switch (automaton_state) {
case 0:
{
// look for the first opening parenthesis
if (current_char == '(') {
add_new_tree_level();
automaton_state = 1; // expecting node name
}
break;
}
case 1: // name
case 3: // branch length
{
// reading name
if (current_char == ':') {
if (automaton_state == 3) {
return generate_error(char_index);
}
automaton_state = 3;
} else if (current_char == ',' || current_char == ')') {
try {
finish_node_definition();
automaton_state = 1;
if (current_char == ',') {
add_new_tree_level();
}
} catch (e) {
return generate_error(char_index);
}
} else if (current_char == '(') {
if (current_node_name.length > 0) {
return generate_error(char_index);
} else {
add_new_tree_level();
}
} else if (current_char in name_quotes) {
if (automaton_state == 1 && current_node_name.length === 0 && current_node_attribute.length === 0 && current_node_annotation.length === 0) {
automaton_state = 2;
quote_delimiter = current_char;
continue;
}
return generate_error(char_index);
} else {
if (current_char == '[') {
if (current_node_annotation.length) {
return generate_error(char_index);
} else {
automaton_state = 4;
}
} else {
if (automaton_state == 3) {
current_node_attribute += current_char;
} else {
if (space.test(current_char)) {
continue;
}
current_node_name += current_char;
}
}
}
break;
}
case 2:
{
if (current_char == quote_delimiter) {
if (char_index < nwk_str.length - 1) {
if (nwk_str[char_index + 1] == quote_delimiter) {
char_index++;
current_node_name += quote_delimiter;
continue;
}
}
quote_delimiter = 0;
automaton_state = 1;
continue;
} else {
current_node_name += current_char;
}
break;
}
case 4:
{
if (current_char == ']') {
automaton_state = 3;
} else {
if (current_char == '[') {
return generate_error(char_index);
}
current_node_annotation += current_char;
}
break;
}
}
} catch (e) {
return generate_error(char_index);
}
}
if (clade_stack.length != 1) {
return generate_error(nwk_str.length - 1);
}
return {
"json": tree_json,
"error": null
};
}
function d3_add_custom_menu(node, name, callback, condition) {
if (!("menu_items" in node)) {
node["menu_items"] = [];
}
if (!node["menu_items"].some(function(d) {
return d[0] == name && d[1] == callback && d[2] == condition;
})) {
node["menu_items"].push([name, callback, condition]);
}
}
function d3_phylotree_rootpath(attr_name, store_name) {
attr_name = attr_name || "attribute";
store_name = store_name || "y_scaled";
if ('parent' in this) {
var my_value = parseFloat(this[attr_name]);
this[store_name] = this.parent[store_name] + (isNaN(my_value) ? 0.1 : my_value);
} else {
this[store_name] = 0.0;
}
return this[store_name];
}
function d3_phylotree_rescale(scale, attr_name) {
attr_name = attr_name || "y_scaled";
if (attr_name in this) {
this[attr_name] *= scale;
}
}
function d3_phylotree_trigger_refresh(tree) {
var event = new CustomEvent(d3_layout_phylotree_event_id, {
'detail': ['refresh', tree]
});
document.dispatchEvent(event);
}
function d3_phylotree_trigger_count_update(tree, counts) {
var event = new CustomEvent(d3_layout_phylotree_event_id, {
'detail': ['count_update', counts, tree.count_handler()]
});
document.dispatchEvent(event);
}
function d3_phylotree_event_listener(event) {
switch (event.detail[0]) {
case 'refresh':
event.detail[1].refresh();
break;
case 'count_update':
event.detail[2](event.detail[1]);
break;
}
return true;
}
function d3_phylotree_add_event_listener() {
document.addEventListener(d3_layout_phylotree_event_id, d3_phylotree_event_listener, false);
}
function d3_phylotree_svg_translate(x) {
if (x && (x[0] !== null || x[1] !== null))
return "translate (" + (x[0] !== null ? x[0] : 0) + "," + (x[1] !== null ? x[1] : 0) + ") ";
return "";
}
function d3_phylotree_svg_rotate(a) {
if (a !== null) {
return "rotate (" + a + ") ";
}
return "";
}
}.call(this));
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