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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width,maximum-scale=2">
<link href="https://code.jquery.com/ui/1.12.1/themes/cupertino/jquery-ui.min.css" rel="stylesheet" type="text/css" media="all" />
<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
<link rel="stylesheet" href="build/pedigreejs.v3.0.0-rc7.css" />
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/jquery.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/d3.min.js" integrity="sha256-yUdn/lyl/rHBn4bD4HkKmnR7S6Fj+tXIO0ozSay1Bik=" crossorigin="anonymous"></script>
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
<script type="module" src="es/pedigree.js"></script>
<style>
a[href^="http://"][target=_blank]:after,
a[href^="https://"][target=_blank]:after,
a[href^="ftp://"][target=_blank]:after {
content: "\f08e";
font-family: FontAwesome;
font-weight: normal;
font-style: normal;
display: inline-block;
text-decoration: none;
padding: 0px 2px;
display:inline;
}
.fa-rotate-45 {
-webkit-transform:rotate(45deg);
-moz-transform:rotate(45deg);
-ms-transform:rotate(45deg);
-o-transform:rotate(45deg);
transform:rotate(45deg);
}
.header {
background-color:#DDD1C1;
margin-right: auto;
margin-left: auto;
margin-bottom: 20px;
}
.btn.btn-primary {
color: #fff;
background-color: #337ab7;
border-color: #2e6da4;
padding: 10px 16px;
font-size: 18px;
line-height: 1.3333333;
border-radius: 6px;
text-decoration: none;
}
.row {
display: flex;
}
.row > div {
margin-right: 10px;
}
.left {
width:140px;
font-weight: bold;
text-align: right;
flex-shrink: 0;
}
/* Clear floats after the columns */
.row:after {
content: "";
display: table;
clear: both;
}
@media screen and (min-width: 768px) {
.header {
padding-top: 20px;
padding-bottom: 20px;
}
.header h1 {
font-size: 63px;
font-weight: 500;
line-height: 1.1;
margin: 10px 0;
}
.header h2 {
font-size: 30px;
margin-top: 20px;
margin-bottom: 10px;
font-weight: 500;
}
}
body {
margin: 0;
font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
font-size: 14px;
line-height: 1.42857143;
color: #333;
background-color: #fff;
}
.container {
width: 90%;
max-width: 1140px;
margin-right: auto;
margin-left: auto;
}
#ped {text-align:center;}
.btn {
color: #333;
background-color: #fff;
border: 1px solid #ccc;
display: inline-block;
padding: 6px 12px;
cursor: pointer;
margin-left: 5px;
border-radius: 4px;
}
.options {
background-color: #F5F5F5;
padding: 10px;
border: 1px solid #ccc;
font-size: 13px;
line-height: 1.42857143;
overflow: auto;word-wrap: normal;
border-radius: 4px;
}
#pedigree_history {
padding: 10px;
}
.text-center {
text-align: center;
padding: 0 20px;
}
</style>
<script type="module">
import * as pedigree from '/es/pedigree.js';
import * as pedcache from '/es/pedcache.js';
import {urlParam, isIE} from '/es/utils.js';
if(isIE()) {
document.write('<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/browser/canvg.min.js"><\/script>');
}
$( document ).ready(function() {
////////////////////
var dataset = [
{"name": "m11", "sex": "M", "top_level": true},
{"name": "f11", "display_name": "Jane", "sex": "F", "status": 1, "top_level": true, "breast_cancer_diagnosis_age":67, "ovarian_cancer_diagnosis_age":63},
{"name": "m12", "sex": "M", "top_level": true},
{"name": "f12", "sex": "F", "top_level": true, "breast_cancer_diagnosis_age":55},
{"name": "m21", "sex": "M", "mother": "f11", "father": "m11", "age": 56},
{"name": "f21", "sex": "F", "mother": "f12", "father": "m12", "breast_cancer_diagnosis_age":55, "breast_cancer2_diagnosis_age": 60, "ovarian_cancer_diagnosis_age":58, "age": 63},
{"name": "ch1", "display_name": "Ana", "sex": "F", "mother": "f21", "father": "m21", "proband": true, "age": 25}
];
$( "#pedigrees" ).append( $( "<div id='pedigree_history'></div>" ) );
$( "#pedigrees" ).append( $( "<div id='pedigree'></div>" ) );
var opts = {
'targetDiv': 'pedigree',
'btn_target': 'pedigree_history',
// 'nodeclick': pedigree_form.nodeclick,
'width': ($(window).width() > 450 ? 1000 : $(window).width()- 30),
'height': 580,
'symbol_size': 30,
'edit': true,
'zoomSrc': ['button'],
'zoomIn': .05,
'zoomOut': 1.5,
'optionalLabels': [
['brca1_gene_test', 'brca2_gene_test', 'palb2_gene_test', 'chek2_gene_test', 'atm_gene_test'],
['rad51d_gene_test', 'rad51c_gene_test', 'brip1_gene_test'],
['er_bc_pathology', 'pr_bc_pathology', 'her2_bc_pathology', 'ck14_bc_pathology', 'ck56_bc_pathology']],
'labels': [['age', 'yob'],
['brca1_gene_test', 'brca2_gene_test', 'palb2_gene_test', 'chek2_gene_test', 'atm_gene_test'],
['rad51d_gene_test', 'rad51c_gene_test', 'brip1_gene_test'],
['er_bc_pathology', 'pr_bc_pathology', 'her2_bc_pathology', 'ck14_bc_pathology', 'ck56_bc_pathology']],
'diseases': [{'type': 'breast_cancer', 'colour': '#F68F35'},
{'type': 'breast_cancer2', 'colour': 'pink'},
{'type': 'ovarian_cancer', 'colour': '#4DAA4D'},
{'type': 'pancreatic_cancer', 'colour': '#4289BA'},
{'type': 'prostate_cancer', 'colour': '#D5494A'}],
'DEBUG': (urlParam('debug') === null ? false : true)};
var local_dataset = pedcache.current(opts);
if (local_dataset !== undefined && local_dataset !== null) {
opts.dataset = local_dataset;
} else {
opts.dataset = dataset;
}
opts = pedigree.build(opts);
});
</script>
</head>
<body>
<!-- HEADER -->
<div class="header">
<div class="container">
<a class="btn btn-primary pull-right" role="button" href="https://github.com/CCGE-BOADICEA/pedigreejs">View on GitHub</a>
<h1>pedigreejs</h1>
<h2>A web tool for building and displaying pedigrees.</h2>
</div>
</div>
<div class="container">
<div>
<!-- EXAMPLE -->
<div style="margin-left:20px;" class="pull-right">
<div class="text-center">
<label class="btn">
<input id="load" type="file" style="display: none;"/>Load
</label>
<label class="btn">
<input id="save" type="button" style="display: none;"/>Save
</label>
<label class="btn">
<input id="print" type="button" style="display: none;"/>Print
</label>
<label class="btn">
<input id="svg_download" type="button" style="display: none;"/>SVG
</label>
<label class="btn">
<input id="png_download" type="button" style="display: none;"/>PNG
</label>
<div id="pedigrees"></div>
<div id="node_properties"></div>
</div>
</div>
<div>
<h2>Overview</h2>
<p>
<strong>pedigreejs</strong> is a JavaScript library used to draw family trees using
<a href="https://www.ncbi.nlm.nih.gov/pubmed/7887430" target="_blank">standard pedigree nomenclature</a>.
It uses the JavaScript <a href="https://d3js.org/" target="_blank">d3</a> library
to layout the hierarchical structure and draw the individual nodes as a SVG image.
The size of the SVG can be configured as well as the colour codes used to denote disease.
It can be used to build the pedigree structure or load in an existing data set.
To assist visualisation and building of larger pedigrees a full screen mode is provided.
</p>
<p>
Browser local storage is used to maintain a history of the steps in building a pedigree
structure. So that at each step of the pedigree building process it can be undone to return
to previous versions.
</p>
<p>See the <a href="docs/developer.html">developer documentation</a> for more details about setting up
pedigreejs.</p>
<p>A demonstration page is available <a href="docs/demo.html">here</a>.
Other example pages and configurations are given below:</p>
<ul>
<li>Example 1: <a href="docs/example1.html">diabetes example</a></li>
<li>Example 2: <a href="docs/example2.html">change background, node colours and using local storage</a></li>
<li>Example 3: <a href="docs/example3.html">change text and node size</a></li>
<li>Example 4: <a href="docs/example4.html">PED file example with genotype data</a></li>
<li>Example 5: <a href="docs/example5.html">consanguineous partners and first and last name labels</a></li>
<li>Example 6: <a href="docs/example6.html">example pedigree validation</a></li>
<li>Example 7: <a href="docs/example7.html">twins, divorced, miscarriage, termination, stillbirth and adoption</a></li>
<li>Example 8: <a href="docs/example8.html">search pedigree data</a></li>
<li>Example 9: <a href="docs/example9.html">consanguineous partners at different levels</a></li>
</ul>
</div>
</div>
<!-- EXAMPLE END -->
<h2>Building Pedigrees</h2>
<p>
Individuals can be added to the pedigree by placing the mouse over an individual to reveal
the widgets used for editing and adding a
partner <i class="fa fa-link" aria-hidden="true"></i> (two people with at least one child),
parents <i class="fa fa-arrow-up" aria-hidden="true"></i>,
a sibling <i class="fa fa-user-plus" aria-hidden="true"></i>,
or a child <i class="fa fa-arrow-down" aria-hidden="true"></i>.
Options are given to add
male <i class="fa fa-square-o" aria-hidden="true"></i>,
female <i class="fa fa-circle-o" aria-hidden="true"></i>,
unknown <i class="fa fa-square-o fa-rotate-45" aria-hidden="true"></i>,
dizygotic (fraternal) twin <i class="fa fa-angle-up" style="font-size:1.5em" aria-hidden="true"></i>
or monozygotic (identical) twin <i class="fa fa-caret-up" style="font-size:1.5em" aria-hidden="true"></i>.
</p>
<p>
If the 'edit' parameter is set in the configuration of pedigreejs then the <i class="fa fa-cog" aria-hidden="true"></i> widget
is also displayed. When this widget is clicked it opens an editor dialog of the attributes associated for the individual. A default
editor is provided that can be overridden and customised.
</p>
<p>Half siblings can be added by creating a new partner (with <i class="fa fa-link" aria-hidden="true"></i>)
for the parent in common to the siblings.
Consanguineous partners can be created between individual's at the same or different levels in the pedigree
tree, <i>e.g.</i> cousins.
This is done by placing the mouse over one of the partners and clicking and dragging the
triple dashed line widget <img alt="handle" src="docs/img/handle.png"> in the direction of their new partner.
</p>
<p>
There are 'undo' <i class="fa fa-undo" aria-hidden="true"></i>,
'redo' <i class="fa fa-redo" aria-hidden="true"></i> and 'reset' <i class="fa fa-refresh" aria-hidden="true"></i>
buttons at the top and a button to enable full screen editing <i class="fa fa-arrows-alt" aria-hidden="true"></i>.
</p>
<h2>Loading and Saving Pedigree Data</h2>
<p>The pedigree can be saved out and loaded back in. Preliminary support is given to loading basic
BOADICEA file format v4 (see the BOADICEA documentation
<a href="https://pluto.srl.cam.ac.uk/bd4/v4/docs/BWA_v4_Appendix_A.pdf" target="_blank">Appendix</a>).</p>
<p>Support for <a href="https://www.cog-genomics.org/plink/1.9/formats#ped">PED file format</a>
has been added, see <a href="docs/example4.html">example 4</a>.<p>
<h2>Future Development</h2>
<p>The following will be looked at:</p>
<ul>
<li>currently the maximum number of partners an individual can be represented to have is 2.</li>
<li><del>the ability to represent consanguineous partners between different levels in the tree.</del></li>
</ul>
<h2 id="config">Configuration and Integration Notes</h2>
<p>The following parameters can be used to configure pedigreejs.
Please also see the <a href="docs/developer.html">developer notes</a> for more details about
programmatically interacting with pedigreejs.
The important parameter to configure is 'targetDiv' which defines the HTML div used for
drawing the pedigree. Default parameters are provided which are documented below.
There is a configuration parameter 'edit' which can take a function, so that a
customised editor can be written to view and edit an individual's attributes (e.g. name, sex).
Alternatively is 'edit' is set to true a default dialog will be displayed showing the
individual's attributes.
</p>
<pre class="options">
var opts = {
'targetDiv': 'pedigree',
'btn_target': 'pedigree_history',
'width': 450,
'height': 320,
'symbol_size': 35,
'store_type': 'array',
'diseases': [
{'type': 'breast_cancer', 'colour': '#F68F35'},
{'type': 'ovarian_cancer', 'colour': '#4DAA4D'},
{'type': 'pancreatic_cancer', 'colour': '#4289BA'},
{'type': 'prostate_cancer', 'colour': '#D5494A'}],
labels: ['age', 'yob'],
font_size: '.75em',
font_family: 'Helvetica',
font_weight: 700,
'DEBUG': (pedigree_util.urlParam('debug') === null ? false : true)
};
var local_dataset = pedcache.current(opts);
if (local_dataset !== undefined && local_dataset !== null) {
opts.dataset = local_dataset;
} else {
opts.dataset = dataset;
}
opts= ptree.build(opts);
</pre>
<h2>Options</h2>
<div class="row" id="targetDiv">
<div class="left">targetDiv</div>
<div>This is the id of the HTML div used for drawing the pedigree, <i>e.g.</i> 'pedigree_edit'.</div>
</div>
<div class="row" id="btn_target">
<div class="left">btn_target</div>
<div>This is the id of the HTML div used for the buttons, <i>e.g.</i> 'pedigree_history'.</div>
</div>
<div class="row" id="dataset">
<div class="left">dataset</div>
<div>The pedigree data to be displayed, <i>e.g.</i>
<pre class="options">
[ {"name": "m21", "sex": "M", "top_level": true},
{"name": "f21", "sex": "F", "top_level": true},
{"name": "ch1", "sex": "F", "mother": "f21", "father": "m21", "breast_cancer": true, "proband": true}]</pre>
</div>
</div>
<div class="row" id="labels">
<div class="left">labels</div>
<div>Array of attributes to display under the individual's symbol, <i>e.g.</i> labels: ['age', 'yob', 'alleles'].</div>
</div>
<div class="row" id="font_size">
<div class="left">font_size</div>
<div>Define the font-size of the labels, <i>e.g.</i> '0.75em' or '10px'.</div>
</div>
<div class="row" id="font_family">
<div class="left">font_family</div>
<div>Define the font-family of the labels, <i>e.g.</i> 'times'.</div>
</div>
<div class="row" id="font_weight">
<div class="left">font_weight</div>
<div>Define the font-weight of the labels, <i>e.g.</i> 400, 700.</div>
</div>
<div class="row" id="width">
<div class="left">width</div>
<div>Width of the SVG element, <i>e.g.</i> 600.</div>
</div>
<div class="row" id="height">
<div class="left">height</div>
<div>Height of the SVG element, <i>e.g.</i> 400.</div>
</div>
<div class="row" id="symbol_size">
<div class="left">symbol_size</div>
<div>Size of the nodes, <i>e.g.</i> 35.</div>
</div>
<div class="row" id="store_type">
<div class="left">store_type</div>
<div>Pedigree storage (for undo, redo functions) set to 'session', 'local' or 'array'.
Default is '<a href="https://www.w3schools.com/html/html5_webstorage.asp">session</a>' browser storage.
Using 'session' will store the data for one session (data is lost when the browser tab is closed).
Using 'local' will store the data with no expiration date.
If session/local storage is not supported then it switches automatically to 'array' (JavaScript array store).</div>
</div>
<div class="row" id="zoomIn">
<div class="left">zoomIn</div>
<div>The factor by which the svg size can be scaled down to, default 1 (no zoom in).</div>
</div>
<div class="row" id="zoomOut">
<div class="left">zoomOut</div>
<div>The factor by which the svg size can be scaled up to, default 1 (no zoom out).</div>
</div>
<div class="row" id="edit">
<div class="left">edit</div>
<div>Set to true for a button to display an individual's details (<i>e.g.</i> age, sex) in a dialog or provide a funtion to handle editing.</div>
</div>
<div class="row" id="diseases">
<div class="left">diseases</div>
<div>Diseases and their colour representation, <i>e.g.</i>
<pre class="options">
[{'type': 'breast_cancer', 'colour': '#F68F35'},
{'type': 'breast_cancer2', 'colour': 'pink'},
{'type': 'ovarian_cancer', 'colour': '#4DAA4D'},
{'type': 'pancreatic_cancer', 'colour': '#4289BA'},
{'type': 'prostate_cancer', 'colour': '#D5494A'}]</pre>
</div>
</div>
<div class="row" id="background">
<div class="left">background</div>
<div>SVG background colour, <i>e.g.</i> #d3d3d3.</div>
</div>
<div class="row" id="node_background">
<div class="left">node_background</div>
<div>Individual's background colour, <i>e.g.</i> #fff.</div>
</div>
<div class="row" id="validate">
<div class="left">validate</div>
<div>Pedigree data validation (default true). This can also take a validation
function to override the in-built validation. The in-built validation throws an error if any
of the following are not true:
<ul>
<li>parents, when defined, exist in the pedigree</li>
<li>mother is female</li>
<li>father is male</li>
</ul>
A warning message it sent to the console if there are any individuals that are not connected
(i.e. a break in the pedigree). See the <a href="docs/developer.html">developer notes</a> for
more details.
</div>
</div>
<div class="row" id="DEBUG">
<div class="left">DEBUG</div>
<div>Debug mode, <i>e.g.</i> false.</div>
</div>
<h2>Publication</h2>
<p><strong>pedigreejs: a web-based graphical pedigree editor</strong><br>
Carver T, Cunningham AP, Babb de Villiers C, Lee A, Hartley S, Tischkowitz M, et al.
<i>Bioinformatics <a href="http://dx.doi.org/10.1093/bioinformatics/btx705" target="_blank">
doi:10.1093/bioinformatics/btx705</a></i></p>
</div>
<p></p>
</body>
</html>