forked from jhmarcus/ggv
-
Notifications
You must be signed in to change notification settings - Fork 5
/
index.html
executable file
·283 lines (245 loc) · 13.6 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
<!doctype html>
<!--[if lt IE 7]> <html class="no-js ie6 oldie" lang="en"> <![endif]-->
<!--[if IE 7]> <html class="no-js ie7 oldie" lang="en"> <![endif]-->
<!--[if IE 8]> <html class="no-js ie8 oldie" lang="en"> <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en"> <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<title>GGV</title>
<link rel="icon" href="/css/map.ico">
<meta name="description" content="">
<meta name="author" content="">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="http://fonts.googleapis.com/css?family=Arvo" rel="stylesheet" type="text/css">
<link rel="stylesheet" href="css/tipsy.css">
<link rel="stylesheet" href="css/bootstrap.css">
<!--<link rel="stylesheet" href="css/Flat-UI-master/css/flat-ui.css">!-->
<link rel="stylesheet" href="css/font-awesome-4.2.0/css/font-awesome.css">
<link rel="stylesheet" href="css/chosen.css">
<link rel="stylesheet" href="//ajax.googleapis.com/ajax/libs/jqueryui/1.11.1/themes/smoothness/jquery-ui.css"/>
<link rel="stylesheet" href="js/jQuery-File-Upload-9.7.1/css/jquery.fileupload.css">
<link rel="stylesheet" href="css/style.css">
<link rel="stylesheet" type="text/css" href="js/igv/ggv-igv-1.0.1.css">
</head>
<body>
<div class="container" id='all'>
<div id="main" role="main">
<a href="https://twitter.com/share" class="twitter-share-button">Tweet</a>
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs');</script>
<h1>Geography of Genetic Variants Browser</h1>
<a data-toggle="modal" data-target="#myModal" id='about'><p id='about'>About / Help</a></p>
<div class="modal fade" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel">About</h4>
</div>
<div class="modal-body">
Welcome to the Geography of Genetic Variants (GGV)
browser! <br><br> To begin, pick a dataset on the
dropdown menu. One can search variants within a dataset
by its rsID or position (Use the format
chromosome#:position, as in, 15:24608502 or
chr15:24608502) and clicking the search button or the
enter key. Click the "random" button to show a random
marker from the chosen dataset.<br><br>
The embedded
IGV browser at the bottom of the page can also also be
used to pick a variant for display. <br> <br>
To
display the population name, minor allele frequency,
minor allele count, and sample size, hover with the
mouse over a data point. Click on the plot title to open
up the UCSC genome browser at that variant.
<br><br>Be sure to note we use a notion of a "frequency scale" to display rare variants and a "transparency scale" to indicate uncertain allele frequencies. These are explained in the legend.
<br><br>
If you use the maps in other works, include the source link: <a href=http://www.popgen.uchicago.edu/ggv/>http://www.popgen.uchicago.edu/ggv</a>
and/or make a formal reference to:<br>
Marcus & Novembre (2016) Visualizing the Geography of Genetic Variants. <it>Bioinformatics</it><a href="http://bioinformatics.oxfordjournals.org/content/early/2016/10/14/bioinformatics.btw643.abstract"><i id='linkIcon' class='fa fa-external-link'></i>.</a>
<br><br>Keep in mind that this
is still an evolving project and many ideas/resources are in progress.
<br><br> Questions/feedback/ideas/critiques are welcomed and appreciated! <br>Contact: josephhmarcus at gmail dot com or jnovembre at uchicago dot edu.
<br><br>
</div>
</div>
</div>
</div>
<div class="modal fade" id="browser" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel">IGV Genome Browser Help</h4>
</div>
<div class="modal-body">
To use the embedded IGV Browser, input the number of the chromosome you would like to look at in the search box and hit enter. You can zoom in/out on the chromosome by clicking on the +/- buttons on the right side of the browser. You can zoom in on a specific section of the chromosome by clicking and dragging along the axis.
<br><br>
To move about the chromosome, you can use the arrow keys to move left or right. You can also click and drag on the genes and variants sections if you would like to make smaller movements. To jump to another section of the chromosome, you can click on areas you would like to look at on the upper chromosome display, and the red window will move there.
<br><br>
If you click on a variant (vertical grey bar) in the variants section, then that variant will be displayed on the map above. Also, if you search for a variant in the upper search box by the map, the browser will switch to the variant's chromosome and zoom into that variant's location along the chromosome.
</div>
</div>
</div>
</div>
<div class="modal fade" id="upload" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel"><i class="fa fa-list-ol"></i></h4>
</div>
<div class="modal-body">
<form id='snpArea'>
copy paste a single column of snps <i class="fa fa-long-arrow-down"></i>. Remeber to select the appropriate dataset!
<textarea id='snp_col' class="form-control" rows="3" type="text"></textarea>
<button id='submitArea' type="button" class="btn btn-default">submit</button>
</form>
</div>
</div>
</div>
</div>
<div class='row' id='settings'>
<div id="dropDown" class='col-sm-4'>
<div id='datasets'>
</div>
</div>
<div class='col-sm-5'>
<div id='variant_settings'>
<div>
<form id='buttons' class='btn-group' onSubmit="return false;">
<input id='search' type="text" class="form-control" placeholder='rsID/chr#:pos'>
<button id='submit' type="button" class="btn btn-default"><i class="fa fa-search"></i></button>
<button id='random' type='button' class="btn btn-default">random</button>
<button id='upload' type='button' class="btn btn-default" data-toggle="modal" data-target="#upload"><i class="fa fa-list-ol"></i></button>
</form>
</div>
</div>
</div>
<div id="layouts" class='col-sm-3'>
Avoid overlap:
<div class='btn-group'>
<a id="true" class="btn btn-default">Off</a>
<a id="charged" class="btn btn-default">On</a>
</div>
</div>
<!-- <button id="true" type="button" class="btn btn-default">True Position</button>
<button id="charged" type="button" class="btn btn-default">Avoid Overlap</button> -->
<div class='col-sm-6' id='slider-holder'>
<div id="slider"></div>
</div>
</div>
<div class="modal fade" id="alert" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
<h4 class="modal-title" id="myModalLabel"><i class="fa fa-exclamation-triangle"></i></h4>
</div>
<div class="modal-body">
Either the SNP you searched is not in the chosen dataset or the search term is formatted incorrectly. <br><br>
When using the query box, acceptable searches by chromosome/pos or rsID look like...<br><br>
<li>chr1:742429</li>
<br>
<li>1:742429</li>
<br>
<li>rs3094315</li>
<br>
When using a url-based query, acceptable searches look like: <br><br>
<li> Query default data (1000 Genomes phase 3) by chromosome and position:<br>
<a href='http://popgen.uchicago.edu/ggv/?chr=10&pos=114900524'>'http://popgen.uchicago.edu/ggv/?chr=10&pos=114900524'</a></li>
<br>
<li> Query default data by rsid:<br>
<a href='http://popgen.uchicago.edu/ggv/?data=1000genomes"&rsid=rs1799983'>'http://popgen.uchicago.edu/ggv/?data=1000genomes"&rsid=rs1799983'</a></li>
<br>
<li> Query default data for a random SNP<br>
<a href='http://popgen.uchicago.edu/ggv/?data="1000genomes"&random_snp=True'>'http://popgen.uchicago.edu/ggv/?data="1000genomes"&random_snp=True'</a></li>
<br>
<li> Query an alternate dataset:<br>
<a href='http://popgen.uchicago.edu/ggv/?data="1000genomes_superpops"&chr=12&pos=11957847'>'http://popgen.uchicago.edu/ggv/?data="1000genomes_superpops"&chr=12&pos=11957847'</a></li>
</div>
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class='col-md-8'>
<div id="vis">
<div id='variant'><h2></h2></div>
</div>
</div>
<div class='col-md-4', id='legend'>
<div class="row">
<div id='freqLegend' class="col-md-12">
<h3></h3>
<p></p>
</div>
</div>
<div class="row">
<div id='transLegend' class="col-md-12">
<h3></h3>
<p></p>
</div>
</div>
<div class="row">
<div id='testLegend' class="col-md-12">
<h3></h3>
<p></p>
</div>
<div class="btn-group">
<a id="pdf" class="btn btn-default">Save Plot As PDF</a>
</div>
</div>
</div>
<!-- <div id="scales">
<h3></h3>
<a data-toggle="modal" data-target="#browser"><p>Help</p></a>
</div> -->
</div>
</div>
<div>
<!-- <h3>Variants Browser</h3> removed JRT 10-14-16 -->
<div id="browserContainer">
</div>
<a data-toggle="modal" data-target="#browser"><p>IGV Browser Help</p></a>
</div>
</div>
<footer id='footer'>
<div id='text'>
<p><a href='http://jnpopgen.org/' target='_blank'>Novembre Lab</a><br>Developed by Joe Marcus and John Novembre with Jeff Tharsen and Alex Mueller<br>Department of Human Genetics, University of Chicago</p>
<!--<a href="http://creativecommons.org/licenses/by/4.0/"><img src='data/by.png' id='cc'></a>!-->
<a href="http://creativecommons.org/licenses/by/4.0/" target='_blank'><i class="fa fa-cc fa-2x"></i></a>
</div>
</footer>
<script src="js/jquery-1.11.0.js"></script>
<script src="js/colorbrewer.v1.min.js"></script>
<script src="js/bootstrap.js"></script>
<script src="js/jquery.tipsy.js"></script>
<script src="js/d3.v3.min.js"></script>
<script src="js/d3.geo.projection.v0.min.js"></script>
<script src="js/topojson.v1.min.js"></script>
<script src="js/chosen.jquery.js"></script>
<script src="//ajax.googleapis.com/ajax/libs/jqueryui/1.11.1/jquery-ui.min.js"></script>
<script src="js/jQuery-File-Upload-9.7.1/js/jquery.iframe-transport.js"></script>
<script src="js/jQuery-File-Upload-9.7.1/js/jquery.fileupload.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jspdf/1.0.272/jspdf.debug.js"></script>
<script type="text/javascript" src="js/pdfkit.js"></script>
<!-- <script src="https://github.com/devongovett/blob-stream/releases/download/v0.1.2/blob-stream-v0.1.2.js"></script> -->
<script type="text/javascript" src="js/blob-stream.js"></script>
<script type="text/javascript" src="js/igv/ggv-igv-1.0.1.js"></script>
<script type="text/javascript" src="js/vis.js"></script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-52770606-1', 'auto');
ga('send', 'pageview');
</script>
<!--[if lt IE 7 ]>
<script src="//ajax.googleapis.com/ajax/libs/chrome-frame/1.0.3/CFInstall.min.js"></script>
<script>window.attachEvent('onload',function(){CFInstall.check({mode:'overlay'})})</script>
<![endif]-->
</body>
</html>