-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
880 lines (837 loc) · 40.6 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
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <script type="application/shiny-singletons"></script> <script type="application/html-dependencies">json2[2014.02.04];jquery[1.12.4];shiny[1.0.1];datatables[1.10.5];datatables-bootstrap[1.10.5];bootstrap[3.3.7]</script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href='StyleSheet.css' rel='stylesheet'/>
<link href="dataTables.bootstrap.css" rel="stylesheet" />
<link href="dataTables.extra.css" rel="stylesheet" />
<link href="bootstrap.min.css" rel="stylesheet" />
<link href='jquery.dataTables.min.css' rel='stylesheet'/>
<!--<link href="shared/shiny.css" rel="stylesheet" /> -->
<script src="json2-min.js"></script>
<script src="jquery.min.js"></script>
<script src="shiny.min.js"></script>
<script type="text/javascript" src="html5shiv.min.js"></script>
<script type="text/javascript" src="respond.min.js"></script>
<script type="text/javascript" src="d3.min.js"></script>
<script type="text/javascript" src='underscore-min.js'></script>
<script type="text/javascript" src="d3-scale-chromatic.v1.min.js"></script>
<script type="text/javascript" src="jquery-3.1.1.min.js"> </script>
<script type='text/javascript' src='jquery.dataTables.min.js'></script>
<script type="text/javascript" src="jquery-ui.js"> </script>
<script type="text/javascript" src="bootstrap.min.js"></script>
<script type="text/javascript" src="init.js"></script>
<script type="text/javascript" src="Create2DNetwork.js"> </script>
<script type="text/javascript" src="LineChart2D.js"></script>
<script type="text/javascript" src="three.js"></script>
<script type="text/javascript" src='FirstPersonControls.js'></script>
<script type="text/javascript" src='TrackballControls.js'></script>
<script type="text/javascript" src='FlyControls.js'></script>
<script type="text/javascript" src='FileSaver.js'></script>
<script type="text/javascript" src='ExportSVGImage.js'></script>
<script type="text/javascript" src='ExportSVGAnimation.js'></script>
<script type="text/javascript" src='d3-recorder.js'></script>
<script type="text/javascript" src="Create3DNetwork.js"></script>
<script type="text/javascript" src="createHTMLtable.js"></script>
<script type="text/javascript" src='createBarPlot.js'></script>
<script type="text/javascript" src='dataTables.deepLink.js'></script>
<script type="text/javascript" src='d3Animation.js'></script>
<script type="text/javascript" src='d3AnimationEdges.js'></script>
<script type="text/javascript" src='d3AnimationNodeEdges.js'></script>
<script type="text/javascript" src="LZWEncoder.js"></script>
<script type="text/javascript" src="NeuQuant.js"></script>
<script type="text/javascript" src="GIFEncoder.js"></script>
<script type='text/javascript' src='colorbrewer.js'></script>
<script type='text/javascript' src='exportHistogramImage.js'></script>
<script type='text/javascript' src='exportLineGraph2D.js'></script>
<script type='text/javascript' src='export3D.js'></script>
<script type='text/javascript' src='ExportPathwayList.js'></script>
<script type='text/javascript' src='createTableDynamicNodes.js'></script>
<script type= "text/javascript">
// When the user clicks on div, open the popup
function myFunction() {
var popup = document.getElementById("myPopup");
popup.classList.toggle("show");
}
var acc = document.getElementsByClassName("accordion");
var i;
for (i = 0; i < acc.length; i++) {
acc[i].addEventListener("click", function() {
/* Toggle between adding and removing the "active" class,
to highlight the button that controls the panel */
this.classList.toggle("active");
/* Toggle between hiding and showing the active panel */
var panel = this.nextElementSibling;
if (panel.style.display === "block") {
panel.style.display = "none";
} else {
panel.style.display = "block";
}
});
}
function showUploadDataDiv(){document.getElementById('DivElementUploadData').style.display='block'
document.getElementById('ParentWelcomeScreen').style.display='none'
document.getElementById('DivElementMouseControls').style.display='none'
document.getElementById('DataDownload').style.display='none'
document.getElementById('Tutorialdata').style.display='none'
}
function showMouseControls(){document.getElementById('DivElementMouseControls').style.display='block'
document.getElementById('ParentWelcomeScreen').style.display='none'
document.getElementById('DivElementUploadData').style.display='none'
document.getElementById('DataDownload').style.display='none'
document.getElementById('Tutorialdata').style.display='none'
}
function Home(){document.getElementById('ParentWelcomeScreen').style.display='block'
document.getElementById('DivElementUploadData').style.display='none'
document.getElementById('DivElementMouseControls').style.display='none'
document.getElementById('DataDownload').style.display='none'
document.getElementById('Tutorialdata').style.display='none'
}
function DownloadData(){document.getElementById('DataDownload').style.display='block'
document.getElementById('ParentWelcomeScreen').style.display='none'
document.getElementById('DivElementUploadData').style.display='none'
document.getElementById('DivElementMouseControls').style.display='none'
document.getElementById('Tutorialdata').style.display='none'
}
function TutorialScreen(){document.getElementById('Tutorialdata').style.display='block'
document.getElementById('ParentWelcomeScreen').style.display='none'
document.getElementById('DivElementUploadData').style.display='none'
document.getElementById('DivElementMouseControls').style.display='none'
document.getElementById('DataDownload').style.display='none'
}
</script>
<title>DynOVis: Network visualization tool</title>
</head>
<body>
<!-- Navigation Bar Menu -->
<nav class="navbar navbar-default navbar-static-top" role="navigation">
<div class="container-fluid">
<div class="navbar-header">
<span class="navbar-brand">DynOVis: Network visualization tool</span>
</div>
<ul class="nav navbar-nav">
<li class="active">
<a href="#tab-7438-1" data-toggle="tab" data-value="Home page">Home page</a>
</li>
<li>
<a href="#tab-7438-2" data-toggle="tab" data-value="User Input Data">User Input Data</a>
</li>
<li>
<a href="#tab-7438-3" data-toggle="tab" data-value="Network visualization">Network visualization</a>
</li>
</ul>
</div>
</nav>
<div class="container-fluid">
<div class="tab-content">
<!-- Tab Panel for Home screen -->
<div class="tab-pane active" data-value="Home page" id="tab-7438-1">
<div class="row">
<div class="col-sm-4">
<div class="well">
<h3>Getting started</h3>
<a href='#' onclick='Home()'> Home </a> <br />
<a href='#' onclick='TutorialScreen()'> Start with the tutorial data </a><br />
<a href='#' onclick='showUploadDataDiv()'> How to upload your data </a> <br />
<a href='#' onclick=' showMouseControls()'> Mouse controls</a> <br />
<a href='#' onclick='DownloadData()'>Where are my images saved?</a> <br />
<!-- Insert tutorial link -->
</div>
</div>
<div class="col-sm-8">
<div id='DivElementMouseControls' style='display:none;'>
<h4> Mouse controls</h4>
<h5><b>Left mouse button</b></h5>
<ul>
<li> single click + hold on node: drag and place node </li>
<li> single click + node: drag and place whole network</li>
<li> Double click: heighlight node and his neighbors</li>
</ul>
<h5><b>Right mouse button</b></h5>
<ul>
<li>single click: show node information hub</li>
</ul>
<h5><b> Mouse wheel</b></h5>
<ul><li>Zoom in/out</li></ul>
</div>
<div id='DivElementUploadData' style='display:none;'>
<h4>Upload your network data</h4>
<p>After navigating to the tab 'User Input Data', you can specify the network file type (figure,panel A):<br>
<ul>
<li>Edge list</li>
<li>Adjacency matrix</li>
<li>Cytoscape sif file</li>
</ul>
<br>
The Cytoscape sif file is the standard output file one can generate in the Cytoscape program and is intended to allow you to visualize your network you've already build in Cytoscape.<br> The adjacency matrix (of dimension MxM) should be of the standard format thus an matrix containing zeros if there is no connection and ones if there is a connection between nodes (figure, panel B).<br> The edge list should be a two column file containing the source node in column 1 and the target node in column 2. (figure, panel C) <br>
</p>
<h4> Upload the experimental data</h4>
<p>
The second step is uploading the experimental data from the dose/time/dose-over-time series. These data values are used to color the nodes in the network, for instance to show the log intensity changes of the genes in a gene regulatory network. Each of the different file, whether it is a dose series or time series has a comparable data file structure. The rows in the file correspond to the different nodes in the network and therefore should have the same name. The columns in the file correspond to the dose, time point or Dose X at time point Y (figure, panel D).<br>
As a last option, the user can upload an interaction file, which is a file that will specify which interactions are present at different time points.<br>
<img source='www/DataUploadPanel.jpeg' height='200'/>
</p>
</div>
<div id="ParentWelcomeScreen" style='display:block;'>
<h4>Welcome at the DynOVis visualization tool for network analysis</h4>
<p>
DynOVis is designed to capture the dynamic nature of biological data due to different perturbations, such as time or dose series experiments.<br />
Integrative visualization can be used to gain more information out of the networks graphs and thereby increase our understanding of the biological data.<br />
<br />
Here, we have integrated a dynamic visualization approach combined with integrated databases, to add biological context to the network. This includes information about related pathways, associated diseases and general gene information.
</p>
<p>
</p>
<p><img src="Graphical abstract.jpg" height='400'/></p>
<p><img src="TGX_logo.jpg" height='100' align='right'/></p>
</div>
<div id='DataDownload' style='display:none;'>
<p>
<h4> Where are my images saved to?</h4>
By default, your images will be downloaded to the standard folder specified by your browser.<br>
In general, this is 'Downloads' folder in your documents directory.<br>
</p>
</div>
<div id='Tutorialdata' style='display:none;'>
<p>
<h4> How to use the tutorial data</h4>
DynOVis has two different tutorial data sets that can be viewed in the tool: i) NFkB pathway exposed to acetaminophen (NFkB data set) and ii) biological network of Fibronectin 1 perturbation after primary human hepatocytes have been exposed to Valproic acid.<br>
<br>
To upload the data, just check one of the two boxed (NFkB exposure or VPA exposure) and press the button ‘Upload data’. The second step will be to select the directionality of the network: directed or undirected. For the Tutorial data sets please select ‘directed’. Finally, you can select if you want to map the genes in the network to the internal database of DynOVis. For the NFkB exposure pathway you can select 'map nodes to database' and select 'Entrez ID'. For the tutorial data set of VPA exposure you should select 'gene Name'. To start the visualization press ‘Build network’. <br />
<br>
A short description of the main functions: <br>
<b> Threshold on node degree:</b> If you click on the menu bar, the panel will drop down and three options sliders become visible to select a threshold on the degree for which a node becomes hidden. The drop menu can be closed again by clicking on 'Threshold on node degree' <br>
<b> Show Expression data:</b> This drop down menu contains the different animation options of DynOVis: i) color nodes with expression ii) Edge interaction over time and iii) color node + edge interaction. The animation controls are used to play the animation ('play button'),pause/resume the animation ('pause'button) and to go frame-by-frame through the network ('forward/backward' button).<br>
For the NFkB data set choose the option: color nodes with expression<br>
For the VPA exposure set choose the option: color nodes + edge interaction <br>
<br>
<b> Start analysis of subselection:</b> Before you can run this option, you first have to double click on a node in the network to highlight the node and its first neighbors. After this step, you can press 'start analysis subselection' which will create a 2D line graph of the expression changes over time or dose.<br />
<br>
<b>A complete tutorial which explains all the functions of the tool in more detail can be found <a href='ManualDynovis.pdf' target=_blank">here</a>.</b><br>
</p>
</div>
</div>
</div>
</div>
<div class="tab-pane" data-value="User Input Data" id="tab-7438-2">
<div class="container-fluid">
<div class="row">
<div class="col-sm-4">
<div class="well">
<h4>Step 1:Upload files</h4>
<h5> Tutorial data<h5>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="NFkBexposure" type="checkbox"/>
<span>NFkB exposure</span>
</label>
</div>
</div>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="VPAexposure" type="checkbox"/>
<span>VPA exposure</span>
</label>
</div>
</div>
<h5>Select network type</h5>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="EdgeList" type="checkbox"/>
<span>Edge list</span>
</label>
</div>
</div>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="AdjMatrix" type="checkbox"/>
<span>Adjacancy matrix</span>
</label>
</div>
</div>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="Cytoscape" type="checkbox"/>
<span>Cytoscape file</span>
</label>
</div>
</div>
<div data-display-if="input.EdgeList==1||input.AdjMatrix==1||input.Cytoscape==1">
<div class="form-group shiny-input-container">
<label>Choose edgelist file</label>
<div class="input-group">
<label class="input-group-btn">
<span class="btn btn-default btn-file">
Browse...
<input id="NetworkFile" name="NetworkFile" type="file" style="display: none;" accept="multiple"/>
</span>
</label>
<input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
</div>
<div id="NetworkFile_progress" class="progress progress-striped active shiny-file-input-progress">
<div class="progress-bar"></div>
</div>
</div>
</div>
<h4>Data type</h4>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="Dose" type="checkbox"/>
<span>Dose experiments</span>
</label>
</div>
</div>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="Time" type="checkbox"/>
<span>Time series experiments</span>
</label>
</div>
</div>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="DoseTime" type="checkbox"/>
<span>Dose with Time series</span>
</label>
</div>
</div>
<div class="form-group shiny-input-container">
<div class="checkbox">
<label>
<input id="EdgeTime" type="checkbox"/>
<span>Interactions</span>
</label>
</div>
</div>
<div data-display-if="input.Dose==1">
<div class="form-group shiny-input-container">
<label>Choose Dose series file(s)</label>
<div class="input-group">
<label class="input-group-btn">
<span class="btn btn-default btn-file">
Browse...
<input id="DoseUpload" name="DoseUpload" type="file" style="display: none;" multiple="multiple"/>
</span>
</label>
<input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
</div>
<div id="DoseUpload_progress" class="progress progress-striped active shiny-file-input-progress">
<div class="progress-bar"></div>
</div>
</div>
</div>
<div data-display-if="input.Time==1">
<div class="form-group shiny-input-container">
<label>Choose Time series file(s)</label>
<div class="input-group">
<label class="input-group-btn">
<span class="btn btn-default btn-file">
Browse...
<input id="TimeUpload" name="TimeUpload" type="file" style="display: none;" multiple="multiple"/>
</span>
</label>
<input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
</div>
<div id="TimeUpload_progress" class="progress progress-striped active shiny-file-input-progress">
<div class="progress-bar"></div>
</div>
</div>
</div>
<div data-display-if="input.DoseTime==1">
<div class="form-group shiny-input-container">
<label>Choose Dose + Time series file(s)</label>
<div class="input-group">
<label class="input-group-btn">
<span class="btn btn-default btn-file">
Browse...
<input id="DoseTimeUpload" name="DoseTimeUpload" type="file" style="display: none;" multiple="multiple"/>
</span>
</label>
<input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
</div>
<div id="DoseTimeUpload_progress" class="progress progress-striped active shiny-file-input-progress">
<div class="progress-bar"></div>
</div>
</div>
</div>
<div data-display-if="input.EdgeTime==1">
<div class="form-group shiny-input-container">
<label>Choose interaction series file(s)</label>
<div class="input-group">
<label class="input-group-btn">
<span class="btn btn-default btn-file">
Browse...
<input id="EdgeInteractionUpload" name="DoseTimeUpload" type="file" style="display: none;" multiple="multiple"/>
</span>
</label>
<input type="text" class="form-control" placeholder="No file selected" readonly="readonly"/>
</div>
<div id="DoseTimeUpload_progress" class="progress progress-striped active shiny-file-input-progress">
<div class="progress-bar"></div>
</div>
</div>
</div>
<button type="button" class="btn btn-default action-button" id='StartAnalysis' onclick='showNetworkStyle()'>Upload data</button>
</div> <!-- well of the panel -->
</div> <!-- close colum 1: data upload part -->
<div class='row'>
<div id='NetworkStyle' class="col-sm-4">
<!-- open colum 3: Set the settings for network creation -->
<div class="well">
<!-- Container for the direction network checkbox -->
<div class="form-group shiny-input-container">
<div class="form-group shiny-input-container">
<h4>Step 2a: Directed/undirected network</h4>
<div class="form-group shiny-input-container" style="padding-left: 2em;"> <br />
<img src="DirectedNetworkPicture.png" alt="Directed" height="20" width="60">
<label>
<input id="Directed" name="Directed" type="checkbox">
<span>Directed</span>
</label>
</div><br />
<div class="form-group shiny-input-container" style="padding-left: 2em;"><br />
<img src="UndirectedNetworkPicture.png" alt="Directed" height="20" width="60">
<label>
<input id="Undirected" name="Undirected" type="checkbox" checked>
<span>Undirected</span>
</label>
</div>
</div>
<br />
<button id='DataMapOptionsChosen' class='btn btn-default action-button' onclick='showMapNetworkTodata()'>Set network characteristics</button>
</div>
</div>
</div>
<div class="col-sm-4" id='MapNetworkToData'> <!-- open colum 2: Mapping options -->
<div class="well" display='none'>
<!-- Container for the mapping checkbox -->
<div class="form-group shiny-input-container">
<h4> Step 2b: Connect network to database</h4>
<h5> Select organism:</h5>
<b> Selection</b>
<select id='inputOrganism'>
<option value='Homo_Sapiens'>Homo Sapiens</option>
<option value='Mus_Musculus'>Mus Musculus</option>
<option value='Rattus_Norvegicus'>Rattus Norvegicus</option>
</select>
<h4> Select gene identifier</h4>
<div class="checkbox">
<label>
<input id="MapGenesToDB" name="MapGenesToDB" type="checkbox" />
<span>Map nodes to database</span>
</label>
</div>
<div data-display-if="input.MapGenesToDB==1">
<div class="checkbox" style="padding-left: 2em;">
<label>
<input id="GeneName" name="GeneName" type="checkbox">
<span>Gene Name</span>
</label>
</div>
<div class="checkbox" style="padding-left: 2em;">
<label>
<input id="EntrezID" name="EntrezID" type="checkbox" checked>
<span>Entrez ID</span>
</label>
</div>
</div>
<button type="button" class="btn btn-default action-button" id='BuildNetwork' onclick='showLoadingButton()'>Build network</button>
</div>
</div>
</div>
</div>
</div>
</div>
<div id='buildingNetwork' style='display:none;'><text><b>building network</b></text></div>
<div id="loader" style="display:none;"></div>
<div id='networkBuildFinished' style='display:none;'><text><b>Network finished<br /> proceed to network visualization tab</b></text></div>
</div>
<script>
document.getElementById('MapNetworkToData').style.display='none'
document.getElementById('NetworkStyle').style.display='none'
function showMapNetworkTodata(){document.getElementById('MapNetworkToData').style.display='block'}
function showNetworkStyle(){document.getElementById('NetworkStyle').style.display='block'}
function showLoadingButton(){document.getElementById('buildingNetwork').style.display='block';document.getElementById('loader').style.display='block'}
</script>
<!-- tab content of the network visualization -->
<div class="tab-pane" data-value="Network visualization" id="tab-7438-3" >
<div class="container-fluid">
<div class="row">
<div class="col-sm-4">
<div class="w3-container" style="position:relative">
<button id='SettingsOptions' title='Set network options' type="button" class="btn btn-default action-button" >
<img src='SettingsButton.png' alt='Settings' />
</button>
<button id='ColorOptions' type="button" title='Set style colors' class="btn btn-default action-button" >
<img src='ColorOptions.png' alt='Color Options' />
</button>
<hr>
<div class='searchwrapper'>
<input type="searchbox" class="search" id="searchbar" placeholder="Search nodes" />
<button id='SearchButton' title='Search nodes in network' type='button' class='btn btn-default action-button'>
<img src='SearchButton.png' alt='Search Button' />
</button>
</div>
</div>
<hr>
<div class="panel-group" id="accordion">
<div class="panel panel-default">
<div class="panel-heading">
<h5 class="panel-title">
<a data-toggle="collapse" href="#collapse1">Threshold on node degree </a>
</h5>
</div>
<div id="collapse1" class="panel-collapse collapse">
<div class="panel-body">
<b> Threshold on node degree </b>
<form>
<b>Threshold degree </b><output name="nRadiusOutputName" id="nRadiusOutput">0</output><br>
<input type="range" value="0" min="0" max="50" id="nRadius" oninput='nRadiusOutput.value=nRadius.value' class="w3-bar-item w3-button" >
</form>
<form>
<b> Threshold on in-degree</b><br>
<b>Threshold indegree </b><output name="inDegreeOutputName" id="inDegreeOutput" >0</output><br>
<input type='range' value='0' min='0' max='50' id='inDegree' oninput='inDegreeOutput.value=inDegree.value' class="w3-bar-item w3-button" > <br>
</form>
<form>
<b> Treshold on out-degree</b><output name="outDegreeOutputName" id="outDegreeOutput" >0</output><br>
<input type='range' value='0' min='0' max='50' id='outDegree' oninput='outDegreeOutput.value=outDegree.value' class="w3-bar-item w3-button"> <br>
</form>
<br />
<b> Set Node size:</b>
<select id='OptionSetNodeSize'>
<option value='Off'>Off</option>
<option value='Degree'>Degree</option>
<option value='inDegree'>inDegree</option>
<option value='outDegree'>outDegree</option>
</select></div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" href="#collapse2">Show expression data</a>
</h4>
</div>
<div id="collapse2" class="panel-collapse collapse">
<div class="panel-body">
<b> Choose animation type </b><br />
<form action=''>
<input type='radio' name='DataControlVideo' value='ColorNodesTime' checked=true>Color nodes with expression <br />
<input type='radio' name='DataControlVideo' value='EdgeInteractionTime' >Edge interaction over time <br />
<input type='radio' name='DataControlVideo' value='NodeEdgeTime'> Color node + edge interaction <br />
<text> Animation control </text><br />
</form>
<button id='playButton' class='PlayerControls' >play</button>
<button id='pauseButton' class='PlayerControls' >pause</button>
<button id='forwardButton' class='PlayerControls'>forward</button>
<button id='backwardButton' class='PlayerControls'>backward</button><br />
<b> Loop Animation ?</b><br />
<form action=''>
<input type='radio' id='LoopAnimation' name='LoopAnimation' value='LoopedAnimation'>Loop animation
</form>
<b> Legend node expression<b><br/>
<div id='ColorBar' width='160px' height='30px'></div>
<b> Time/Dose point<b><br />
<div id='TimeStep2D'></div>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" href="#collapse3">Network analysis/ 3D network</a>
</h4>
</div>
<div id="collapse3" class="panel-collapse collapse">
<div class="panel-body">
<b> Subselection analysis</b><br />
<button id="Create2DlineGraph" class='btn btn-default action-button'> start analysis subselection </button><br/>
<b> Generate 3D network</b><br />
<button id='Generate3DNetwork' class='btn btn-default action-button'>Generate 3D network</button><br />
<b> Pathway histogram</b><br />
<button id='PathwayHist' type="button" class="btn btn-default action-button">Pathway histogram </button><br />
<b> identify HUB nodes </b><br />
<button id='HUBNodes' type="button" class="btn btn-default action-button" > HUB nodes </button><br />
<b> Dynamic HUB nodes </b><br />
<button id='HUBDynamic' type="button" class="btn btn-default action-button" > Dynamic HUB </button>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h4 class="panel-title">
<a data-toggle="collapse" href="#collapse4">Export image/animation</a>
</h4>
<div id="collapse4" class="panel-collapse collapse">
<button id='ExportImage' class='btn btn-default action-button'> export svg as image </button>
<button id='ExportAnimation' class='btn btn-default action-button'> export animation </button>
</div>
</div>
</div>
</div>
</div>
<div class="col-sm-8">
<div id="network-area"></div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="modal fade" id="2DLineGraphModal" role="dialog">
<div class="modal-dialog modal-lg">
<!-- Modal content-->
<div class="modal-content">
<div class="modal-header">
<text> 2D graph of log values</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<button id='ExportThisButton'type='button' class='close'>Export image</button>
<div id='PlotArea'></div>
</div>
</div>
</div>
</div>
<div class="modal fade" id="PathwayPlot" role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<text> Pathway histogram</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<button id='ExportPathwayList' type='button' class='close' style="marging:5px;">Export List Pathways </button>
<button id='ExportPathway'type='button' class='close'>Export image</button>
<div id='PlotPathwayBars' width='100%'></div>
</div>
</div>
</div>
</div>
<div class="modal fade" id="3DNetworkVisualizationModal" role="dialog">
<div class='modal-dialog modal-lg'>
<div class="modal-content">
<div class="modal-header" >
<button type="button" class="close" data-dismiss="modal">×</button>
<div class="tab-pane" data-value="3D visualization" id="tab-7438-5" >
<div class="container-fluid">
<div class='button-panel'>
<button id='TimeAnimation' class='toggle-data-btn'>Time animation</button>
<button id='PauseAnimation' class='toggle-data-btn'>Pause</button>
<button id='ForwardFrame' class='toggle-data-btn'>Forward</button>
<button id='BackwardFrame' class='toggle-data-btn'>Backward</button>
<div id='TimeStep'></div>
</div>
</div>
</div>
</div>
<div class="modal-body">
<div id='3Dnetworkvisualization' width='1500' height='700'></div>
</div>
</div>
</div>
</div>
<div class='modal fade' id= "ExportImageModal" role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<text> Export image</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<div class="form-group">
<label for="input-fileName">File name</label>
<input type="text" class="form-control" id="input-fileNameImage" value="Network" placeholder="Enter file name">
</div>
<button id='SaveImage'> Save </button>
</div>
</div>
</div>
</div>
<div class='modal fade' id= "ExportHistogram" role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<text> Export image</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<div class="form-group">
<label for="input-fileName">File name</label>
<input type="text" class="form-control" id="input-fileIHistogram" value="Histogram" placeholder="Enter file name">
</div>
<button id='ExportPathwayFile'> Save Graph </button>
</div>
</div>
</div>
</div>
<div class='modal fade' id="ExportLineGraph" role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<text> Export line graph</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<div class="form-group">
<label for="input-fileName">File name</label>
<input type="text" class="form-control" id="input-fileLineGraph" value="LineGraph" placeholder="Enter file name">
</div>
<button id='ExportLineGraphButton'> Save Graph </button>
</div>
</div>
</div>
</div>
<div class='modal fade' id='ExportAnimationModal' role= dialog >
<div class='modal-dialog modal-lg'>
<div class='modal-content'>
<div class='modal-header'>
<text> Export animation gif</text>
<button type='button' class='close' data-dismiss='modal'>×</button>
</div>
<div class='modal-body'>
<div class= 'form-group'>
<label for='input-fileName'>File name</label>
<input type='text' class='form-control' id='input-fileNameAnimation' value='NetworkAnimation' placeholder='Enter file Name'>
</div>
<button id='SaveAnimation' class='btn btn-default action-button'>Save</button>
</div>
</div>
</div>
</div>
<div class='modal fade' id= "DataAnalysisHUB" role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<text> Export image</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<div class="form-group">
<table id='DataTableHUB' class='display' width='100%'>
<thead>
<tr>
<th>GeneID</th>
<th>TotalDegree</th>
<th>Innerdegree</th>
<th>OuterDegree</th>
</tr>
</thead>
</table>
</div>
</div>
</div>
</div>
</div>
<div class='modal fade' id= "DataAnalysisHUBDynamic" role="dialog">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<text> Export image</text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class="modal-body">
<div class="form-group">
<table id='DataTableHUBDynamic' class='display' width='100%'>
<thead>
<tr>
<th>GeneID</th>
<th>Time point 1</th>
<th>Time point 2</th>
<th>Time point 3</th>
<th>Time point 4</th>
</tr>
</thead>
</table>
</div>
</div>
</div>
</div>
</div>
<div class='modal fade' id='NetworkSettingsModal' role='dialog'>
<div class='Modal-dialog modal-styleoptions'>
<div class='modal-content'>
<div class='modal-header'>
<text> Network style settings </text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class='modal-body'>
<table>
<tr>
<td><span>node size:</span></td>
<td><input id="NodeSizeNumber" type="number" value='4' width='49%' class='InputField'></td>
</tr>
<tr>
<td><span>Line style:</span><
<td><select id='LineStyle'>
<option value='Solid'>Solid line</option>
<option value='Dashed'>Dashed line</option>
<select>
</td>
</tr>
<tr>
<tr>
<td><span> link stroke color: </span></td>
<td><select id='LinkStrokeColor'>
<option value='Grey'>Grey</option>
<option value='Black'>Black</option>
<option value='Red'>Red</option>
<option value='Blue'>Blue</option>
<option value='Green'>Green</option>
<option value='Purple'>Purple</option>
<option value='White'>White</option>
</select></td>
</tr>
</table>
<button id='UploadChangesStyle'> Apply changes </button>
</div>
</div>
</div>
</div>
<div class='modal fade' id='ColorSettingsModal' role='dialog'>
<div class='Modal-dialog modal-styleoptions'>
<div class='modal-content'>
<div class='modal-header'>
<text> Color settings </text>
<button type="button" class="close" data-dismiss="modal">×</button>
</div>
<div class='modal-body'>
<table>
<tr>
<td><span>Node colorscale</span></td>
<td>
<select id='NodeExpressionColorStyle'>
<option value='RedGreenScale'>Red-Green scale</option>
<option value='RedBlueScale'>Red-Blue scale</option>
<option value='BrownGreenScale'> Brown-Green scale </option>
<option value='PurpleOrangeScale'> Purple-Orange scale </option>
<option value='SpectralScale'> Spectral scale </option>
<option value="RNASequencing"> RNAseq data</option>
</select>
</td>
</tr>
<tr>
<td><span> Background color: </span></td>
<td> <select id='BackgroundColorOptions'>
<option value='White'>White</option>
<option value='Black'>Black</option>
</select></td>
</tr>
</table>
<button id='UploadChangesStyle2'> Apply changes </button>
</div>
</div>
</div>
</div>
</body>
</html>