-
Notifications
You must be signed in to change notification settings - Fork 1
/
JRomanowska_2024-08-09.html
1153 lines (1040 loc) · 85.8 KB
/
JRomanowska_2024-08-09.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
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html lang="en"><head>
<script src="JRomanowska_2024-08-09_files/libs/clipboard/clipboard.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/quarto-html/tabby.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/quarto-html/popper.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="JRomanowska_2024-08-09_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="JRomanowska_2024-08-09_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="JRomanowska_2024-08-09_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="JRomanowska_2024-08-09_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.5.56">
<meta name="author" content="Julia Romanowska">
<meta name="dcterms.date" content="2024-08-09">
<title>mQTLs in ART</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="JRomanowska_2024-08-09_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="JRomanowska_2024-08-09_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
</style>
<link rel="stylesheet" href="JRomanowska_2024-08-09_files/libs/revealjs/dist/theme/quarto.css">
<link rel="stylesheet" href="extra.css">
<link href="JRomanowska_2024-08-09_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="JRomanowska_2024-08-09_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="JRomanowska_2024-08-09_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="JRomanowska_2024-08-09_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-titled.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-titled) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-titled .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-titled .callout-title p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-titled.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-titled.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-title {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-title {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-titled .callout-body > .callout-content > :last-child {
padding-bottom: 0.5rem;
margin-bottom: 0;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
}
div.callout-important .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-important.callout-style-default .callout-title {
background-color: #f7dddc
}
div.callout-warning {
border-left-color: #f0ad4e !important;
}
div.callout-warning .callout-icon::before {
background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAAAXNSR0IArs4c6QAAAERlWElmTU0AKgAAAAgAAYdpAAQAAAABAAAAGgAAAAAAA6ABAAMAAAABAAEAAKACAAQAAAABAAAAIKADAAQAAAABAAAAIAAAAACshmLzAAAETklEQVRYCeVWW2gcVRg+58yaTUnizqbipZeX4uWhBEniBaoUX1Ioze52t7sRq6APio9V9MEaoWlVsFasRq0gltaAPuxms8lu0gcviE/FFOstVbSIxgcv6SU7EZqmdc7v9+9mJtNks51NTUH84ed889/PP+cmxP+d5FIbMJmNbpREu4WUkiTtCicKny0l1pIKmBzovF2S+hIJHX8iEu3hZJ5lNZGqyRrGSIQpq15AzF28jgpeY6yk6GVdrfFqdrD6Iw+QlB8g0YS2g7dyQmXM/IDhBhT0UCiRf59lfqmmDvzRt6kByV/m4JjtzuaujMUM2c5Z2d6JdKrRb3K2q6mA+oYVz8JnDdKPmmNthzkAk/lN63sYPgevrguc72aZX/L9C6x09GYyxBgCX4NlvyGUHOKELlm5rXeR1kchuChJt4SSwyddZRXgvwMGvYo4QSlk3/zkHD8UHxwVJA6zjZZqP8v8kK8OWLnIZtLyCAJagYC4rTGW/9Pqj92N/c+LUaAj27movwbi19tk/whRCIE7Q9vyI6yvRpftAKVTdUjOW40X3h5OXsKCdmFcx0xlLJoSuQngnrJe7Kcjm4OMq9FlC7CMmScQANuNvjfP3PjGXDBaUQmbp296S5L4DrpbrHN1T87ZVEZVCzg1FF0Ft+dKrlLukI+/c9ENo+TvlTDbYFvuKPtQ9+l052rXrgKoWkDAFnvh0wTOmYn8R5f4k/jN/fZiCM1tQx9jQQ4ANhqG4hiL0qIFTGViG9DKB7GYzgubnpofgYRwO+DFjh0Zin2m4b/97EDkXkc+f6xYAPX0KK2I/7fUQuwzuwo/L3AkcjugPNixC8cHf0FyPjWlItmLxWw4Ou9YsQCr5fijMGoD/zpdRy95HRysyXA74MWOnscpO4j2y3HAVisw85hX5+AFBRSHt4ShfLFkIMXTqyKFc46xdzQM6XbAi702a7sy04J0+feReMFKp5q9esYLCqAZYw/k14E/xcLLsFElaornTuJB0svMuJINy8xkIYuL+xPAlWRceH6+HX7THJ0djLUom46zREu7tTkxwmf/FdOZ/sh6Q8qvEAiHpm4PJ4a/doJe0gH1t+aHRgCzOvBvJedEK5OFE5jpm4AGP2a8Dxe3gGJ/pAutug9Gp6he92CsSsWBaEcxGx0FHytmIpuqGkOpldqNYQK8cSoXvd+xLxXADw0kf6UkJNFtdo5MOgaLjiQOQHcn+A6h5NuL2s0qsC2LOM75PcF3yr5STuBSAcGG+meA14K/CI21HcS4LBT6tv0QAh8Dr5l93AhZzG5ZJ4VxAqdZUEl9z7WJ4aN+svMvwHHL21UKTd1mqvChH7/Za5xzXBBKrUcB0TQ+Ulgkfbi/H/YT5EptrGzsEK7tR1B7ln9BBwckYfMiuSqklSznIuoIIOM42MQO+QnduCoFCI0bpkzjCjddHPN/F+2Yu+sd9bKNpVwHhbS3LluK/0zgfwD0xYI5dXuzlQAAAABJRU5ErkJggg==');
}
div.callout-warning.callout-style-default .callout-title {
background-color: #fcefdc
}
div.callout-tip {
border-left-color: #02b875 !important;
}
div.callout-tip .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-tip.callout-style-default .callout-title {
background-color: #ccf1e3
}
div.callout-caution {
border-left-color: #fd7e14 !important;
}
div.callout-caution .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-caution.callout-style-default .callout-title {
background-color: #ffe5d0
}
</style>
<style type="text/css">
.reveal div.sourceCode {
margin: 0;
overflow: auto;
}
.reveal div.hanging-indent {
margin-left: 1em;
text-indent: -1em;
}
.reveal .slide:not(.center) {
height: 100%;
}
.reveal .slide.scrollable {
overflow-y: auto;
}
.reveal .footnotes {
height: 100%;
overflow-y: auto;
}
.reveal .slide .absolute {
position: absolute;
display: block;
}
.reveal .footnotes ol {
counter-reset: ol;
list-style-type: none;
margin-left: 0;
}
.reveal .footnotes ol li:before {
counter-increment: ol;
content: counter(ol) ". ";
}
.reveal .footnotes ol li > p:first-child {
display: inline-block;
}
.reveal .slide ul,
.reveal .slide ol {
margin-bottom: 0.5em;
}
.reveal .slide ul li,
.reveal .slide ol li {
margin-top: 0.4em;
margin-bottom: 0.2em;
}
.reveal .slide ul[role="tablist"] li {
margin-bottom: 0;
}
.reveal .slide ul li > *:first-child,
.reveal .slide ol li > *:first-child {
margin-block-start: 0;
}
.reveal .slide ul li > *:last-child,
.reveal .slide ol li > *:last-child {
margin-block-end: 0;
}
.reveal .slide .columns:nth-child(3) {
margin-block-start: 0.8em;
}
.reveal blockquote {
box-shadow: none;
}
.reveal .tippy-content>* {
margin-top: 0.2em;
margin-bottom: 0.7em;
}
.reveal .tippy-content>*:last-child {
margin-bottom: 0.2em;
}
.reveal .slide > img.stretch.quarto-figure-center,
.reveal .slide > img.r-stretch.quarto-figure-center {
display: block;
margin-left: auto;
margin-right: auto;
}
.reveal .slide > img.stretch.quarto-figure-left,
.reveal .slide > img.r-stretch.quarto-figure-left {
display: block;
margin-left: 0;
margin-right: auto;
}
.reveal .slide > img.stretch.quarto-figure-right,
.reveal .slide > img.r-stretch.quarto-figure-right {
display: block;
margin-left: auto;
margin-right: 0;
}
</style>
<link href="JRomanowska_2024-08-09_files/libs/htmltools-fill-0.5.8.1/fill.css" rel="stylesheet">
<script src="JRomanowska_2024-08-09_files/libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/d3-bundle-5.16.0/d3-bundle.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/d3-lasso-0.0.5/d3-lasso.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/save-svg-as-png-1.4.17/save-svg-as-png.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/flatbush-4.4.0/flatbush.min.js"></script>
<link href="JRomanowska_2024-08-09_files/libs/ggiraphjs-0.8.10/ggiraphjs.min.css" rel="stylesheet">
<script src="JRomanowska_2024-08-09_files/libs/ggiraphjs-0.8.10/ggiraphjs.min.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/girafe-binding-0.8.10/girafe.js"></script>
</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" data-background-image="figs/sergei-gussev-MFPrDj-9czI-unsplash.jpg" data-background-opacity="0.5" data-background-size="stretch" class="center">
<div class="left-column-title-slide">
<h1 class="title">mQTLs in ART</h1>
<p class="title">parents vs children</p>
<br>
<br>
<br>
<p class="author">Julia Romanowska</p>
<p class="date">2024-08-09</p>
</div>
<p style="position: absolute; bottom: 1px; right: 1px; font-size: small;">
Photo by <a href="https://unsplash.com/@sergei_gussev?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Sergei Gussev</a> on <a href="https://unsplash.com/photos/a-roller-coaster-going-down-a-hill-at-sunset-MFPrDj-9czI?utm_content=creditCopyText&utm_medium=referral&utm_source=unsplash">Unsplash</a>
</p>
</section>
<section id="outline" class="slide level2">
<h2>OUTLINE</h2>
<h3 id="mqtls"><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M160 32c0-17.7 14.3-32 32-32h32c17.7 0 32 14.3 32 32c17.7 0 32 14.3 32 32V288c0 17.7-14.3 32-32 32c0 17.7-14.3 32-32 32H192c-17.7 0-32-14.3-32-32c-17.7 0-32-14.3-32-32V64c0-17.7 14.3-32 32-32zM32 448H320c70.7 0 128-57.3 128-128s-57.3-128-128-128V128c106 0 192 86 192 192c0 49.2-18.5 94-48.9 128H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H320 32c-17.7 0-32-14.3-32-32s14.3-32 32-32zm80-64H304c8.8 0 16 7.2 16 16s-7.2 16-16 16H112c-8.8 0-16-7.2-16-16s7.2-16 16-16z"></path></svg> mQTLs</h3>
<h3 id="dnam-reprogramming"><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M160 32c0-17.7 14.3-32 32-32h32c17.7 0 32 14.3 32 32c17.7 0 32 14.3 32 32V288c0 17.7-14.3 32-32 32c0 17.7-14.3 32-32 32H192c-17.7 0-32-14.3-32-32c-17.7 0-32-14.3-32-32V64c0-17.7 14.3-32 32-32zM32 448H320c70.7 0 128-57.3 128-128s-57.3-128-128-128V128c106 0 192 86 192 192c0 49.2-18.5 94-48.9 128H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H320 32c-17.7 0-32-14.3-32-32s14.3-32 32-32zm80-64H304c8.8 0 16 7.2 16 16s-7.2 16-16 16H112c-8.8 0-16-7.2-16-16s7.2-16 16-16z"></path></svg> DNAm reprogramming</h3>
<h3 id="methods"><svg aria-hidden="true" role="img" viewbox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M64 96c0-35.3 28.7-64 64-64H512c35.3 0 64 28.7 64 64V352H512V96H128V352H64V96zM0 403.2C0 392.6 8.6 384 19.2 384H620.8c10.6 0 19.2 8.6 19.2 19.2c0 42.4-34.4 76.8-76.8 76.8H76.8C34.4 480 0 445.6 0 403.2zM281 209l-31 31 31 31c9.4 9.4 9.4 24.6 0 33.9s-24.6 9.4-33.9 0l-48-48c-9.4-9.4-9.4-24.6 0-33.9l48-48c9.4-9.4 24.6-9.4 33.9 0s9.4 24.6 0 33.9zM393 175l48 48c9.4 9.4 9.4 24.6 0 33.9l-48 48c-9.4 9.4-24.6 9.4-33.9 0s-9.4-24.6 0-33.9l31-31-31-31c-9.4-9.4-9.4-24.6 0-33.9s24.6-9.4 33.9 0z"></path></svg> methods</h3>
<h3 id="some-results"><svg aria-hidden="true" role="img" viewbox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M339.3 367.1c27.3-3.9 51.9-19.4 67.2-42.9L568.2 74.1c12.6-19.5 9.4-45.3-7.6-61.2S517.7-4.4 499.1 9.6L262.4 187.2c-24 18-38.2 46.1-38.4 76.1L339.3 367.1zm-19.6 25.4l-116-104.4C143.9 290.3 96 339.6 96 400c0 3.9 .2 7.8 .6 11.6C98.4 429.1 86.4 448 68.8 448H64c-17.7 0-32 14.3-32 32s14.3 32 32 32H208c61.9 0 112-50.1 112-112c0-2.5-.1-5-.2-7.5z"></path></svg> some results</h3>
<h3 id="discussion"><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M464 256A208 208 0 1 0 48 256a208 208 0 1 0 416 0zM0 256a256 256 0 1 1 512 0A256 256 0 1 1 0 256zm169.8-90.7c7.9-22.3 29.1-37.3 52.8-37.3h58.3c34.9 0 63.1 28.3 63.1 63.1c0 22.6-12.1 43.5-31.7 54.8L280 264.4c-.2 13-10.9 23.6-24 23.6c-13.3 0-24-10.7-24-24V250.5c0-8.6 4.6-16.5 12.1-20.8l44.3-25.4c4.7-2.7 7.6-7.7 7.6-13.1c0-8.4-6.8-15.1-15.1-15.1H222.6c-3.4 0-6.4 2.1-7.5 5.3l-.4 1.2c-4.4 12.5-18.2 19-30.6 14.6s-19-18.2-14.6-30.6l.4-1.2zM224 352a32 32 0 1 1 64 0 32 32 0 1 1 -64 0z"></path></svg> discussion</h3>
</section>
<section id="mqtl" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M160 32c0-17.7 14.3-32 32-32h32c17.7 0 32 14.3 32 32c17.7 0 32 14.3 32 32V288c0 17.7-14.3 32-32 32c0 17.7-14.3 32-32 32H192c-17.7 0-32-14.3-32-32c-17.7 0-32-14.3-32-32V64c0-17.7 14.3-32 32-32zM32 448H320c70.7 0 128-57.3 128-128s-57.3-128-128-128V128c106 0 192 86 192 192c0 49.2-18.5 94-48.9 128H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H320 32c-17.7 0-32-14.3-32-32s14.3-32 32-32zm80-64H304c8.8 0 16 7.2 16 16s-7.2 16-16 16H112c-8.8 0-16-7.2-16-16s7.2-16 16-16z"></path></svg> mQTL</h2>
<div class="center-box">
<p>SNP–CpG pair</p>
</div>
<ul>
<li><p><em>cis</em>-mQTLs and <em>trans</em>-mQTLs</p></li>
<li><p>indicating a functional connection between<br>
<em>methylation</em> status of that CpG and<br>
<em>allele</em> at that SNP</p></li>
</ul>
</section>
<section id="dnam-reprogramming-1" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M160 32c0-17.7 14.3-32 32-32h32c17.7 0 32 14.3 32 32c17.7 0 32 14.3 32 32V288c0 17.7-14.3 32-32 32c0 17.7-14.3 32-32 32H192c-17.7 0-32-14.3-32-32c-17.7 0-32-14.3-32-32V64c0-17.7 14.3-32 32-32zM32 448H320c70.7 0 128-57.3 128-128s-57.3-128-128-128V128c106 0 192 86 192 192c0 49.2-18.5 94-48.9 128H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H320 32c-17.7 0-32-14.3-32-32s14.3-32 32-32zm80-64H304c8.8 0 16 7.2 16 16s-7.2 16-16 16H112c-8.8 0-16-7.2-16-16s7.2-16 16-16z"></path></svg> DNAm reprogramming</h2>
<div class="center-box">
<p>wave of demethylation followed by rapid re-methylation</p>
</div>
<ul>
<li><p>paternal DNA is <em>demethylated</em> faster than maternal</p></li>
<li><p>at <strong>blastocyst</strong> stage, DNAm level is lowest (ca.20% of all CpGs)</p></li>
<li><p>freezing of eggs could influence de-methylation and differentiation</p></li>
</ul>
<p style="position: absolute; font-size: small; bottom: 10px; left: 5px;">
[src: Albert and Greenberg, Development (2023); Greenberg, Front.Cell Develop.Biol. (2021)]
</p>
<aside class="notes">
<p>Blastocyst = naive pluripotency stage; only imprinted regions and <em>transpose elements</em> (TEs) are methylated!</p>
<p>However, a lot of signalling is also done by methylation of histones!</p>
<style type="text/css">
span.MJX_Assistive_MathML {
position:absolute!important;
clip: rect(1px, 1px, 1px, 1px);
padding: 1px 0 0 0!important;
border: 0!important;
height: 1px!important;
width: 1px!important;
overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="aim" class="slide level2">
<h2>Aim</h2>
<div class="center-box">
<p><em>to check for differences in existence of mQTLs</em> between:</p>
</div>
<ul>
<li><p>parents <em>vs</em> children</p></li>
<li><p>ART <em>vs</em> non-ART</p></li>
</ul>
</section>
<section id="methods-1" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M64 96c0-35.3 28.7-64 64-64H512c35.3 0 64 28.7 64 64V352H512V96H128V352H64V96zM0 403.2C0 392.6 8.6 384 19.2 384H620.8c10.6 0 19.2 8.6 19.2 19.2c0 42.4-34.4 76.8-76.8 76.8H76.8C34.4 480 0 445.6 0 403.2zM281 209l-31 31 31 31c9.4 9.4 9.4 24.6 0 33.9s-24.6 9.4-33.9 0l-48-48c-9.4-9.4-9.4-24.6 0-33.9l48-48c9.4-9.4 24.6-9.4 33.9 0s9.4 24.6 0 33.9zM393 175l48 48c9.4 9.4 9.4 24.6 0 33.9l-48 48c-9.4 9.4-24.6 9.4-33.9 0s-9.4-24.6 0-33.9l31-31-31-31c-9.4-9.4-9.4-24.6 0-33.9s24.6-9.4 33.9 0z"></path></svg> methods</h2>
<h3 id="data"><svg aria-hidden="true" role="img" viewbox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M448 80v48c0 44.2-100.3 80-224 80S0 172.2 0 128V80C0 35.8 100.3 0 224 0S448 35.8 448 80zM393.2 214.7c20.8-7.4 39.9-16.9 54.8-28.6V288c0 44.2-100.3 80-224 80S0 332.2 0 288V186.1c14.9 11.8 34 21.2 54.8 28.6C99.7 230.7 159.5 240 224 240s124.3-9.3 169.2-25.3zM0 346.1c14.9 11.8 34 21.2 54.8 28.6C99.7 390.7 159.5 400 224 400s124.3-9.3 169.2-25.3c20.8-7.4 39.9-16.9 54.8-28.6V432c0 44.2-100.3 80-224 80S0 476.2 0 432V346.1z"></path></svg> data</h3>
<ul>
<li><p><strong>genetic data</strong> - MoBa</p></li>
<li><p><strong>epigenetic data</strong> - START</p></li>
</ul>
<img data-src="JRomanowska_2024-08-09_files/figure-revealjs/samples_final-1.png" alt="Boxplot showing that number of samples available in each category is comparable: 819 non-ART mothers, 779 ART mothers, 808 non-ART fathers, 784 ART fathers, 911 non-ART children, and 847 ART children." width="960" class="r-stretch"></section>
<section id="methods-2" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M64 96c0-35.3 28.7-64 64-64H512c35.3 0 64 28.7 64 64V352H512V96H128V352H64V96zM0 403.2C0 392.6 8.6 384 19.2 384H620.8c10.6 0 19.2 8.6 19.2 19.2c0 42.4-34.4 76.8-76.8 76.8H76.8C34.4 480 0 445.6 0 403.2zM281 209l-31 31 31 31c9.4 9.4 9.4 24.6 0 33.9s-24.6 9.4-33.9 0l-48-48c-9.4-9.4-9.4-24.6 0-33.9l48-48c9.4-9.4 24.6-9.4 33.9 0s9.4 24.6 0 33.9zM393 175l48 48c9.4 9.4 9.4 24.6 0 33.9l-48 48c-9.4 9.4-24.6 9.4-33.9 0s-9.4-24.6 0-33.9l31-31-31-31c-9.4-9.4-9.4-24.6 0-33.9s24.6-9.4 33.9 0z"></path></svg> methods</h2>
<h3 id="tools"><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M78.6 5C69.1-2.4 55.6-1.5 47 7L7 47c-8.5 8.5-9.4 22-2.1 31.6l80 104c4.5 5.9 11.6 9.4 19 9.4h54.1l109 109c-14.7 29-10 65.4 14.3 89.6l112 112c12.5 12.5 32.8 12.5 45.3 0l64-64c12.5-12.5 12.5-32.8 0-45.3l-112-112c-24.2-24.2-60.6-29-89.6-14.3l-109-109V104c0-7.5-3.5-14.5-9.4-19L78.6 5zM19.9 396.1C7.2 408.8 0 426.1 0 444.1C0 481.6 30.4 512 67.9 512c18 0 35.3-7.2 48-19.9L233.7 374.3c-7.8-20.9-9-43.6-3.6-65.1l-61.7-61.7L19.9 396.1zM512 144c0-10.5-1.1-20.7-3.2-30.5c-2.4-11.2-16.1-14.1-24.2-6l-63.9 63.9c-3 3-7.1 4.7-11.3 4.7H352c-8.8 0-16-7.2-16-16V102.6c0-4.2 1.7-8.3 4.7-11.3l63.9-63.9c8.1-8.1 5.2-21.8-6-24.2C388.7 1.1 378.5 0 368 0C288.5 0 224 64.5 224 144l0 .8 85.3 85.3c36-9.1 75.8 .5 104 28.7L429 274.5c49-23 83-72.8 83-130.5zM56 432a24 24 0 1 1 48 0 24 24 0 1 1 -48 0z"></path></svg> tools</h3>
<ul>
<li><p><code>PLINK</code></p></li>
<li><p><svg aria-hidden="true" role="img" viewbox="0 0 581 512" style="height:1em;width:1.13em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> (<code>MatrixEQTL</code> package)</p></li>
<li><p><code>snakemake</code></p></li>
</ul>
<aside class="notes">
<ul>
<li><code>JuliaLang</code></li>
</ul>
<style type="text/css">
span.MJX_Assistive_MathML {
position:absolute!important;
clip: rect(1px, 1px, 1px, 1px);
padding: 1px 0 0 0!important;
border: 0!important;
height: 1px!important;
width: 1px!important;
overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="methods-3" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M64 96c0-35.3 28.7-64 64-64H512c35.3 0 64 28.7 64 64V352H512V96H128V352H64V96zM0 403.2C0 392.6 8.6 384 19.2 384H620.8c10.6 0 19.2 8.6 19.2 19.2c0 42.4-34.4 76.8-76.8 76.8H76.8C34.4 480 0 445.6 0 403.2zM281 209l-31 31 31 31c9.4 9.4 9.4 24.6 0 33.9s-24.6 9.4-33.9 0l-48-48c-9.4-9.4-9.4-24.6 0-33.9l48-48c9.4-9.4 24.6-9.4 33.9 0s9.4 24.6 0 33.9zM393 175l48 48c9.4 9.4 9.4 24.6 0 33.9l-48 48c-9.4 9.4-24.6 9.4-33.9 0s-9.4-24.6 0-33.9l31-31-31-31c-9.4-9.4-9.4-24.6 0-33.9s24.6-9.4 33.9 0z"></path></svg> methods</h2>
<ol type="1">
<li><p>agnostic search for mQTLs <em>in parents</em></p></li>
<li><p>select the significant mQTLs</p></li>
<li><p>check for association <em>in children</em><br>
using two models:</p></li>
</ol>
<ul>
<li>DNAm <span class="math inline">\(\sim\)</span> SNP <span class="math inline">\(+\)</span> case_control_status</li>
<li>DNAm <span class="math inline">\(\sim\)</span> SNP <span class="math inline">\(\times\)</span> case_control_status</li>
</ul>
</section>
<section>
<section id="results" class="title-slide slide level1 center">
<h1><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M416 208c0 45.9-14.9 88.3-40 122.7L502.6 457.4c12.5 12.5 12.5 32.8 0 45.3s-32.8 12.5-45.3 0L330.7 376c-34.4 25.2-76.8 40-122.7 40C93.1 416 0 322.9 0 208S93.1 0 208 0S416 93.1 416 208zm-312 8v64c0 13.3 10.7 24 24 24s24-10.7 24-24l0-64c0-13.3-10.7-24-24-24s-24 10.7-24 24zm80-96V280c0 13.3 10.7 24 24 24s24-10.7 24-24V120c0-13.3-10.7-24-24-24s-24 10.7-24 24zm80 64v96c0 13.3 10.7 24 24 24s24-10.7 24-24V184c0-13.3-10.7-24-24-24s-24 10.7-24 24z"></path></svg> Results</h1>
<div style="font-size: 1.2em; font-weight: bold;">
<p><em>mQTLs in parents</em></p>
</div>
</section>
<section id="how-many-mqtl-pairs" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M64 0C28.7 0 0 28.7 0 64V448c0 35.3 28.7 64 64 64H320c35.3 0 64-28.7 64-64V64c0-35.3-28.7-64-64-64H64zM96 64H288c17.7 0 32 14.3 32 32v32c0 17.7-14.3 32-32 32H96c-17.7 0-32-14.3-32-32V96c0-17.7 14.3-32 32-32zm32 160a32 32 0 1 1 -64 0 32 32 0 1 1 64 0zM96 352a32 32 0 1 1 0-64 32 32 0 1 1 0 64zM64 416c0-17.7 14.3-32 32-32h96c17.7 0 32 14.3 32 32s-14.3 32-32 32H96c-17.7 0-32-14.3-32-32zM192 256a32 32 0 1 1 0-64 32 32 0 1 1 0 64zm32 64a32 32 0 1 1 -64 0 32 32 0 1 1 64 0zm64-64a32 32 0 1 1 0-64 32 32 0 1 1 0 64zm32 64a32 32 0 1 1 -64 0 32 32 0 1 1 64 0zM288 448a32 32 0 1 1 0-64 32 32 0 1 1 0 64z"></path></svg> How many mQTL pairs?</h2>
<blockquote>
<p><em>for chromosome 20 only!</em></p>
</blockquote>
<div class="cell">
<div class="cell-output-display">
<table class="caption-top">
<thead>
<tr class="header">
<th style="text-align: left;"></th>
<th style="text-align: right;"># tests</th>
<th style="text-align: right;"># all mQTLs</th>
<th style="text-align: right;"># signif mQTLs[*]</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">cis</td>
<td style="text-align: right;">107225852</td>
<td style="text-align: right;">107225852</td>
<td style="text-align: right;">6175</td>
</tr>
<tr class="even">
<td style="text-align: left;">trans</td>
<td style="text-align: right;">3191581264</td>
<td style="text-align: right;">256233</td>
<td style="text-align: right;">9105</td>
</tr>
</tbody>
</table>
</div>
</div>
<aside><div>
<p>[*] significance for <em>cis</em> based on FDR, for <em>trans</em>, based on Bonferroni</p>
</div></aside></section>
<section id="where-are-the-significant-mqtl-pairs" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M256 0c17.7 0 32 14.3 32 32V66.7C368.4 80.1 431.9 143.6 445.3 224H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H445.3C431.9 368.4 368.4 431.9 288 445.3V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V445.3C143.6 431.9 80.1 368.4 66.7 288H32c-17.7 0-32-14.3-32-32s14.3-32 32-32H66.7C80.1 143.6 143.6 80.1 224 66.7V32c0-17.7 14.3-32 32-32zM128 256a128 128 0 1 0 256 0 128 128 0 1 0 -256 0zm128-80a80 80 0 1 1 0 160 80 80 0 1 1 0-160z"></path></svg> Where are the significant mQTL pairs?</h2>
<div class="panel-tabset">
<ul id="tabset-1" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-1-1">Genomic position</a></li><li><a href="#tabset-1-2">Relative distance</a></li></ul>
<div class="tab-content">
<div id="tabset-1-1">
<div class="cell">
<div class="cell-output-display">
<div>
<figure>
<p><img data-src="JRomanowska_2024-08-09_files/figure-revealjs/plot_position-1.png" style="width:110.0%"></p>
</figure>
</div>
</div>
</div>
</div>
<div id="tabset-1-2">
<div class="cell">
<div class="cell-output-display">
<div>
<figure>
<p><img data-src="JRomanowska_2024-08-09_files/figure-revealjs/unnamed-chunk-5-1.png" width="960"></p>
</figure>
</div>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="how-many-connections" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M418.4 157.9c35.3-8.3 61.6-40 61.6-77.9c0-44.2-35.8-80-80-80c-43.4 0-78.7 34.5-80 77.5L136.2 151.1C121.7 136.8 101.9 128 80 128c-44.2 0-80 35.8-80 80s35.8 80 80 80c12.2 0 23.8-2.7 34.1-7.6L259.7 407.8c-2.4 7.6-3.7 15.8-3.7 24.2c0 44.2 35.8 80 80 80s80-35.8 80-80c0-27.7-14-52.1-35.4-66.4l37.8-207.7zM156.3 232.2c2.2-6.9 3.5-14.2 3.7-21.7l183.8-73.5c3.6 3.5 7.4 6.7 11.6 9.5L317.6 354.1c-5.5 1.3-10.8 3.1-15.8 5.5L156.3 232.2z"></path></svg> How many connections?</h2>
<div class="panel-tabset">
<ul id="tabset-2" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-2-1">Per SNP</a></li><li><a href="#tabset-2-2">Per CpG</a></li></ul>
<div class="tab-content">
<div id="tabset-2-1">
<div class="cell">
<div class="cell-output-display">
<div class="girafe html-widget html-fill-item" id="htmlwidget-39511acf20db24aeb285" style="width:110%;height:480px;"></div>
<script type="application/json" data-for="htmlwidget-39511acf20db24aeb285">{"x":{"html":"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' class='ggiraph-svg' role='graphics-document' id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a' viewBox='0 0 720 360'>\n <defs id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_defs'>\n <clipPath id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_c1'>\n <rect x='0' y='0' width='720' height='360'/>\n <\/clipPath>\n <clipPath id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_c2'>\n <rect x='146.84' y='0' width='426.32' height='360'/>\n <\/clipPath>\n <clipPath id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_c3'>\n <rect x='199.87' y='23.32' width='294.78' height='304.97'/>\n <\/clipPath>\n <\/defs>\n <g id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_rootg' class='ggiraph-svg-rootg'>\n <g clip-path='url(#svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_c1)'>\n <rect x='0' y='0' width='720' height='360' fill='#FFFFFF' fill-opacity='1' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.75' stroke-linejoin='round' stroke-linecap='round' class='ggiraph-svg-bg'/>\n <\/g>\n <g clip-path='url(#svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_c3)'>\n <polyline points='199.87,288.04 494.65,288.04' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='0.53' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='199.87,198.08 494.65,198.08' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='0.53' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='199.87,108.13 494.65,108.13' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='0.53' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='234.15,328.29 234.15,23.32' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='0.53' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='324.11,328.29 324.11,23.32' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='0.53' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='414.06,328.29 414.06,23.32' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='0.53' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='199.87,243.06 494.65,243.06' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='1.07' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='199.87,153.11 494.65,153.11' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='1.07' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='199.87,63.16 494.65,63.16' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='1.07' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='279.13,328.29 279.13,23.32' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='1.07' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='369.08,328.29 369.08,23.32' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='1.07' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='459.03,328.29 459.03,23.32' fill='none' stroke='#EBEBEB' stroke-opacity='1' stroke-width='1.07' stroke-linejoin='round' stroke-linecap='butt'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e1' cx='213.27' cy='314.43' r='1.87pt' fill='#193854' fill-opacity='1' stroke='none' title='SNP: rs75912699;&lt;br/&gt; CpG: cg26824325'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e2' cx='213.27' cy='301.22' r='1.87pt' fill='#152F49' fill-opacity='1' stroke='none' title='SNP: rs75912699;&lt;br/&gt; CpG: cg03595951'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e3' cx='213.27' cy='301.17' r='1.87pt' fill='#275278' fill-opacity='1' stroke='none' title='SNP: rs75912699;&lt;br/&gt; CpG: cg12512053'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e4' cx='213.27' cy='300.96' r='1.87pt' fill='#18344F' fill-opacity='1' stroke='none' title='SNP: rs75912699;&lt;br/&gt; CpG: cg20618996'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e5' cx='233.95' cy='297.03' r='1.87pt' fill='#3D7FB4' fill-opacity='1' stroke='none' title='SNP: rs373775601;&lt;br/&gt; CpG: cg20564458'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e6' cx='233.95' cy='297.03' r='1.87pt' fill='#3874A5' fill-opacity='1' stroke='none' title='SNP: rs373775601;&lt;br/&gt; CpG: cg05298461'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e7' cx='233.95' cy='295.31' r='1.87pt' fill='#1A3855' fill-opacity='1' stroke='none' title='SNP: rs373775601;&lt;br/&gt; CpG: cg22433521'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e8' cx='233.95' cy='287.06' r='1.87pt' fill='#265075' fill-opacity='1' stroke='none' title='SNP: rs373775601;&lt;br/&gt; CpG: cg02335030'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e9' cx='319.12' cy='207.47' r='1.87pt' fill='#132B43' fill-opacity='1' stroke='none' title='SNP: rs113035198;&lt;br/&gt; CpG: cg22984938'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e10' cx='319.12' cy='200.12' r='1.87pt' fill='#22496B' fill-opacity='1' stroke='none' title='SNP: rs113035198;&lt;br/&gt; CpG: cg12611551'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e11' cx='319.12' cy='197.77' r='1.87pt' fill='#3671A1' fill-opacity='1' stroke='none' title='SNP: rs113035198;&lt;br/&gt; CpG: cg05913229'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e12' cx='319.12' cy='196.18' r='1.87pt' fill='#204566' fill-opacity='1' stroke='none' title='SNP: rs113035198;&lt;br/&gt; CpG: cg12127137'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e13' cx='431.67' cy='96.5' r='1.87pt' fill='#4792CE' fill-opacity='1' stroke='none' title='SNP: rs142445519;&lt;br/&gt; CpG: cg17414900'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e14' cx='431.67' cy='96.5' r='1.87pt' fill='#448DC7' fill-opacity='1' stroke='none' title='SNP: rs142445519;&lt;br/&gt; CpG: cg01595162'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e15' cx='431.67' cy='92.8' r='1.87pt' fill='#204567' fill-opacity='1' stroke='none' title='SNP: rs142445519;&lt;br/&gt; CpG: cg14417820'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e16' cx='431.67' cy='91.51' r='1.87pt' fill='#244D71' fill-opacity='1' stroke='none' title='SNP: rs142445519;&lt;br/&gt; CpG: cg12720148'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e17' cx='466.67' cy='63.15' r='1.87pt' fill='#1D405F' fill-opacity='1' stroke='none' title='SNP: rs117045061;&lt;br/&gt; CpG: cg09618988'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e18' cx='466.67' cy='62.49' r='1.87pt' fill='#214668' fill-opacity='1' stroke='none' title='SNP: rs117045061;&lt;br/&gt; CpG: cg04863665'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e19' cx='466.67' cy='54.57' r='1.87pt' fill='#234C6F' fill-opacity='1' stroke='none' title='SNP: rs117045061;&lt;br/&gt; CpG: cg02524833'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e20' cx='466.67' cy='50.24' r='1.87pt' fill='#56B1F7' fill-opacity='1' stroke='none' title='SNP: rs117045061;&lt;br/&gt; CpG: cg03070473'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e21' cx='481.26' cy='41.2' r='1.87pt' fill='#244C70' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg06491828'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e22' cx='480.69' cy='37.19' r='1.87pt' fill='#4895D2' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg04630848'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e23' cx='480.96' cy='37.19' r='1.87pt' fill='#4792CE' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg04630848'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e24' cx='481.26' cy='37.19' r='1.87pt' fill='#4996D3' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg04630848'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e25' cx='480.69' cy='37.19' r='1.87pt' fill='#4B9AD9' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg13218906'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e26' cx='480.96' cy='37.19' r='1.87pt' fill='#4998D5' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg13218906'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e27' cx='481.17' cy='37.19' r='1.87pt' fill='#458FCA' fill-opacity='1' stroke='none' title='SNP: rs6011172;&lt;br/&gt; CpG: cg13218906'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e28' cx='481.25' cy='37.19' r='1.87pt' fill='#4894D0' fill-opacity='1' stroke='none' title='SNP: rs62219910;&lt;br/&gt; CpG: cg13218906'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e29' cx='481.26' cy='37.19' r='1.87pt' fill='#4C9DDC' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg13218906'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e30' cx='480.69' cy='37.19' r='1.87pt' fill='#438AC3' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg01182084'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e31' cx='480.96' cy='37.19' r='1.87pt' fill='#4288C0' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg01182084'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e32' cx='481.25' cy='37.19' r='1.87pt' fill='#4186BE' fill-opacity='1' stroke='none' title='SNP: rs62219910;&lt;br/&gt; CpG: cg01182084'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e33' cx='481.26' cy='37.19' r='1.87pt' fill='#448DC6' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg01182084'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e34' cx='480.69' cy='37.19' r='1.87pt' fill='#448EC8' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg26468205'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e35' cx='480.96' cy='37.19' r='1.87pt' fill='#438BC5' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg26468205'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e36' cx='481.17' cy='37.19' r='1.87pt' fill='#4186BD' fill-opacity='1' stroke='none' title='SNP: rs6011172;&lt;br/&gt; CpG: cg26468205'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e37' cx='481.25' cy='37.19' r='1.87pt' fill='#4289C1' fill-opacity='1' stroke='none' title='SNP: rs62219910;&lt;br/&gt; CpG: cg26468205'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e38' cx='481.26' cy='37.19' r='1.87pt' fill='#4590CA' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg26468205'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e39' cx='480.69' cy='37.19' r='1.87pt' fill='#3A78AA' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg08116199'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e40' cx='480.96' cy='37.19' r='1.87pt' fill='#3977A9' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg08116199'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e41' cx='481.17' cy='37.19' r='1.87pt' fill='#3875A7' fill-opacity='1' stroke='none' title='SNP: rs6011172;&lt;br/&gt; CpG: cg08116199'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e42' cx='481.25' cy='37.19' r='1.87pt' fill='#3976A8' fill-opacity='1' stroke='none' title='SNP: rs62219910;&lt;br/&gt; CpG: cg08116199'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e43' cx='481.26' cy='37.19' r='1.87pt' fill='#3A79AB' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg08116199'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e44' cx='480.69' cy='37.18' r='1.87pt' fill='#4996D3' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg27392956'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e45' cx='480.96' cy='37.18' r='1.87pt' fill='#4793CF' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg27392956'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e46' cx='481.17' cy='37.18' r='1.87pt' fill='#438AC2' fill-opacity='1' stroke='none' title='SNP: rs6011172;&lt;br/&gt; CpG: cg27392956'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e47' cx='481.25' cy='37.18' r='1.87pt' fill='#4690CB' fill-opacity='1' stroke='none' title='SNP: rs62219910;&lt;br/&gt; CpG: cg27392956'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e48' cx='481.26' cy='37.18' r='1.87pt' fill='#4A98D6' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg27392956'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e49' cx='480.69' cy='37.18' r='1.87pt' fill='#448CC5' fill-opacity='1' stroke='none' title='SNP: rs35738769;&lt;br/&gt; CpG: cg04820387'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e50' cx='480.96' cy='37.18' r='1.87pt' fill='#438AC3' fill-opacity='1' stroke='none' title='SNP: rs62219894;&lt;br/&gt; CpG: cg04820387'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e51' cx='481.17' cy='37.18' r='1.87pt' fill='#4084BA' fill-opacity='1' stroke='none' title='SNP: rs6011172;&lt;br/&gt; CpG: cg04820387'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e52' cx='481.25' cy='37.18' r='1.87pt' fill='#4288C0' fill-opacity='1' stroke='none' title='SNP: rs62219910;&lt;br/&gt; CpG: cg04820387'/>\n <circle id='svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_e53' cx='481.26' cy='37.18' r='1.87pt' fill='#458EC9' fill-opacity='1' stroke='none' title='SNP: rs11905704;&lt;br/&gt; CpG: cg04820387'/>\n <\/g>\n <g clip-path='url(#svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a_c1)'>\n <text x='165.37' y='246.27' font-size='6.6pt' font-family='DejaVu Sans' fill='#4D4D4D' fill-opacity='1'>4e+07<\/text>\n <text x='165.37' y='156.32' font-size='6.6pt' font-family='DejaVu Sans' fill='#4D4D4D' fill-opacity='1'>5e+07<\/text>\n <text x='165.37' y='66.37' font-size='6.6pt' font-family='DejaVu Sans' fill='#4D4D4D' fill-opacity='1'>6e+07<\/text>\n <text x='264.35' y='339.64' font-size='6.6pt' font-family='DejaVu Sans' fill='#4D4D4D' fill-opacity='1'>4e+07<\/text>\n <text x='354.3' y='339.64' font-size='6.6pt' font-family='DejaVu Sans' fill='#4D4D4D' fill-opacity='1'>5e+07<\/text>\n <text x='444.25' y='339.64' font-size='6.6pt' font-family='DejaVu Sans' fill='#4D4D4D' fill-opacity='1'>6e+07<\/text>\n <text x='323.87' y='352.23' font-size='8.25pt' font-family='DejaVu Sans'>SNP_pos<\/text>\n <text transform='translate(160.34,199.88) rotate(-90.00)' font-size='8.25pt' font-family='DejaVu Sans'>CpG_pos<\/text>\n <text x='511.09' y='106.38' font-size='8.25pt' font-family='DejaVu Sans'>type<\/text>\n <circle cx='519.73' cy='121.65' r='1.87pt' fill='#000000' fill-opacity='1' stroke='none'/>\n <text x='533.85' y='124.86' font-size='6.6pt' font-family='DejaVu Sans'>cis<\/text>\n <text x='511.09' y='161.37' font-size='8.25pt' font-family='DejaVu Sans'>beta<\/text>\n <image x='511.09' y='168' width='17.28' height='86.4' preserveAspectRatio='none' xlink:href='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAEsCAYAAAACUNnVAAAAmElEQVQ4ja2UQRLDMAgDd3hk/tnX5agcknFaCoa0vnkMCEnGsL12GQhDYDpPwoDrpBFlRDWi/9Wu6AHC9FkLYLrzlhD3oJ3mDvRHRYy7IC8A7bCK8gpWKYDzeQVArDcDyD2YAnSofZvzaOA6Q7Oahp/dmRuVTQ0xU5TGP2o8Waool1obVuv1q8qP9xPvg633XlGLDtfIhNUBcBeA5ss0BXMAAAAASUVORK5CYII=' xmlns:xlink='http://www.w3.org/1999/xlink'/>\n <polyline points='524.92,249.93 528.37,249.93' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='524.92,229.90 528.37,229.90' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='524.92,209.87 528.37,209.87' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='524.92,189.84 528.37,189.84' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='524.92,169.81 528.37,169.81' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='514.55,249.93 511.09,249.93' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='514.55,229.90 511.09,229.90' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='514.55,209.87 511.09,209.87' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='514.55,189.84 511.09,189.84' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <polyline points='514.55,169.81 511.09,169.81' fill='none' stroke='#FFFFFF' stroke-opacity='1' stroke-width='0.37' stroke-linejoin='round' stroke-linecap='butt'/>\n <text x='533.85' y='253.14' font-size='6.6pt' font-family='DejaVu Sans'>-0.010<\/text>\n <text x='533.85' y='233.11' font-size='6.6pt' font-family='DejaVu Sans'>-0.005<\/text>\n <text x='533.85' y='213.08' font-size='6.6pt' font-family='DejaVu Sans'>0.000<\/text>\n <text x='533.85' y='193.05' font-size='6.6pt' font-family='DejaVu Sans'>0.005<\/text>\n <text x='533.85' y='173.02' font-size='6.6pt' font-family='DejaVu Sans'>0.010<\/text>\n <text x='199.87' y='15.1' font-size='9.9pt' font-family='DejaVu Sans'>most connected SNPs<\/text>\n <\/g>\n <\/g>\n<\/svg>","js":null,"uid":"svg_a7e3be35_e06f_4c2f_8b52_b2a7e0e6961a","ratio":2,"settings":{"tooltip":{"css":".tooltip_SVGID_ { padding:5px;background:black;color:white;border-radius:2px;text-align:left; ; position:absolute;pointer-events:none;z-index:999;}","placement":"doc","opacity":0.9,"offx":10,"offy":10,"use_cursor_pos":true,"use_fill":false,"use_stroke":false,"delay_over":200,"delay_out":500},"hover":{"css":".hover_data_SVGID_ { fill:orange;stroke:black;cursor:pointer; }\ntext.hover_data_SVGID_ { stroke:none;fill:orange; }\ncircle.hover_data_SVGID_ { fill:orange;stroke:black; }\nline.hover_data_SVGID_, polyline.hover_data_SVGID_ { fill:none;stroke:orange; }\nrect.hover_data_SVGID_, polygon.hover_data_SVGID_, path.hover_data_SVGID_ { fill:orange;stroke:none; }\nimage.hover_data_SVGID_ { stroke:orange; }","reactive":true,"nearest_distance":null},"hover_inv":{"css":""},"hover_key":{"css":".hover_key_SVGID_ { fill:orange;stroke:black;cursor:pointer; }\ntext.hover_key_SVGID_ { stroke:none;fill:orange; }\ncircle.hover_key_SVGID_ { fill:orange;stroke:black; }\nline.hover_key_SVGID_, polyline.hover_key_SVGID_ { fill:none;stroke:orange; }\nrect.hover_key_SVGID_, polygon.hover_key_SVGID_, path.hover_key_SVGID_ { fill:orange;stroke:none; }\nimage.hover_key_SVGID_ { stroke:orange; }","reactive":true},"hover_theme":{"css":".hover_theme_SVGID_ { fill:orange;stroke:black;cursor:pointer; }\ntext.hover_theme_SVGID_ { stroke:none;fill:orange; }\ncircle.hover_theme_SVGID_ { fill:orange;stroke:black; }\nline.hover_theme_SVGID_, polyline.hover_theme_SVGID_ { fill:none;stroke:orange; }\nrect.hover_theme_SVGID_, polygon.hover_theme_SVGID_, path.hover_theme_SVGID_ { fill:orange;stroke:none; }\nimage.hover_theme_SVGID_ { stroke:orange; }","reactive":true},"select":{"css":".select_data_SVGID_ { fill:red;stroke:black;cursor:pointer; }\ntext.select_data_SVGID_ { stroke:none;fill:red; }\ncircle.select_data_SVGID_ { fill:red;stroke:black; }\nline.select_data_SVGID_, polyline.select_data_SVGID_ { fill:none;stroke:red; }\nrect.select_data_SVGID_, polygon.select_data_SVGID_, path.select_data_SVGID_ { fill:red;stroke:none; }\nimage.select_data_SVGID_ { stroke:red; }","type":"multiple","only_shiny":true,"selected":[]},"select_inv":{"css":""},"select_key":{"css":".select_key_SVGID_ { fill:red;stroke:black;cursor:pointer; }\ntext.select_key_SVGID_ { stroke:none;fill:red; }\ncircle.select_key_SVGID_ { fill:red;stroke:black; }\nline.select_key_SVGID_, polyline.select_key_SVGID_ { fill:none;stroke:red; }\nrect.select_key_SVGID_, polygon.select_key_SVGID_, path.select_key_SVGID_ { fill:red;stroke:none; }\nimage.select_key_SVGID_ { stroke:red; }","type":"single","only_shiny":true,"selected":[]},"select_theme":{"css":".select_theme_SVGID_ { fill:red;stroke:black;cursor:pointer; }\ntext.select_theme_SVGID_ { stroke:none;fill:red; }\ncircle.select_theme_SVGID_ { fill:red;stroke:black; }\nline.select_theme_SVGID_, polyline.select_theme_SVGID_ { fill:none;stroke:red; }\nrect.select_theme_SVGID_, polygon.select_theme_SVGID_, path.select_theme_SVGID_ { fill:red;stroke:none; }\nimage.select_theme_SVGID_ { stroke:red; }","type":"single","only_shiny":true,"selected":[]},"zoom":{"min":1,"max":1,"duration":300},"toolbar":{"position":"topright","pngname":"diagram","tooltips":null,"fixed":false,"hidden":[],"delay_over":200,"delay_out":500},"sizing":{"rescale":true,"width":1}}},"evals":[],"jsHooks":[]}</script>
</div>
</div>
</div>
<div id="tabset-2-2">
<div class="cell">
<div class="cell-output-display">
<div>
<figure>
<p><img data-src="JRomanowska_2024-08-09_files/figure-revealjs/plot_position_most_connected_cpg-1.png" style="width:110.0%"></p>
</figure>
</div>
</div>
</div>
</div>
</div>
</div>
</section></section>
<section>
<section id="results-1" class="title-slide slide level1 center">
<h1><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M416 208c0 45.9-14.9 88.3-40 122.7L502.6 457.4c12.5 12.5 12.5 32.8 0 45.3s-32.8 12.5-45.3 0L330.7 376c-34.4 25.2-76.8 40-122.7 40C93.1 416 0 322.9 0 208S93.1 0 208 0S416 93.1 416 208zm-312 8v64c0 13.3 10.7 24 24 24s24-10.7 24-24l0-64c0-13.3-10.7-24-24-24s-24 10.7-24 24zm80-96V280c0 13.3 10.7 24 24 24s24-10.7 24-24V120c0-13.3-10.7-24-24-24s-24 10.7-24 24zm80 64v96c0 13.3 10.7 24 24 24s24-10.7 24-24V184c0-13.3-10.7-24-24-24s-24 10.7-24 24z"></path></svg> Results</h1>
<div style="font-size: 1.2em; font-weight: bold;">
<p><em>mQTLs in children</em></p>
</div>
</section>
<section id="where-are-the-confirmed-mqtls" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M256 0c17.7 0 32 14.3 32 32V66.7C368.4 80.1 431.9 143.6 445.3 224H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H445.3C431.9 368.4 368.4 431.9 288 445.3V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V445.3C143.6 431.9 80.1 368.4 66.7 288H32c-17.7 0-32-14.3-32-32s14.3-32 32-32H66.7C80.1 143.6 143.6 80.1 224 66.7V32c0-17.7 14.3-32 32-32zM128 256a128 128 0 1 0 256 0 128 128 0 1 0 -256 0zm128-80a80 80 0 1 1 0 160 80 80 0 1 1 0-160z"></path></svg> Where are the confirmed mQTLs?</h2>
<p><em>model:</em> additive</p>
<p>296 mQTLs (out of 6175) were confirmed <em>in children</em></p>
<img data-src="JRomanowska_2024-08-09_files/figure-revealjs/plot_signif_mqtls_confirmed_add_model-1.png" style="width:110.0%" alt="Only some of the cis-mQTLs found to be significant in parents were confirmed with the additive model. This plot shows that there is no clustering of those confirmed mQTLs within chromosome 20." class="r-stretch"></section>
<section id="where-are-the-mqtls-with-interaction" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M256 0c17.7 0 32 14.3 32 32V66.7C368.4 80.1 431.9 143.6 445.3 224H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H445.3C431.9 368.4 368.4 431.9 288 445.3V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V445.3C143.6 431.9 80.1 368.4 66.7 288H32c-17.7 0-32-14.3-32-32s14.3-32 32-32H66.7C80.1 143.6 143.6 80.1 224 66.7V32c0-17.7 14.3-32 32-32zM128 256a128 128 0 1 0 256 0 128 128 0 1 0 -256 0zm128-80a80 80 0 1 1 0 160 80 80 0 1 1 0-160z"></path></svg> Where are the mQTLs with interaction?</h2>
<div style="font-size: 0.8em;">
<p><em>model:</em> interaction</p>
<p>314 mQTLs (out of 6175) had significant interaction with ART-status <em>in children</em></p>
</div>
<img data-src="JRomanowska_2024-08-09_files/figure-revealjs/plot_signif_mqtls_confirmed_interact_model-1.png" style="width:110.0%" alt="Only some of the cis-mQTLs found to be significant in parents had significant interaction with ART-status in children. This plot shows that there is no clustering of those mQTLs within chromosome 20." class="r-stretch"></section>
<section id="zooming-in" class="slide level2">
<h2><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M416 208c0 45.9-14.9 88.3-40 122.7L502.6 457.4c12.5 12.5 12.5 32.8 0 45.3s-32.8 12.5-45.3 0L330.7 376c-34.4 25.2-76.8 40-122.7 40C93.1 416 0 322.9 0 208S93.1 0 208 0S416 93.1 416 208zM288 176c0-44.2-35.8-80-80-80s-80 35.8-80 80c0 48.8 46.5 111.6 68.6 138.6c6 7.3 16.8 7.3 22.7 0c22.1-27 68.6-89.8 68.6-138.6zm-112 0a32 32 0 1 1 64 0 32 32 0 1 1 -64 0z"></path></svg> Zooming in…</h2>
<div class="panel-tabset">
<ul id="tabset-3" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-3-1">Part 1</a></li><li><a href="#tabset-3-2">Part 2</a></li><li><a href="#tabset-3-3">Part 3</a></li></ul>
<div class="tab-content">
<div id="tabset-3-1">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="figs/genes_and_loops_part1.png"></p>
<figcaption>Part1</figcaption>
</figure>
</div>
</div>
<div id="tabset-3-2">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="figs/genes_and_loops_part2.png"></p>
<figcaption>Part2</figcaption>
</figure>
</div>
</div>
<div id="tabset-3-3">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="figs/genes_and_loops_part3.png"></p>
<figcaption>Part3</figcaption>
</figure>
</div>
</div>
</div>
</div>
</section></section>
<section id="discussion-1" class="title-slide slide level1 center">
<h1><svg aria-hidden="true" role="img" viewbox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M464 256A208 208 0 1 0 48 256a208 208 0 1 0 416 0zM0 256a256 256 0 1 1 512 0A256 256 0 1 1 0 256zm169.8-90.7c7.9-22.3 29.1-37.3 52.8-37.3h58.3c34.9 0 63.1 28.3 63.1 63.1c0 22.6-12.1 43.5-31.7 54.8L280 264.4c-.2 13-10.9 23.6-24 23.6c-13.3 0-24-10.7-24-24V250.5c0-8.6 4.6-16.5 12.1-20.8l44.3-25.4c4.7-2.7 7.6-7.7 7.6-13.1c0-8.4-6.8-15.1-15.1-15.1H222.6c-3.4 0-6.4 2.1-7.5 5.3l-.4 1.2c-4.4 12.5-18.2 19-30.6 14.6s-19-18.2-14.6-30.6l.4-1.2zM224 352a32 32 0 1 1 64 0 32 32 0 1 1 -64 0z"></path></svg> Discussion</h1>
<aside class="notes">
<p>DNAmethylation depends on a lot of variables! e.g., folate supplement or vitamin supplement during pregnancy</p>
<style type="text/css">
span.MJX_Assistive_MathML {
position:absolute!important;
clip: rect(1px, 1px, 1px, 1px);
padding: 1px 0 0 0!important;
border: 0!important;
height: 1px!important;
width: 1px!important;
overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section>
<section id="extra-slides" class="title-slide slide level1 center">
<h1><svg aria-hidden="true" role="img" viewbox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M287.9 0c9.2 0 17.6 5.2 21.6 13.5l68.6 141.3 153.2 22.6c9 1.3 16.5 7.6 19.3 16.3s.5 18.1-5.9 24.5L433.6 328.4l26.2 155.6c1.5 9-2.2 18.1-9.6 23.5s-17.3 6-25.3 1.7l-137-73.2L151 509.1c-8.1 4.3-17.9 3.7-25.3-1.7s-11.2-14.5-9.7-23.5l26.2-155.6L31.1 218.2c-6.5-6.4-8.7-15.9-5.9-24.5s10.3-14.9 19.3-16.3l153.2-22.6L266.3 13.5C270.4 5.2 278.7 0 287.9 0zm0 79L235.4 187.2c-3.5 7.1-10.2 12.1-18.1 13.3L99 217.9 184.9 303c5.5 5.5 8.1 13.3 6.8 21L171.4 443.7l105.2-56.2c7.1-3.8 15.6-3.8 22.6 0l105.2 56.2L384.2 324.1c-1.3-7.7 1.2-15.5 6.8-21l85.9-85.1L358.6 200.5c-7.8-1.2-14.6-6.1-18.1-13.3L287.9 79z"></path></svg> Extra slides</h1>
</section>
<section id="strongest-associations-additive-model" class="slide level2">
<h2>‘Strongest’ associations, additive model</h2>
<div class="cell">
<div class="cell-output cell-output-stdout">
<pre><code> SNP gene term estimate std.error statistic p.value
<char> <char> <char> <num> <num> <num> <num>
1: rs142527558 cg10797920 SNP1 0.03434030 0.007438696 4.616441 4.187951e-06
2: rs79359164 cg26680502 SNP1 0.01845339 0.006365479 2.898980 3.790711e-03
3: rs79033469 cg00794607 SNP1 -0.01758346 0.008407823 -2.091322 3.664345e-02
4: rs35849074 cg26680502 SNP1 0.01739812 0.006135291 2.835745 4.624445e-03
5: rs188100838 cg26680502 SNP1 0.01596453 0.005673459 2.813898 4.949335e-03
6: rs8126087 cg20937230 SNP1 -0.01574302 0.007539033 -2.088202 3.692445e-02
conf.low conf.high SNP_pos CpG_pos
<num> <num> <int> <int>
1: 0.019750642 0.0489299635 61586712 62495449
2: 0.005968599 0.0309381864 37764667 37433765
3: -0.034073923 -0.0010930005 30953516 30143151
4: 0.005364851 0.0294313831 37659385 37433765
5: 0.004837043 0.0270920202 37462351 37433765
6: -0.030529526 -0.0009565226 976128 725968</code></pre>
</div>
<div class="cell-output cell-output-stdout">
<pre><code> SNP gene term estimate std.error statistic
<char> <char> <char> <num> <num> <num>
1: rs142892531 cg04446876 SNP1 -0.009995664 0.001500043 -6.663587
2: rs41278236 cg11145914 SNP1 -0.010154342 0.001545462 -6.570425
3: rs16987038 cg20606255 SNP1 0.011110467 0.001986969 5.591665
4: rs45555040 cg20606255 SNP1 0.011083456 0.001986446 5.579541
5: rs144117172 cg10817792 SNP1 -0.005553789 0.001184940 -4.686979
6: rs142527558 cg10797920 SNP1 0.034340303 0.007438696 4.616441
p.value conf.low conf.high SNP_pos CpG_pos
<num> <num> <num> <int> <int>
1: 3.577903e-11 -0.012937746 -0.007053582 59699754 60630424
2: 6.595683e-11 -0.013185485 -0.007123199 62641605 62564447
3: 2.604532e-08 0.007213384 0.015007551 36551349 36839442
4: 2.789096e-08 0.007187401 0.014979512 36794916 36839442
5: 2.988150e-06 -0.007877844 -0.003229734 57292298 57004379
6: 4.187951e-06 0.019750642 0.048929963 61586712 62495449</code></pre>
</div>
</div>
</section>
<section id="volcano-plot-additive-model" class="slide level2">
<h2>Volcano plot, additive model</h2>
<img data-src="JRomanowska_2024-08-09_files/figure-revealjs/volcano_plot_additive_model-1.png" width="960" class="r-stretch"></section>
<section id="strongest-associations-interaction-model" class="slide level2">
<h2>‘Strongest’ associations, interaction model</h2>
<div class="cell">
<div class="cell-output cell-output-stdout">
<pre><code> SNP gene term estimate std.error
<char> <char> <char> <num> <num>
1: rs142892531 cg04446876 SNP1:case_controlSTART 0.01944484 0.002965239
2: rs16987038 cg20606255 SNP1:case_controlSTART -0.02364613 0.003937080
3: rs45555040 cg20606255 SNP1:case_controlSTART -0.02352914 0.003936437
4: rs117654917 cg12204262 SNP1:case_controlSTART 0.02264140 0.004103064
5: rs144117172 cg10817792 SNP1:case_controlSTART -0.01298584 0.002358332
6: rs41278236 cg11145914 SNP1:case_controlSTART -0.01432727 0.003105520
7: rs142527558 cg10797920 SNP1:case_controlSTART -0.06688452 0.014945962
8: rs117226334 cg19122601 SNP1:case_controlSTART 0.01394780 0.003153570
9: rs117696074 cg09453598 SNP1:case_controlSTART 0.01940239 0.004410773
10: rs182484229 cg06448079 SNP1:case_controlSTART 0.01415210 0.003286212
statistic p.value conf.low conf.high SNP_pos CpG_pos
<num> <num> <num> <num> <int> <int>
1: 6.557597 7.194759e-11 0.013629022 0.025260666 59699754 60630424
2: -6.006009 2.307551e-09 -0.031368012 -0.015924256 36551349 36839442
3: -5.977269 2.743626e-09 -0.031249754 -0.015808525 36794916 36839442
4: 5.518168 3.939374e-08 0.014593963 0.030688837 2106677 1249928
5: -5.506367 4.209472e-08 -0.017611304 -0.008360381 57292298 57004379
6: -4.613485 4.247084e-06 -0.020418188 -0.008236356 62641605 62564447
7: -4.475089 8.130124e-06 -0.096198338 -0.037570694 61586712 62495449
8: 4.422859 1.034044e-05 0.007762630 0.020132964 55517482 56254598
9: 4.398864 1.154167e-05 0.010751414 0.028053370 38891003 39288278
10: 4.306509 1.750905e-05 0.007706764 0.020597434 57327746 57565177</code></pre>
</div>
</div>
<div class="quarto-auto-generated-content">
<p><img src="figs/UiBmerke_grayscaleV8_black_transp.png" class="slide-logo"></p>
<div class="footer footer-default">
</div>
</div>
</section></section>
</div>
</div>
<script>window.backupDefine = window.define; window.define = undefined;</script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/dist/reveal.js"></script>
<!-- reveal.js plugins -->
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/pdf-export/pdfexport.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/reveal-menu/menu.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/reveal-menu/quarto-menu.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/quarto-support/support.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/notes/notes.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/search/search.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/zoom/zoom.js"></script>
<script src="JRomanowska_2024-08-09_files/libs/revealjs/plugin/math/math.js"></script>
<script>window.define = window.backupDefine; window.backupDefine = undefined;</script>
<script>
// Full list of configuration options available at:
// https://revealjs.com/config/
Reveal.initialize({
'controlsAuto': true,
'previewLinksAuto': false,
'pdfSeparateFragments': false,
'autoAnimateEasing': "ease",
'autoAnimateDuration': 1,
'autoAnimateUnmatched': true,
'menu': {"side":"left","useTextContentForMissingTitles":true,"markers":false,"loadIcons":false,"custom":[{"title":"Tools","icon":"<i class=\"fas fa-gear\"></i>","content":"<ul class=\"slide-menu-items\">\n<li class=\"slide-tool-item active\" data-item=\"0\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.fullscreen(event)\"><kbd>f</kbd> Fullscreen</a></li>\n<li class=\"slide-tool-item\" data-item=\"1\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.speakerMode(event)\"><kbd>s</kbd> Speaker View</a></li>\n<li class=\"slide-tool-item\" data-item=\"2\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.overview(event)\"><kbd>o</kbd> Slide Overview</a></li>\n<li class=\"slide-tool-item\" data-item=\"3\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.togglePdfExport(event)\"><kbd>e</kbd> PDF Export Mode</a></li>\n<li class=\"slide-tool-item\" data-item=\"4\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.keyboardHelp(event)\"><kbd>?</kbd> Keyboard Help</a></li>\n</ul>"}],"openButton":true},
'smaller': false,
// Display controls in the bottom right corner
controls: false,
// Help the user learn the controls by providing hints, for example by
// bouncing the down arrow when they first encounter a vertical slide
controlsTutorial: false,
// Determines where controls appear, "edges" or "bottom-right"
controlsLayout: 'edges',
// Visibility rule for backwards navigation arrows; "faded", "hidden"
// or "visible"
controlsBackArrows: 'faded',
// Display a presentation progress bar
progress: true,
// Display the page number of the current slide
slideNumber: false,
// 'all', 'print', or 'speaker'
showSlideNumber: 'all',
// Add the current slide number to the URL hash so that reloading the
// page/copying the URL will return you to the same slide
hash: true,
// Start with 1 for the hash rather than 0
hashOneBasedIndex: false,
// Flags if we should monitor the hash and change slides accordingly
respondToHashChanges: true,
// Push each slide change to the browser history
history: true,
// Enable keyboard shortcuts for navigation
keyboard: true,
// Enable the slide overview mode
overview: true,
// Disables the default reveal.js slide layout (scaling and centering)
// so that you can use custom CSS layout
disableLayout: false,
// Vertical centering of slides
center: false,
// Enables touch navigation on devices with touch input
touch: true,
// Loop the presentation
loop: false,
// Change the presentation direction to be RTL
rtl: false,
// see https://revealjs.com/vertical-slides/#navigation-mode
navigationMode: 'linear',
// Randomizes the order of slides each time the presentation loads
shuffle: false,
// Turns fragments on and off globally
fragments: true,
// Flags whether to include the current fragment in the URL,
// so that reloading brings you to the same fragment position
fragmentInURL: false,
// Flags if the presentation is running in an embedded mode,
// i.e. contained within a limited portion of the screen
embedded: false,
// Flags if we should show a help overlay when the questionmark
// key is pressed
help: true,
// Flags if it should be possible to pause the presentation (blackout)
pause: true,
// Flags if speaker notes should be visible to all viewers
showNotes: false,
// Global override for autoplaying embedded media (null/true/false)
autoPlayMedia: null,
// Global override for preloading lazy-loaded iframes (null/true/false)
preloadIframes: null,
// Number of milliseconds between automatically proceeding to the
// next slide, disabled when set to 0, this value can be overwritten
// by using a data-autoslide attribute on your slides
autoSlide: 0,
// Stop auto-sliding after user input
autoSlideStoppable: true,
// Use this method for navigation when auto-sliding
autoSlideMethod: null,
// Specify the average time in seconds that you think you will spend
// presenting each slide. This is used to show a pacing timer in the
// speaker view
defaultTiming: null,
// Enable slide navigation via mouse wheel
mouseWheel: false,
// The display mode that will be used to show slides
display: 'block',
// Hide cursor if inactive
hideInactiveCursor: true,
// Time before the cursor is hidden (in ms)
hideCursorTime: 5000,
// Opens links in an iframe preview overlay
previewLinks: false,
// Transition style (none/fade/slide/convex/concave/zoom)
transition: 'none',
// Transition speed (default/fast/slow)
transitionSpeed: 'default',
// Transition style for full page slide backgrounds
// (none/fade/slide/convex/concave/zoom)
backgroundTransition: 'none',
// Number of slides away from the current that are visible
viewDistance: 3,
// Number of slides away from the current that are visible on mobile
// devices. It is advisable to set this to a lower number than
// viewDistance in order to save resources.
mobileViewDistance: 2,
// The "normal" size of the presentation, aspect ratio will be preserved
// when the presentation is scaled to fit different resolutions. Can be
// specified using percentage units.
width: 1050,
height: 700,
// Factor of the display size that should remain empty around the content
margin: 0.1,
math: {
mathjax: 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js',
config: 'TeX-AMS_HTML-full',
tex2jax: {
inlineMath: [['\\(','\\)']],
displayMath: [['\\[','\\]']],
balanceBraces: true,
processEscapes: false,
processRefs: true,
processEnvironments: true,
preview: 'TeX',
skipTags: ['script','noscript','style','textarea','pre','code'],
ignoreClass: 'tex2jax_ignore',
processClass: 'tex2jax_process'
},
},
// reveal.js plugins
plugins: [QuartoLineHighlight, PdfExport, RevealMenu, QuartoSupport,
RevealMath,
RevealNotes,
RevealSearch,
RevealZoom
]
});
</script>
<script>
// htmlwidgets need to know to resize themselves when slides are shown/hidden.
// Fire the "slideenter" event (handled by htmlwidgets.js) when the current
// slide changes (different for each slide format).
(function () {
// dispatch for htmlwidgets
function fireSlideEnter() {
const event = window.document.createEvent("Event");
event.initEvent("slideenter", true, true);
window.document.dispatchEvent(event);
}
function fireSlideChanged(previousSlide, currentSlide) {
fireSlideEnter();
// dispatch for shiny
if (window.jQuery) {
if (previousSlide) {
window.jQuery(previousSlide).trigger("hidden");
}
if (currentSlide) {
window.jQuery(currentSlide).trigger("shown");
}
}
}
// hookup for slidy
if (window.w3c_slidy) {
window.w3c_slidy.add_observer(function (slide_num) {
// slide_num starts at position 1
fireSlideChanged(null, w3c_slidy.slides[slide_num - 1]);
});
}
})();
</script>
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const tabsets = window.document.querySelectorAll(".panel-tabset-tabby")
tabsets.forEach(function(tabset) {
const tabby = new Tabby('#' + tabset.id);
});
const isCodeAnnotation = (el) => {
for (const clz of el.classList) {
if (clz.startsWith('code-annotation-')) {
return true;
}
}
return false;
}
const onCopySuccess = function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();