-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrapportMbio.html
587 lines (503 loc) · 31.5 KB
/
rapportMbio.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
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta name="author" content="CHARRIAT Florian" />
<title>Visulaisation de la qualité des assemblages issue de la littérature</title>
<script src="site_libs/jquery-1.12.4/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cerulean.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/htmlwidgets-1.3/htmlwidgets.js"></script>
<link href="site_libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet" />
<script src="site_libs/datatables-binding-0.5/datatables.js"></script>
<link href="site_libs/dt-core-1.10.16/css/jquery.dataTables.min.css" rel="stylesheet" />
<link href="site_libs/dt-core-1.10.16/css/jquery.dataTables.extra.css" rel="stylesheet" />
<script src="site_libs/dt-core-1.10.16/js/jquery.dataTables.min.js"></script>
<script src="site_libs/jszip-1.10.16/jszip.min.js"></script>
<script src="site_libs/pdfmake-1.10.16/pdfmake.min.js"></script>
<script src="site_libs/pdfmake-1.10.16/vfs_fonts.js"></script>
<link href="site_libs/dt-ext-buttons-1.10.16/css/buttons.dataTables.min.css" rel="stylesheet" />
<script src="site_libs/dt-ext-buttons-1.10.16/js/dataTables.buttons.min.js"></script>
<script src="site_libs/dt-ext-buttons-1.10.16/js/buttons.flash.min.js"></script>
<script src="site_libs/dt-ext-buttons-1.10.16/js/buttons.html5.min.js"></script>
<script src="site_libs/dt-ext-buttons-1.10.16/js/buttons.colVis.min.js"></script>
<script src="site_libs/dt-ext-buttons-1.10.16/js/buttons.print.min.js"></script>
<link href="site_libs/crosstalk-1.0.0/css/crosstalk.css" rel="stylesheet" />
<script src="site_libs/crosstalk-1.0.0/js/crosstalk.min.js"></script>
<link href="site_libs/font-awesome-5.0.13/css/fa-svg-with-js.css" rel="stylesheet" />
<script src="site_libs/font-awesome-5.0.13/js/fontawesome-all.min.js"></script>
<script src="site_libs/font-awesome-5.0.13/js/fa-v4-shims.min.js"></script>
<link href="site_libs/ionicons-2.0.1/css/ionicons.min.css" rel="stylesheet" />
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
div.sourceCode { overflow-x: auto; }
table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode {
margin: 0; padding: 0; vertical-align: baseline; border: none; }
table.sourceCode { width: 100%; line-height: 100%; background-color: #303030; color: #cccccc; }
td.lineNumbers { text-align: right; padding-right: 4px; padding-left: 4px; }
td.sourceCode { padding-left: 5px; }
pre, code { color: #cccccc; background-color: #303030; }
code > span.kw { color: #f0dfaf; } /* Keyword */
code > span.dt { color: #dfdfbf; } /* DataType */
code > span.dv { color: #dcdccc; } /* DecVal */
code > span.bn { color: #dca3a3; } /* BaseN */
code > span.fl { color: #c0bed1; } /* Float */
code > span.ch { color: #dca3a3; } /* Char */
code > span.st { color: #cc9393; } /* String */
code > span.co { color: #7f9f7f; } /* Comment */
code > span.ot { color: #efef8f; } /* Other */
code > span.al { color: #ffcfaf; } /* Alert */
code > span.fu { color: #efef8f; } /* Function */
code > span.er { color: #c3bf9f; } /* Error */
code > span.wa { color: #7f9f7f; font-weight: bold; } /* Warning */
code > span.cn { color: #dca3a3; font-weight: bold; } /* Constant */
code > span.sc { color: #dca3a3; } /* SpecialChar */
code > span.vs { color: #cc9393; } /* VerbatimString */
code > span.ss { color: #cc9393; } /* SpecialString */
code > span.im { } /* Import */
code > span.va { } /* Variable */
code > span.cf { color: #f0dfaf; } /* ControlFlow */
code > span.op { color: #f0efd0; } /* Operator */
code > span.bu { } /* BuiltIn */
code > span.ex { } /* Extension */
code > span.pp { color: #ffcfaf; font-weight: bold; } /* Preprocessor */
code > span.at { } /* Attribute */
code > span.do { color: #7f9f7f; } /* Documentation */
code > span.an { color: #7f9f7f; font-weight: bold; } /* Annotation */
code > span.cv { color: #7f9f7f; font-weight: bold; } /* CommentVar */
code > span.in { color: #7f9f7f; font-weight: bold; } /* Information */
div.sourceCode {
overflow-x: visible;
}
</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<div class="container-fluid main-container">
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<script>
$(document).ready(function () {
window.initializeCodeFolding("hide" === "show");
});
</script>
<script>
$(document).ready(function () {
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
// establish options
var options = {
selectors: "h1,h2,h3,h4,h5",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = true;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
padding-left: 25px;
text-indent: 0;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Rapport Florian</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="info.html">
<span class="fa fa-info"></span>
Information
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-folder-open"></span>
Rapport
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="rapport30.html">Assemblages des souches terrasses</a>
</li>
<li>
<a href="assembleSoucheAdel.html">Assemblages des souches d'Adel</a>
</li>
<li>
<a href="assembleMagMAXSPE.html">Assemblages des séquencées à Toulouse (MagMAX)</a>
</li>
<li>
<a href="allAssemblage.html">Visualisation de la qualité de tout les assemblages</a>
</li>
<li>
<a href="rapportMbio.html">Visulaisation de la qualité des assemblages issue de la littérature</a>
</li>
<li>
<a href="repeatMasquer.html">Masquer les éléments répétés</a>
</li>
<li>
<a href="comparaison_assemblage.html">Choix du meilleurs Assemblages</a>
</li>
<li>
<a href="Annotation.html">Annotation</a>
</li>
<li>
<a href="Secretome.html">Prédiction du sécrétome</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="ion ion-easel"></span>
Présentation
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="Presentation/presentation_03_04_2018.html">Presentation du 3 avril 2018</a>
</li>
<li>
<a href="Presentation/presentation_17_04_2018.html">Presentation du 17 avril 2018</a>
</li>
<li>
<a href="Presentation/presentation_CBS.html">Présentation au CBS du 1 juin 2018</a>
</li>
</ul>
</li>
<li>
<a href="biblio.html">
<span class="fa fa-book"></span>
Bibliographie
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="ion ion-cube"></span>
App
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://floriancha.shinyapps.io/Open_File_with_R_v2/">File Visualizer v2</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="about.html">
<span class="fa fa-info-circle"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div class="btn-group pull-right">
<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
</div>
<h1 class="title toc-ignore">Visulaisation de la qualité des assemblages issue de la littérature</h1>
<h4 class="author"><em>CHARRIAT Florian</em></h4>
<h4 class="date"><em>20 mars 2018</em></h4>
</div>
<div id="traitement-des-donnees" class="section level1">
<h1>Traitement des données</h1>
<p style="text-align:justify" ;>
Les données sont importées dans R afin de pouvoir ensuite les traiter.
</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dataQuality <-<span class="kw">c</span>()
WD <-<span class="st"> 'StatQuality'</span>
file.quality <-<span class="st"> </span><span class="kw">file.path</span>(WD,<span class="st">'QualityMbio.txt'</span>)
dataQ <-<span class="st"> </span><span class="kw">read.table</span>(<span class="dt">file=</span>file.quality, <span class="dt">sep=</span><span class="st">"</span><span class="ch">\t</span><span class="st">"</span>, <span class="dt">header=</span><span class="ot">TRUE</span>)
idS <-<span class="st"> </span><span class="kw">c</span>()
idSouche <-<span class="st"> </span><span class="kw">c</span>()
<span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="op">:</span><span class="kw">nrow</span>(dataQ))
{
idS<-<span class="st"> </span><span class="kw">toString</span>(dataQ[i,<span class="dv">11</span>])
idSouche <-<span class="st"> </span><span class="kw">c</span>(idSouche,<span class="kw">substr</span>(idS,<span class="dv">0</span>,<span class="dv">9</span>))
}
dataQ[,<span class="dv">11</span>] <-<span class="st"> </span>idSouche
dataQuality <-dataQ[,<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>]
<span class="kw">rownames</span>(dataQuality) <-<span class="st"> </span>idSouche</code></pre></div>
</div>
<div id="visualisation-des-donnees" class="section level1">
<h1>Visualisation des données</h1>
<div id="donnees-qualite" class="section level2">
<h2>Données qualité</h2>
<p>Ici le tableau montre les données qualités récupéré à l’aide du script <a href='https://floriancha.github.io/Script/index.html' target='_blank'>QualityAssemblage</a>.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">datatable</span>(dataQuality, <span class="dt">caption =</span><span class="st">" Tableau n°1: Tableau des statistiques de qualité de tous les assemblages"</span>,<span class="dt">colnames =</span> <span class="kw">c</span>(<span class="st">'Id'</span>, <span class="kw">colnames</span>(dataQuality)),<span class="dt">extensions =</span> <span class="st">'Buttons'</span>, <span class="dt">options =</span> <span class="kw">list</span>(<span class="dt">dom =</span> <span class="st">'Blfrtip'</span>,<span class="dt">buttons =</span> <span class="kw">c</span>(<span class="st">'copy'</span>, <span class="st">'csv'</span>, <span class="st">'excel'</span>, <span class="st">'pdf'</span>, <span class="st">'print'</span>))) </code></pre></div>
<div id="htmlwidget-b9104794c41d78d1d6e0" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-b9104794c41d78d1d6e0">{"x":{"filter":"none","extensions":["Buttons"],"caption":"<caption> Tableau n°1: Tableau des statistiques de qualité de tous les assemblages<\/caption>","data":[["INA168","TH3","SSFL14-3","B51","GFSI1-7-2","PY5003","Br48","PY6025","Br62","Pm1","Br130","WBKY11","BR29","Bd8401","CHW","IE1K","P28","IC17","PY86-1","PY36-1","PY5010","US0071","HO","P3","EI9411","KANSV1-4-","PgKY","PY6045","GY11","SSFL02","B71","SA05-43","PL2-1","IA1","GRF52","Y34","LpKY97","SV9623","PH42","IB49","ML33","Dig41","Br7","Z2-1","98-06","P131","PH0014-rn","PGPA","EI9604","G17","FR13","87-120","IB33","BR0032","BdBar","CHRF","PY6017","CD0156","DsLIZ","FH","Br80","SA05-144","BdMeh","TH0016","SV9610","BdJes","T25","Bm88324","WHTQ","V0107","PY5033","B2","GG11","Ken53-33","PL3-1","Arcadia","TF05-1","TH0012-rn","P29","PY0925","Pg1213-22","Br58","G22","P-2"],[1811,9687,2638,2390,1910,2565,2082,64347,2317,4091,2436,115,16,2901,790,1722,1665,2438,3209,740,2290,220,1760,833,1661,10061,3858,1671,1964,1277,667,11994,811,2257,3606,1198,5572,1514,1673,2076,3439,3970,1215,2048,284,1822,711,3403,1346,1803,2051,2714,1589,111,6205,889,1654,237,1508,2346,724,31922,1365,171,1546,3007,1277,1732,3094,33028,2012,2491,1463,7987,1949,1399,1720,940,1472,2191,1390,2057,2460,6787],[1810,8322,1751,2390,1908,1676,2082,31772,1332,2377,2435,115,16,1559,790,1225,1102,2438,1282,397,962,220,1143,833,1656,7842,1967,898,1964,1277,667,9163,811,2257,1374,1198,3608,1513,1673,2076,2134,3968,1215,2048,284,1822,711,1681,1344,1350,2051,1390,1589,111,3796,889,757,237,1508,1693,724,19631,1365,171,1544,3007,1277,1087,3092,3233,1005,2102,1023,5980,1456,1399,1238,940,980,820,1390,2053,1783,5029],[128,1452,168,411,125,213,121,16027,88,207,265,5,6,56,93,79,47,392,71,47,59,12,84,87,137,1197,141,66,60,169,67,1552,79,358,102,92,335,78,250,309,120,509,166,173,10,159,20,71,116,113,124,64,202,7,343,84,47,13,227,207,78,5540,170,11,70,571,210,43,306,411,61,288,97,785,171,181,121,21,52,56,165,119,160,594],[500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500,500],[22533,2881,24900,12332,29866,25810,30181,431,47619,19640,18727,964958,1126513,65409,52207,27201,68827,11401,63173,116558,73335,189768,47118,51057,29305,3215,32385,73917,23706,28702,67266,2579,50715,12545,36231,27710,13178,49778,21276,14303,21424,10005,32441,25322,300936,21994,158106,47734,38777,40829,25027,44486,18823,629663,12841,47348,100124,362046,24690,27736,58053,868,26871,254700,47278,9120,29171,78995,13706,10066,75844,19499,42179,4498,31398,22984,37434,44331,83588,81855,28697,31341,26741,5576],[75886,7034,72801,27865,88519,62930,97014,814,141061,63795,47088,3962041,1625795,204898,120224,127734,218204,28200,167541,272947,204456,813981,123633,138921,81416,8523,89888,184726,187276,71208,181707,6778,141200,30490,105252,106863,35955,145603,50217,37864,83862,24063,74276,64080,1530397,62822,697115,155029,100075,105667,101645,161911,53069,1760460,35256,134224,261084,1066457,60910,61997,134171,2008,68617,938544,154236,20309,62883,267242,37555,31142,181875,46715,114865,12612,72795,62325,104709,590463,232896,208439,79461,91276,72869,16224],[183877,14175,155736,54286,191376,106714,206346,1468,264563,138369,84748,5497615,2515496,446141,254330,297522,612082,53859,346593,499125,422346,2923703,322088,264224,168993,18487,180852,394005,556686,138121,410105,13777,303736,60886,238957,272116,73278,297475,95898,71670,205617,48178,146622,138342,2329954,144057,2025323,378242,214057,214011,205760,417379,109623,4391730,73775,287447,553654,1912116,112355,118980,348737,3953,151850,1977323,315634,39181,113360,507540,80974,60143,421604,81433,253694,27991,142376,139998,203933,1560965,479846,447203,141217,198526,158590,37772],[108778,9213,92073,35360,113597,74864,121507,1033,177399,84310,54675,3658792,1664034,267642,159223,175827,416479,35807,240988,339042,264221,1242610,222618,181118,111316,11703,107275,240613,294033,86490,235291,8918,232761,39280,141208,150459,46150,179272,62254,46394,121123,30353,90946,84848,1441269,91184,924050,229422,133707,136026,123244,215817,70935,2160658,46016,189570,343427,1149990,73139,76205,255311,2586,88018,1186259,212724,25569,74163,371025,52724,38273,268137,54185,173318,18164,93851,83270,135534,775519,321357,314929,89133,130263,95661,22747],[400585,48311,323986,156141,393777,330048,476436,20244,665316,410669,208622,6783147,2523387,1076705,587934,621508,1778806,193775,1159164,1123756,881373,3113975,1431250,906733,501659,69768,384410,1082052,1102691,347231,823909,62709,1483421,188050,505245,708350,196461,585182,228111,313329,627475,149066,331884,371027,3511474,459401,2495708,937392,472660,564916,557675,620948,280346,4783357,227268,927143,1185762,2814965,308435,262988,1643104,20665,257108,3133578,948369,125452,269925,1679996,292920,212535,1214743,219930,966222,103689,413171,303158,703161,2302051,1188465,1607382,310331,641189,390726,105622],[38122422,35382215,42715770,38908646,39152295,42727676,40783269,42113116,42951273,47701690,40014084,43381641,22834969,41269396,40418923,39603376,43582558,37809379,43594932,42166263,42821371,41206925,43035775,41631577,40306145,37014292,42094423,42459583,46326187,40269483,43067233,36922728,42551839,37559418,39910600,38872417,42494433,39376824,42256740,38214410,39494099,41519068,41336942,39609439,42306689,37955031,49819876,42669742,41601338,41186569,43065003,39290202,38573393,41858488,42808240,41693228,43103128,42691742,44435812,42973384,42345624,37894689,41292141,39126391,39325514,38930738,42297954,41379780,42249780,43299204,42778215,42489196,42565249,36918208,42519598,40595029,43536331,48539267,43272941,43095444,41150008,40301183,41423750,36656921]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>Id<\/th>\n <th>n<\/th>\n <th>n.500<\/th>\n <th>L50<\/th>\n <th>min<\/th>\n <th>N80<\/th>\n <th>N50<\/th>\n <th>N20<\/th>\n <th>E.size<\/th>\n <th>max<\/th>\n <th>sum<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"Blfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[1,2,3,4,5,6,7,8,9,10]}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p> </p>
</div>
</div>
<div id="visualisation-des-graph" class="section level1">
<h1>Visualisation des graph</h1>
<p>Les données sont ensuite comme visualisées à l’aide de différent graphique.</p>
<div id="graph-n50-generale" class="section level3">
<h3>Graph N50 générale</h3>
<p style="text-align:justify" ;>
Dans un premier temps on visualise le N50 de chaque souche. On constate qu’il y a de grande différence de N50 entre les différentes souches. C’est pour cela qu’un autre graphique est crée afin de visualiser les plus petites valeurs de N50.
</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">x.kmère <-<span class="st"> </span><span class="kw">c</span>()
<span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="op">:</span>(<span class="kw">nrow</span>(dataQ)))
{
x.kmère <-<span class="st"> </span><span class="kw">c</span>(x.kmère,<span class="kw">rep</span>(i))
}
select.kmère <-<span class="st"> </span><span class="kw">c</span>()
N50max <-<span class="st"> </span><span class="dv">25000</span> <span class="co"># Selection des assemblage avec un N50 supérieur à 25 000</span>
<span class="kw">plot</span>(<span class="dt">x =</span> x.kmère, <span class="dt">y =</span> dataQ<span class="op">$</span>N50, <span class="dt">ylab =</span><span class="st">'N50'</span>,<span class="dt">xlab =</span> <span class="st">'souche'</span>,<span class="dt">xaxt=</span><span class="st">"n"</span>,<span class="dt">main =</span><span class="st">'Graphique n°1 : Assemblage de chaque souche en fonction du N50'</span>, <span class="dt">cex =</span> <span class="fl">0.3</span>)
<span class="kw">axis</span>(<span class="dt">side =</span> <span class="dv">1</span>,<span class="dt">at =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(dataQ<span class="op">$</span>name), <span class="dt">labels =</span> dataQ<span class="op">$</span>name, <span class="dt">las =</span><span class="dv">2</span>, <span class="dt">cex.axis =</span> <span class="fl">0.6</span>)
<span class="kw">abline</span>(<span class="dt">h=</span>N50max,<span class="dt">col=</span><span class="st">"red"</span>)</code></pre></div>
<p><img src="rapportMbio_files/figure-html/plot%20N50%20g%C3%A9n%C3%A9ral-1.png" width="960" style="display: block; margin: auto;" /></p>
</div>
<div id="graph-n50-zoom" class="section level3">
<h3>Graph N50 zoom</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">x.kmère <-<span class="st"> </span><span class="kw">c</span>()
<span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="op">:</span>(<span class="kw">nrow</span>(dataQ)))
{
x.kmère <-<span class="st"> </span><span class="kw">c</span>(x.kmère,<span class="kw">rep</span>(i))
}
select.kmère <-<span class="st"> </span><span class="kw">c</span>()
N50max <-<span class="st"> </span><span class="dv">25000</span> <span class="co"># Selection des assemblage avec un N50 supérieur à 25 000</span>
<span class="kw">plot</span>(<span class="dt">x =</span> x.kmère, <span class="dt">y =</span> dataQ<span class="op">$</span>N50, <span class="dt">ylab =</span><span class="st">'N50'</span>,<span class="dt">xlab =</span> <span class="st">'souche'</span>,<span class="dt">xaxt=</span><span class="st">"n"</span> ,<span class="dt">ylim=</span><span class="kw">c</span>(<span class="dv">100</span>,<span class="dv">250000</span>) ,<span class="dt">main =</span><span class="st">'Visualisation du N50 de tous les assemblages issue de la litterature'</span>, <span class="dt">cex =</span> <span class="fl">0.3</span>)
<span class="kw">axis</span>(<span class="dt">side =</span> <span class="dv">1</span>,<span class="dt">at =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(dataQ<span class="op">$</span>name), <span class="dt">labels =</span> dataQ<span class="op">$</span>name, <span class="dt">las =</span><span class="dv">2</span>, <span class="dt">cex.axis =</span> <span class="fl">0.6</span>)
<span class="kw">abline</span>(<span class="dt">h=</span>N50max,<span class="dt">col=</span><span class="st">"red"</span>)</code></pre></div>
<p><img src="rapportMbio_files/figure-html/plot%20N50%20zoom-1.png" width="960" style="display: block; margin: auto;" /></p>
</div>
<div id="graph-l50" class="section level3">
<h3>Graph L50</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(<span class="dt">x =</span> x.kmère , <span class="dt">y =</span> dataQuality<span class="op">$</span>L50, <span class="dt">ylab =</span><span class="st">'L50'</span>, <span class="dt">xlab =</span> <span class="st">'souche'</span>, <span class="dt">xaxt=</span><span class="st">"n"</span> , <span class="dt">main =</span><span class="st">'Graphique n°2 : Assemblage de chaque souche en fonction du L50'</span>, <span class="dt">cex =</span> <span class="fl">0.1</span>)
<span class="kw">axis</span>(<span class="dt">side =</span> <span class="dv">1</span>,<span class="dt">at =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(dataQ<span class="op">$</span>name), <span class="dt">labels =</span> dataQ<span class="op">$</span>name, <span class="dt">las =</span><span class="dv">2</span>, <span class="dt">cex.axis =</span> <span class="fl">0.6</span>)</code></pre></div>
<p><img src="rapportMbio_files/figure-html/plot%20L50-1.png" width="960" style="display: block; margin: auto;" /></p>
</div>
<div id="graph-e-size" class="section level3">
<h3>Graph E-size</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(<span class="dt">x =</span> x.kmère, <span class="dt">y =</span> dataQuality<span class="op">$</span>E.size,<span class="dt">ylab =</span><span class="st">'E.size'</span>,<span class="dt">xlab =</span> <span class="st">'souche'</span>,<span class="dt">xaxt=</span><span class="st">"n"</span>, <span class="dt">main =</span><span class="st">"Graphique n°3 : Assemblage de chaque souche en fonction de l'E-size"</span>, <span class="dt">cex =</span> <span class="fl">0.3</span>)
<span class="kw">axis</span>(<span class="dt">side =</span> <span class="dv">1</span>,<span class="dt">at =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(dataQ<span class="op">$</span>name), <span class="dt">labels =</span> dataQ<span class="op">$</span>name, <span class="dt">las =</span><span class="dv">2</span>, <span class="dt">cex.axis =</span> <span class="fl">0.6</span>)</code></pre></div>
<p><img src="rapportMbio_files/figure-html/plot%20E-size-1.png" width="960" style="display: block; margin: auto;" /></p>
</div>
<div id="graph-longueur-max" class="section level3">
<h3>Graph Longueur max</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(<span class="dt">x =</span> x.kmère, <span class="dt">y =</span> dataQuality<span class="op">$</span>max,<span class="dt">ylab =</span><span class="st">'max'</span>,<span class="dt">xlab =</span> <span class="st">'souche'</span>, <span class="dt">xaxt=</span><span class="st">"n"</span> , <span class="dt">main =</span><span class="st">'Graphique n°4 : Assemblage de chaque souche en fonction de la longueur max des contigs'</span>, <span class="dt">cex =</span> <span class="fl">0.3</span>)
<span class="kw">axis</span>(<span class="dt">side =</span> <span class="dv">1</span>,<span class="dt">at =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(dataQ<span class="op">$</span>name), <span class="dt">labels =</span> dataQ<span class="op">$</span>name, <span class="dt">las =</span><span class="dv">2</span>, <span class="dt">cex.axis =</span> <span class="fl">0.6</span>)</code></pre></div>
<p><img src="rapportMbio_files/figure-html/plot%20longuer%20max%20du%20contigs-1.png" width="960" style="display: block; margin: auto;" /></p>
</div>
<div id="graph-n500" class="section level3">
<h3>Graph n:500</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(<span class="dt">x =</span> x.kmère, <span class="dt">y =</span> dataQuality<span class="op">$</span>n.<span class="dv">500</span>,<span class="dt">ylab =</span><span class="st">'n.500'</span>,<span class="dt">xlab =</span> <span class="st">'souche'</span>, <span class="dt">xaxt=</span><span class="st">"n"</span> , <span class="dt">main =</span><span class="st">'Graphique n°5 : Assemblage de chaque souche en fonction du nombre de contigs supérieur à 500'</span>, <span class="dt">cex =</span> <span class="fl">0.3</span>)
<span class="kw">axis</span>(<span class="dt">side =</span> <span class="dv">1</span>,<span class="dt">at =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(dataQ<span class="op">$</span>name), <span class="dt">labels =</span> dataQ<span class="op">$</span>name, <span class="dt">las =</span><span class="dv">2</span>, <span class="dt">cex.axis =</span> <span class="fl">0.6</span>)</code></pre></div>
<p><img src="rapportMbio_files/figure-html/plot%20n500%20avant%20selection%20kmere-1.png" width="960" style="display: block; margin: auto;" /></p>
</div>
</div>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>