This repository has been archived by the owner on Aug 12, 2021. It is now read-only.
/
index.html
344 lines (298 loc) · 21.7 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
<head>
<meta http-equiv="refresh" content="0;URL=https://yulab-smu.top/biomedical-knowledge-mining-book/index.html">
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>clusterProfiler: universal enrichment tool for functional and comparative study</title>
<meta name="description" content="clusterProfiler: universal enrichment tool for functional and comparative study" />
<meta name="generator" content="bookdown 0.16 and GitBook 2.6.7" />
<meta property="og:title" content="clusterProfiler: universal enrichment tool for functional and comparative study" />
<meta property="og:type" content="book" />
<meta name="twitter:card" content="summary" />
<meta name="twitter:title" content="clusterProfiler: universal enrichment tool for functional and comparative study" />
<meta name="author" content="Guangchuang Yu" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black" />
<link rel="next" href="chapter1.html"/>
<script src="libs/jquery-2.2.3/jquery.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
<script src="libs/htmlwidgets-1.5.1/htmlwidgets.js"></script>
<link href="libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet" />
<script src="libs/datatables-binding-0.9/datatables.js"></script>
<link href="libs/dt-core-1.10.19/css/jquery.dataTables.min.css" rel="stylesheet" />
<link href="libs/dt-core-1.10.19/css/jquery.dataTables.extra.css" rel="stylesheet" />
<script src="libs/dt-core-1.10.19/js/jquery.dataTables.min.js"></script>
<link href="libs/crosstalk-1.0.0/css/crosstalk.css" rel="stylesheet" />
<script src="libs/crosstalk-1.0.0/js/crosstalk.min.js"></script>
<style type="text/css">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
</head>
<body>
<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preface</a></li>
<li class="chapter" data-level="1" data-path="chapter1.html"><a href="chapter1.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
<li class="chapter" data-level="1.1" data-path="chapter1.html"><a href="chapter1.html#terminology"><i class="fa fa-check"></i><b>1.1</b> Terminology</a><ul>
<li class="chapter" data-level="1.1.1" data-path="chapter1.html"><a href="chapter1.html#gene-sets-and-pathway"><i class="fa fa-check"></i><b>1.1.1</b> Gene sets and pathway</a></li>
<li class="chapter" data-level="1.1.2" data-path="chapter1.html"><a href="chapter1.html#gene-ontology-go"><i class="fa fa-check"></i><b>1.1.2</b> Gene Ontology (GO)</a></li>
<li class="chapter" data-level="1.1.3" data-path="chapter1.html"><a href="chapter1.html#kyoto-encyclopedia-of-genes-and-genomes-kegg"><i class="fa fa-check"></i><b>1.1.3</b> Kyoto Encyclopedia of Genes and Genomes (KEGG)</a></li>
<li class="chapter" data-level="1.1.4" data-path="chapter1.html"><a href="chapter1.html#other-gene-sets"><i class="fa fa-check"></i><b>1.1.4</b> Other gene sets</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="2" data-path="chapter2.html"><a href="chapter2.html"><i class="fa fa-check"></i><b>2</b> Functional Enrichment Analysis Methods</a><ul>
<li class="chapter" data-level="2.1" data-path="chapter2.html"><a href="chapter2.html#over-representation-analysis"><i class="fa fa-check"></i><b>2.1</b> Over Representation Analysis</a></li>
<li class="chapter" data-level="2.2" data-path="chapter2.html"><a href="chapter2.html#gene-set-enrichment-analysis"><i class="fa fa-check"></i><b>2.2</b> Gene Set Enrichment Analysis</a></li>
<li class="chapter" data-level="2.3" data-path="chapter2.html"><a href="chapter2.html#leading-edge-analysis-and-core-enriched-genes"><i class="fa fa-check"></i><b>2.3</b> Leading edge analysis and core enriched genes</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="chapter3.html"><a href="chapter3.html"><i class="fa fa-check"></i><b>3</b> Universal enrichment analysis</a><ul>
<li class="chapter" data-level="3.1" data-path="chapter3.html"><a href="chapter3.html#input-data"><i class="fa fa-check"></i><b>3.1</b> Input data</a></li>
<li class="chapter" data-level="3.2" data-path="chapter3.html"><a href="chapter3.html#wikipathways-analysis"><i class="fa fa-check"></i><b>3.2</b> WikiPathways analysis</a></li>
<li class="chapter" data-level="3.3" data-path="chapter3.html"><a href="chapter3.html#cell-marker"><i class="fa fa-check"></i><b>3.3</b> Cell Marker</a></li>
<li class="chapter" data-level="3.4" data-path="chapter3.html"><a href="chapter3.html#msigdb-analysis"><i class="fa fa-check"></i><b>3.4</b> MSigDb analysis</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="chapter4.html"><a href="chapter4.html"><i class="fa fa-check"></i><b>4</b> Disease analysis</a><ul>
<li class="chapter" data-level="4.1" data-path="chapter4.html"><a href="chapter4.html#enrichdo-function"><i class="fa fa-check"></i><b>4.1</b> <code>enrichDO</code> function</a></li>
<li class="chapter" data-level="4.2" data-path="chapter4.html"><a href="chapter4.html#enrichncg-function"><i class="fa fa-check"></i><b>4.2</b> <code>enrichNCG</code> function</a></li>
<li class="chapter" data-level="4.3" data-path="chapter4.html"><a href="chapter4.html#enrichdgn-and-enrichdgnv-functions"><i class="fa fa-check"></i><b>4.3</b> <code>enrichDGN</code> and <code>enrichDGNv</code> functions</a></li>
<li class="chapter" data-level="4.4" data-path="chapter4.html"><a href="chapter4.html#gsedo-fuction"><i class="fa fa-check"></i><b>4.4</b> <code>gseDO</code> fuction</a></li>
<li class="chapter" data-level="4.5" data-path="chapter4.html"><a href="chapter4.html#gsencg-fuction"><i class="fa fa-check"></i><b>4.5</b> <code>gseNCG</code> fuction</a></li>
<li class="chapter" data-level="4.6" data-path="chapter4.html"><a href="chapter4.html#gsedgn-fuction"><i class="fa fa-check"></i><b>4.6</b> <code>gseDGN</code> fuction</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="chapter5.html"><a href="chapter5.html"><i class="fa fa-check"></i><b>5</b> Gene Ontology Analysis</a><ul>
<li class="chapter" data-level="5.1" data-path="chapter5.html"><a href="chapter5.html#supported-organisms"><i class="fa fa-check"></i><b>5.1</b> Supported organisms</a></li>
<li class="chapter" data-level="5.2" data-path="chapter5.html"><a href="chapter5.html#go-classification"><i class="fa fa-check"></i><b>5.2</b> GO classification</a></li>
<li class="chapter" data-level="5.3" data-path="chapter5.html"><a href="chapter5.html#go-over-representation-test"><i class="fa fa-check"></i><b>5.3</b> GO over-representation test</a><ul>
<li class="chapter" data-level="5.3.1" data-path="chapter5.html"><a href="chapter5.html#drop-specific-go-terms-or-level"><i class="fa fa-check"></i><b>5.3.1</b> drop specific GO terms or level</a></li>
<li class="chapter" data-level="5.3.2" data-path="chapter5.html"><a href="chapter5.html#test-go-at-sepcific-level"><i class="fa fa-check"></i><b>5.3.2</b> test GO at sepcific level</a></li>
<li class="chapter" data-level="5.3.3" data-path="chapter5.html"><a href="chapter5.html#reduce-redundancy-of-enriched-go-terms"><i class="fa fa-check"></i><b>5.3.3</b> reduce redundancy of enriched GO terms</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="chapter5.html"><a href="chapter5.html#go-gene-set-enrichment-analysis"><i class="fa fa-check"></i><b>5.4</b> GO Gene Set Enrichment Analysis</a></li>
<li class="chapter" data-level="5.5" data-path="chapter5.html"><a href="chapter5.html#go-semantic-similarity-analysis"><i class="fa fa-check"></i><b>5.5</b> GO Semantic Similarity Analysis</a><ul>
<li class="chapter" data-level="5.5.1" data-path="chapter5.html"><a href="chapter5.html#go-analysis-for-non-model-organisms"><i class="fa fa-check"></i><b>5.5.1</b> GO analysis for non-model organisms</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="chapter6.html"><a href="chapter6.html"><i class="fa fa-check"></i><b>6</b> KEGG analysis</a><ul>
<li class="chapter" data-level="6.1" data-path="chapter6.html"><a href="chapter6.html#kegg-over-representation-test"><i class="fa fa-check"></i><b>6.1</b> KEGG over-representation test</a></li>
<li class="chapter" data-level="6.2" data-path="chapter6.html"><a href="chapter6.html#kegg-gene-set-enrichment-analysis"><i class="fa fa-check"></i><b>6.2</b> KEGG Gene Set Enrichment Analysis</a></li>
<li class="chapter" data-level="6.3" data-path="chapter6.html"><a href="chapter6.html#kegg-module-over-representation-test"><i class="fa fa-check"></i><b>6.3</b> KEGG Module over-representation test</a></li>
<li class="chapter" data-level="6.4" data-path="chapter6.html"><a href="chapter6.html#kegg-module-gene-set-enrichment-analysis"><i class="fa fa-check"></i><b>6.4</b> KEGG Module Gene Set Enrichment Analysis</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="chapter7.html"><a href="chapter7.html"><i class="fa fa-check"></i><b>7</b> MSigDb analysis</a></li>
<li class="chapter" data-level="8" data-path="chapter8.html"><a href="chapter8.html"><i class="fa fa-check"></i><b>8</b> Reactome pathway analysis</a></li>
<li class="chapter" data-level="9" data-path="chapter9.html"><a href="chapter9.html"><i class="fa fa-check"></i><b>9</b> MeSH Enrichment Analysis</a></li>
<li class="chapter" data-level="10" data-path="chapter10.html"><a href="chapter10.html"><i class="fa fa-check"></i><b>10</b> Functional enrichment analysis of genomic coordinations</a></li>
<li class="chapter" data-level="11" data-path="chapter11.html"><a href="chapter11.html"><i class="fa fa-check"></i><b>11</b> Biological theme comparison</a><ul>
<li class="chapter" data-level="11.1" data-path="chapter11.html"><a href="chapter11.html#formula-interface-of-comparecluster"><i class="fa fa-check"></i><b>11.1</b> Formula interface of compareCluster</a></li>
<li class="chapter" data-level="11.2" data-path="chapter11.html"><a href="chapter11.html#visualization-of-profile-comparison"><i class="fa fa-check"></i><b>11.2</b> Visualization of profile comparison</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="chapter12.html"><a href="chapter12.html"><i class="fa fa-check"></i><b>12</b> Visualization of Functional Enrichment Result</a><ul>
<li class="chapter" data-level="12.1" data-path="chapter12.html"><a href="chapter12.html#bar-plot"><i class="fa fa-check"></i><b>12.1</b> Bar Plot</a></li>
<li class="chapter" data-level="12.2" data-path="chapter12.html"><a href="chapter12.html#dot-plot"><i class="fa fa-check"></i><b>12.2</b> Dot plot</a></li>
<li class="chapter" data-level="12.3" data-path="chapter12.html"><a href="chapter12.html#gene-concept-network"><i class="fa fa-check"></i><b>12.3</b> Gene-Concept Network</a></li>
<li class="chapter" data-level="12.4" data-path="chapter12.html"><a href="chapter12.html#heatmap-like-functional-classification"><i class="fa fa-check"></i><b>12.4</b> Heatmap-like functional classification</a></li>
<li class="chapter" data-level="12.5" data-path="chapter12.html"><a href="chapter12.html#enrichment-map"><i class="fa fa-check"></i><b>12.5</b> Enrichment Map</a></li>
<li class="chapter" data-level="12.6" data-path="chapter12.html"><a href="chapter12.html#upset-plot"><i class="fa fa-check"></i><b>12.6</b> UpSet Plot</a></li>
<li class="chapter" data-level="12.7" data-path="chapter12.html"><a href="chapter12.html#ridgeline-plot-for-expression-distribution-of-gsea-result"><i class="fa fa-check"></i><b>12.7</b> ridgeline plot for expression distribution of GSEA result</a></li>
<li class="chapter" data-level="12.8" data-path="chapter12.html"><a href="chapter12.html#running-score-and-preranked-list-of-gsea-result"><i class="fa fa-check"></i><b>12.8</b> running score and preranked list of GSEA result</a></li>
<li class="chapter" data-level="12.9" data-path="chapter12.html"><a href="chapter12.html#pubmed-trend-of-enriched-terms"><i class="fa fa-check"></i><b>12.9</b> pubmed trend of enriched terms</a></li>
<li class="chapter" data-level="12.10" data-path="chapter12.html"><a href="chapter12.html#goplot"><i class="fa fa-check"></i><b>12.10</b> goplot</a></li>
<li class="chapter" data-level="12.11" data-path="chapter12.html"><a href="chapter12.html#browsekegg"><i class="fa fa-check"></i><b>12.11</b> browseKEGG</a></li>
<li class="chapter" data-level="12.12" data-path="chapter12.html"><a href="chapter12.html#pathview-from-pathview-package"><i class="fa fa-check"></i><b>12.12</b> pathview from pathview package</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="chapter13.html"><a href="chapter13.html"><i class="fa fa-check"></i><b>13</b> dplyr verbs for clusterProfiler</a><ul>
<li class="chapter" data-level="13.1" data-path="chapter13.html"><a href="chapter13.html#filter"><i class="fa fa-check"></i><b>13.1</b> filter</a></li>
<li class="chapter" data-level="13.2" data-path="chapter13.html"><a href="chapter13.html#arrange"><i class="fa fa-check"></i><b>13.2</b> arrange</a></li>
<li class="chapter" data-level="13.3" data-path="chapter13.html"><a href="chapter13.html#select"><i class="fa fa-check"></i><b>13.3</b> select</a></li>
<li class="chapter" data-level="13.4" data-path="chapter13.html"><a href="chapter13.html#mutate"><i class="fa fa-check"></i><b>13.4</b> mutate</a></li>
<li class="chapter" data-level="13.5" data-path="chapter13.html"><a href="chapter13.html#slice"><i class="fa fa-check"></i><b>13.5</b> slice</a></li>
<li class="chapter" data-level="13.6" data-path="chapter13.html"><a href="chapter13.html#summarise"><i class="fa fa-check"></i><b>13.6</b> summarise</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="chapter14.html"><a href="chapter14.html"><i class="fa fa-check"></i><b>14</b> Useful utilities</a><ul>
<li class="chapter" data-level="14.1" data-path="chapter14.html"><a href="chapter14.html#bitr"><i class="fa fa-check"></i><b>14.1</b> <code>bitr</code>: Biological Id TranslatoR</a><ul>
<li class="chapter" data-level="14.1.1" data-path="chapter14.html"><a href="chapter14.html#bitr_kegg"><i class="fa fa-check"></i><b>14.1.1</b> <code>bitr_kegg</code>: converting biological IDs using KEGG API</a></li>
</ul></li>
<li class="chapter" data-level="14.2" data-path="chapter14.html"><a href="chapter14.html#setReadable"><i class="fa fa-check"></i><b>14.2</b> <code>setReadable</code>: translating gene IDs to human readable symbols</a></li>
</ul></li>
<li class="appendix"><span><b>Appendix</b></span></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
</ul>
</nav>
</div>
<div class="book-body">
<div class="body-inner">
<div class="book-header" role="navigation">
<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">clusterProfiler: universal enrichment tool for functional and comparative study</a>
</h1>
</div>
<div class="page-wrapper" tabindex="-1" role="main">
<div class="page-inner">
<section class="normal" id="section-">
<div id="header">
<h1 class="title">clusterProfiler: universal enrichment tool for functional and comparative study</h1>
<p class="author"><em>Guangchuang Yu</em></p>
</div>
<div id="preface" class="section level1 unnumbered">
<h1>Preface</h1>
<p>hello</p>
<p><img src="figures/clusterProfiler-diagram.png" /></p>
<!--
In recently years, high-throughput experimental techniques such as
microarray, RNA-Seq and mass spectrometry can detect cellular
molecules at systems-level. These kinds of analyses generate huge
quantitaties of data, which need to be given a biological
interpretation. A commonly used approach is via clustering in the gene
dimension for grouping different genes based on their similarities[@yu2010].
To search for shared functions among genes, a common way is to
incorporate the biological knowledge, such as Gene Ontology (GO) and
Kyoto Encyclopedia of Genes and Genomes (KEGG), for identifying
predominant biological themes of a collection of genes.
After clustering analysis, researchers not only want to determine
whether there is a common theme of a particular gene cluster, but also
to compare the biological themes among gene clusters. The manual step
to choose interesting clusters followed by enrichment analysis on each
selected cluster is slow and tedious. To bridge this gap, we designed
[clusterProfiler](https://www.bioconductor.org/packages/clusterProfiler)[@yu2012], for comparing and visualizing functional
profiles among gene clusters.
-->
</div>
</section>
</div>
</div>
</div>
<a href="chapter1.html" class="navigation navigation-next navigation-unique" aria-label="Next page"><i class="fa fa-angle-right"></i></a>
</div>
</div>
<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
<script src="libs/gitbook-2.6.7/js/lunr.js"></script>
<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
<script>
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": true,
"twitter": true,
"linkedin": false,
"weibo": false,
"instapaper": false,
"vk": false,
"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
},
"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
},
"edit": {
"link": null,
"text": null
},
"history": {
"link": null,
"text": null
},
"view": {
"link": null,
"text": null
},
"download": null,
"toc": {
"collapse": "subsection"
}
});
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
var src = "true";
if (src === "" || src === "true") src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML";
if (location.protocol !== "file:")
if (/^https?:/.test(src))
src = src.replace(/^https?:/, '');
script.src = src;
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>