forked from mortenarendt/MicrobiomeDataAnalysis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathhm.html
457 lines (390 loc) · 12.3 KB
/
hm.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
<!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" />
<title>Heatmaps</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.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/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<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;
}
summary {
display: list-item;
}
</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;
}
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</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 -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
<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">Microbiome Data Analysis</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="about.html">Home</a>
</li>
<li>
<a href="pkgs.html">Installation</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Descriptives
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="prepro.html">Preprocessing</a>
</li>
<li>
<a href="alphadiv.html">alpha diversity</a>
</li>
<li>
<a href="betadiv.html">beta diversity</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Statistical inference
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="DA.html">Differential Abundance</a>
</li>
<li>
<a href="adonistest.html">ANOVA on beta diversity</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Supervised Multivariate models
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="hm.html">Heatmaps</a>
</li>
<li>
<a href="cca.html">Canonical Correlation Analysis</a>
</li>
</ul>
</li>
<li>
<a href="https://github.com/mortenarendt/MicrobiomeDataAnalysis/tree/master/data">Data</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Heatmaps</h1>
</div>
<p>In order to answer biological questions, often a combination of high-throughput data is generated. Especially in combination with microbiome types of data, the associated metabolome is naturally of interest, as these two sources together reflects <em>who are there</em> and <em>what do they do</em>.</p>
<p>In the analysis of such data a natural starting point is to look for common structure. That is; which types of bacteria are correlated to a certain type of metabolites.</p>
<div id="correlation-heat-map" class="section level1 unnumbered">
<h1>Correlation Heat map</h1>
<p>A natural starting point for such an analysis is to produce all pairwise correlations between the OTU table and the metabolite table, and visualize it in a heat map. The build in heatmap() function in R provides a quick initial overview of the data.</p>
<div id="preprocess-the-data" class="section level2 unnumbered">
<h2>Preprocess the data</h2>
<pre class="r"><code>library(phyloseq)
library(tidyverse)
load('./data/Rats_inulin.RData')
phyXpp <- subset_samples(phyX, !is.na(Acetate))
phyXpp <- filter_taxa(phyXpp, function(x) sum(x>0)>0, TRUE)
phyXpp <- transform_sample_counts(phyXpp, function(x) x/sum(x))
OTUtb <- data.frame(t(otu_table(phyXpp)))
Mtb <- sample_data(phyXpp)[,c("Acetate","Butyrate","Fructose","Glucose","Lactate","Propionate","Xylose")]
# preprocess the Mtb data
Mtb$Xylose <- Mtb$Xylose + 0.141/2 # there is zeros for this one - so to fix log we need to add a bit.
Mtb <- log(Mtb)</code></pre>
</div>
<div id="pairwise-correlations" class="section level2 unnumbered">
<h2>Pairwise correlations</h2>
<p>Compute all pairwise correlations</p>
<pre class="r"><code>cr <- cor(OTUtb,Mtb)</code></pre>
</div>
<div id="visualize" class="section level2 unnumbered">
<h2>Visualize</h2>
<pre class="r"><code>heatmap(cr)</code></pre>
<p><img src="hm_files/figure-html/unnamed-chunk-2-1.png" width="672" /></p>
<p>The ordering of the coloumns and rows for this heatmap is based on correlations structure of the <em>correlation matrix</em>. I.e. it is <em>NOT</em> based on similarity of OTUs and metabolites respectively. This might lead to a wrong interpretation. So instead the dendrograms for the rows is based on the correlations of the OTUs and the dendrogram for the coloumns are based on the correlations of the metabolites.</p>
<pre class="r"><code>rd<-dist(t(OTUtb))
rc<-hclust(rd)
cd<-dist(t(Mtb))
cc<-hclust(cd)
heatmap(cr, Rowv=as.dendrogram(rc), Colv=as.dendrogram(cc))</code></pre>
<p><img src="hm_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
</div>
</div>
<div id="exercises" class="section level1">
<h1><span class="header-section-number">1</span> Exercises</h1>
<div id="heatmaps" class="section level2">
<h2><span class="header-section-number">1.1</span> Heatmaps</h2>
<p>Import and run the codes above for generating heatmaps</p>
</div>
<div id="labels" class="section level2">
<h2><span class="header-section-number">1.2</span> Labels</h2>
<p>You might want to change the labels for the bacteria to something more intuitive, and furhter export the plot to pdf for zooming. Try to do this and answer whether you see structure in relation to taxonomic level.</p>
<pre class="r"><code>Txtb <- data.frame(tax_table(phyX))
colnames(OTUtb) <- Txtb$Rank5 # use Rank5 as labels</code></pre>
</div>
<div id="effect-of-preprocessing" class="section level2">
<h2><span class="header-section-number">1.3</span> Effect of Preprocessing</h2>
<p>Try to change the preprocessing such as adding log tranform, and plot histograms of the two versions of the obtained correlations. What do you see?</p>
</div>
<div id="a-zoom-in" class="section level2">
<h2><span class="header-section-number">1.4</span> A zoom-in!</h2>
<p>Digg out OTU_154 and Acetate and plot those against each other. Add log-tranform with a pseudo-count and see what happends. try to add diet info… does that explain anything?</p>
<pre class="r"><code>phyXsel <- subset_samples(phyX, !is.na(Acetate))
OTUsel <- data.frame(t(otu_table(phyXsel)))
df <- cbind(OTUsel,Mtb)
g1 <- ggplot(data = df, aes(OTU_154,Acetate)) + geom_point() + stat_smooth(method = lm) + ggtitle('raw')
g2 <- ggplot(data = df, aes(log2(OTU_154 + 0.1),Acetate)) + geom_point() + stat_smooth(method = lm) + ggtitle('log(count + pc)')
gridExtra::grid.arrange(g1,g2, nrow = 1)</code></pre>
<p>What do you learn from this? … Should be a kinda scarry insight!</p>
</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>