forked from mnemiopsis/mnemiopsis.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
analysis2hpaAllR.html
executable file
·462 lines (386 loc) · 26 KB
/
analysis2hpaAllR.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
<!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="Kirsten Gotting" />
<title>2 hpa Control - All Replicates</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/sandstone.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>
<style type="text/css">code{white-space: pre;}</style>
<link rel="stylesheet"
href="site_libs/highlight/textmate.css"
type="text/css" />
<script src="site_libs/highlight/highlight.js"></script>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs && 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;
}
#rmd-source-code {
display: none;
}
</style>
<link rel="stylesheet" href="styles.css" type="text/css" />
</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;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 61px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 66px;
margin-top: -66px;
}
.section h2 {
padding-top: 66px;
margin-top: -66px;
}
.section h3 {
padding-top: 66px;
margin-top: -66px;
}
.section h4 {
padding-top: 66px;
margin-top: -66px;
}
.section h5 {
padding-top: 66px;
margin-top: -66px;
}
.section h6 {
padding-top: 66px;
margin-top: -66px;
}
</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 src="site_libs/navigation-1.1/tabsets.js"></script>
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: -22px; }
.code-folding-btn.collapsed { margin-bottom: 4px; }
</style>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/navigation-1.1/FileSaver.min.js"></script>
<script src="site_libs/navigation-1.1/sourceembed.js"></script>
<script>
$(document).ready(function () {
window.initializeSourceEmbed("analysis2hpaAllR.Rmd");
});
</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",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = false;
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: 0.9em;
padding-left: 5px;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
padding-left: 10px;
}
</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"><em>Mnemiopsis leidyi</em></a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="experiment.html">Experiment</a>
</li>
<li>
<a href="transcriptome.html">Transcriptome</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Quality Control
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="analysis8hpaAllR.html">8hpa Control First Pass</a>
</li>
<li>
<a href="analysis8hpa5RR.html">8hpa Control Second Pass</a>
</li>
<li>
<a href="analysis2hpaAllR.html">2hpa Control First Pass</a>
</li>
<li>
<a href="analysis2hpa2RR.html">2hpa Control Second Pass</a>
</li>
<li>
<a href="analysisStepwise.html">Stepwise Test</a>
</li>
</ul>
</li>
<li>
<a href="StoryOfInitialAnalysis.html">Differential Expression</a>
</li>
<li>
<a href="downloads.html">Downloads</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-download-source" href="#">Download Rmd</a></li>
</ul>
</div>
<h1 class="title toc-ignore">2 hpa Control - All Replicates</h1>
<h4 class="author"><em>Kirsten Gotting</em></h4>
</div>
<div id="overview" class="section level1">
<h1>Overview</h1>
<p>Differential expression analysis with 2hpa control and all replicates.</p>
</div>
<div id="spearman-correlation" class="section level1">
<h1>Spearman Correlation</h1>
<p>Spearman’s rank correlation coefficient is a nonparametric measure of rank correlation, recommended for data that does not necessarily come from a bivariate normal distribution (Wikipedia). Below, we plot the Spearman correlation of the RPM (reads per million) for all genes that have an average RPM ≥ 1.</p>
<p><img src="figures/spearman_correlation2hpaControlAllReplicates-1.png" width="672" /></p>
</div>
<div id="pairwise-pca" class="section level1">
<h1>Pairwise PCA</h1>
<p>Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components (Wikipedia). Below is a PCA of the 8hpf control versus the other developmental timepoints.</p>
<p><img src="figures/PCA2hpaControlAllReplicates-1.png" width="960" /></p>
</div>
<div id="ma-and-volcano-plots" class="section level1 tabset">
<h1>MA and Volcano plots</h1>
<p>MA plot: The log2 fold change (M) plotted against the log2 average (A) of the normalized read count for each gene. Significantly differentially expressed genes are plotted in red.</p>
<p>Volcano plot: The log2 fold change (M) plotted against the -log10 (eg. 1e^-10 = 10) of the adjusted p-value.</p>
<div id="hpf2hpf" class="section level2">
<h2>1hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-1.png" width="1920" /></p>
</div>
<div id="hpf2hpf-1" class="section level2">
<h2>3hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-2.png" width="1920" /></p>
</div>
<div id="hpf2hpf-2" class="section level2">
<h2>4hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-3.png" width="1920" /></p>
</div>
<div id="hpf2hpf-3" class="section level2">
<h2>5hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-4.png" width="1920" /></p>
</div>
<div id="hpf2hpf-4" class="section level2">
<h2>6hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-5.png" width="1920" /></p>
</div>
<div id="hpf2hpf-5" class="section level2">
<h2>7hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-6.png" width="1920" /></p>
</div>
<div id="hpf2hpf-6" class="section level2">
<h2>8hpf/2hpf</h2>
<p><img src="figures/plotmavol2hpaControlAllReplicates-7.png" width="1920" /></p>
</div>
</div>
<div id="heatmaps" class="section level1">
<h1>Heatmaps</h1>
<p>The first heatmap was made by hierarchically clustering the euclidean distances of the log2 fold change for genes with p-values less than 1e^-5 at any time point.</p>
<p>The second heatmap uses the same hierarchical method to cluster timepoints as well as genes.</p>
</div>
<div id="r-session-information" class="section level1">
<h1><a href="sessionInfo/2hpaAllSessionInfo.txt">R-session information</a></h1>
</div>
<div id="rmd-source-code">---
title: "2 hpa Control - All Replicates" 
author: "Kirsten Gotting"
output:
  html_document:
      code_download: true
      toc: true
      toc_depth: 2
      toc_float:
        collapsed: false
---


```{r initializeData2hpaControlAllReplicates, echo = FALSE, results = "hide", message = FALSE, error = FALSE, warning = FALSE, cache = FALSE}

## user input to 'DESeq2All.Rdata'

load("./output/DESeq2All2hpaAll.Rdata")
setwd("./")

## First list the R libraries I want to use
libraries        <- c("DESeq2", "gplots", "RColorBrewer", 'knitr', 'grid', 'gridExtra', "tidyverse", 'kiRsten')

## Now read in the libraries
lapply(libraries, function(x){
    library(x, character.only = TRUE, quietly = TRUE)
    })

## Initialize knitr options
opts_chunk$set(echo=FALSE, message=FALSE, results="hide", fig.keep="all", warning=FALSE, error=FALSE, fig.path="figures/", cache = TRUE)
opts_knit$set(root.dir = "./")


```


# Overview

Differential expression analysis with 2hpa control and all replicates.

#Spearman Correlation

Spearman's rank correlation coefficient is a nonparametric measure of rank correlation, recommended for data that does not necessarily come from a bivariate normal distribution (Wikipedia). Below, we plot the Spearman correlation of the RPM (reads per million) for all genes that have an average RPM &#8805; 1.


```{r spearman_correlation2hpaControlAllReplicates, fig.cap = ""}

## Make a spearman plot


filteredRPMs <- normCounts %>% group_by(ID) %>% mutate(rpmFlag = ifelse((mean(rpm) >= 1), yes = 'yes', no = 'no')) %>% ungroup() %>%
    filter(rpmFlag == 'yes') %>% select(ID, Sample, rpm) %>% spread(Sample, rpm)



rpmfilt        <- data.frame(select(filteredRPMs, -ID), row.names = filteredRPMs$ID, check.names = FALSE)
spearman       <- data.frame(cor(rpmfilt, method = 'spearman'), check.names = FALSE)
spearman$ID    <- rownames(spearman)
spearmanTidy   <- spearman %>% gather(Sample, correlation, -ID)

## and plot it!

ggplot(data = spearmanTidy, aes(x = ID, y = Sample, fill = correlation)) + geom_tile() +
    scale_fill_gradient2(low = "yellow", mid = 'white', high = "purple4", midpoint = 0.8, limit = c(0,1)) +
        ggtitle('Spearman Correlation of Samples') + xlab('') + ylab('') +
            theme(axis.text.x = element_text(angle = 90, hjust = 1))
```


# Pairwise PCA


Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components (Wikipedia). Below is a PCA of the 8hpf control versus the other developmental timepoints. 


```{r PCA2hpaControlAllReplicates, fig.fullwidth = TRUE, fig.width = 10, fig.height = 10}

pcas_data <- lapply(contrast_names, function(x){
    y <- plotPCA(rld_all[[x]], returnData = TRUE, ntop = 10000)
    y$ID <- x
    y
})

pca_data <- bind_rows(pcas_data)

ggplot(data = pca_data, aes(x = PC1, y = PC2, label = name, colour = factor(condition))) +
            geom_point(size = 3) + theme_bw() + geom_text(hjust = 0, vjust = -0.4) +
            xlab("PC 1") + ylab("PC 2") + 
            scale_x_continuous(expand = c(0.98, 0))  +
            scale_y_continuous(expand = c(0.2, 0)) +
            theme(legend.position="none") +
            facet_wrap(~ ID, scales = "free")

```



# MA and Volcano plots {.tabset}

MA plot: The log2 fold change (M) plotted against the log2 average (A) of the normalized read count for each gene. Significantly differentially expressed genes are plotted in red.

Volcano plot: The log2 fold change (M) plotted against the -log10 (eg. 1e^-10 = 10) of the adjusted p-value.

```{r mavol2hpaControlAllReplicates}


x <- contrast_names[[1]]

plots <- lapply(contrast_names, function(x){
    df      <- all_results_tidyDF %>% filter(contrastID == x) %>% spread(dea_ID, dea_Value) %>% mutate(logbaseMean = log(baseMean))
    pval    <- as.numeric(pval)
    if(is.null(df)){
        message(paste0("Pvalue too stringent for ", contrast, ". MA/Volcano plot ommited.\n"))
    } else {
        pval                  <- as.numeric(pval)
        lower_label           <- paste0("Genes with Counts: ", nrow(df), "\nUp: ",#create the label of the legend
                                  nrow(subset(df, log2FoldChange > 0 & padj < pval)),
                                  ", Down: ", nrow(subset(df, log2FoldChange < 0 & padj < pval)), "\n")
  
        df <- df %>% mutate(significance_group = ifelse(padj <= pval, yes = 'yes', no = 'no'))
  
        legend_labels        <- c(paste0("padj > ", pval,": ", nrow(filter(df, significance_group == 'no'))),
                                  paste0("padj < ", pval,": ", nrow(filter(df, significance_group == 'yes'))))
        ma.plot <-   ggplot(df, aes(x = logbaseMean, y = log2FoldChange, group = significance_group, colour = significance_group)) +
                      geom_point() + theme_bw() +
                      ggtitle('MA plot') + scale_x_continuous(expand = c(0, 0)) +
                      xlab("A = Mean of log2(Abundance)") + ylab("M = log2(Fold Change)") +
                      scale_color_manual(values = c("gray24", "red"), name = lower_label, breaks = c("gray24", "red"), labels = legend_labels) +
                      geom_hline(aes(yintercept = 0), colour = "black", linetype = "dashed") +
                      geom_hline(aes(yintercept = 1), colour = "gray66", linetype = "dashed") +
                      geom_hline(aes(yintercept = -1), colour = "gray66", linetype="dashed") +
                      theme(legend.position = 'none', text = element_text(size=20))
        volcano.plot <-   ggplot(df, aes(x = log2FoldChange, y = -log(padj, base = c(10)), group = significance_group, colour = significance_group)) +
                          geom_point() +
                          ggtitle('Volcano plot') +
                          xlab("M = log2(Fold Change)") + ylab("-log10(Adjusted P-Value)") + 
                          scale_color_manual(values = c("gray24", "red"), labels = legend_labels, name=lower_label) +
                          theme_bw() +
                          theme(legend.title = element_text(size = 16, face = "bold"), legend.text = element_text(size = 20),  text = element_text(size=20))
     grob <-   marrangeGrob(list(ma.plot,
                          volcano.plot),
                          top = textGrob(x, gp = gpar(fonsize = 40, fontface = 'bold', cex = 2), hjust = 1.8),
                          nrow = 1, ncol = 2,
                          widths=c(0.38, 0.62))
     invisible(grob)
    }
})

names(plots) <- contrast_names
```

```{r plotmavol2hpaControlAllReplicates, fig.keep = "all", fig.height = 10, fig.width = 20, echo=FALSE, results='asis'}

for(i in contrast_names){
  cat(paste0("\n\n\n##", i, "\n"))
  print(plots[[i]])
}

```


#Heatmaps



The first heatmap was made by hierarchically clustering the euclidean distances of the log2 fold change for genes with p-values less than  1e^-5 at any time point.

The second heatmap uses the same hierarchical method to cluster timepoints as well as genes.


```{r pairwiseHeatmaps2hpaControlAllReplicates, results = "hide", fig.cap = "", fig.keep = "high"}


lfc_table <- all_results_tidyDF %>%
  mutate(significant = ifelse(dea_ID == 'padj' & dea_Value <= pval, yes = TRUE, no = FALSE)) %>% # label all significant genes
  group_by(contrastID, Gene) %>% # label the # of times genes that are significant
  ungroup()  %>%
  group_by(Gene) %>%
  filter(any(significant), dea_ID == 'log2FoldChange') %>%
  select(-significant) %>% unite(colname, contrastID, dea_ID) %>% # make the table wide formatted
  spread(colname, dea_Value)


## create a table of significant genes with the cluster colors assigned

sign.table <- all_results_tidyDF  %>% 
  spread(key = dea_ID, value = dea_Value)  %>% 
  filter(Gene %in% lfc_table$Gene) %>%
  group_by(contrastID, Gene) %>% 
  mutate(sortby = -log(padj, base = c(10))*sign(log2FoldChange)) %>% 
  ungroup() %>% gather(dea_ID, dea_Value, -Gene, -contrastID) %>% 
  unite(idAll, contrastID, dea_ID) %>% spread(key = idAll, value = dea_Value) %>%
  dplyr::rename('TranscriptID' = Gene)


heatmap.input.table           <- data.frame(lfc_table)
rownames(heatmap.input.table) <- lfc_table$Gene
heatmap.input.table$Gene      <- NULL
heatmap.input.table           <- na.omit(data.matrix(heatmap.input.table[which(rownames(heatmap.input.table) %in% sign.table$TranscriptID), ]))
colnames(heatmap.input.table) <- contrast_names


prettycolors  <- colorRampPalette(rev(brewer.pal(11, "Spectral")))
col.breaks    <- seq(-3, 3, length.out = ncol(heatmap.input.table))


## Make two heatmaps, allow custimizable graphing
if(nrow(heatmap.input.table) >2){
hr <- hclust(dist(heatmap.input.table), method="complete") # Creates row dendrogram
hc <- hclust(dist(t(heatmap.input.table)), method="complete") # Creates column dendrogram

myclr     <- cutree(hr, k = 7) # set up where the groups will be, change 'k' for more or less groups
mycolr    <- c("Green", "Red", "Blue", "Orange", "Purple", "Pink", "Yellow") # must be the same length as 'k'
mycolr    <- mycolr[as.vector(myclr)] # pull out the colors assigned to each gene
mycolr.df <- data.frame(Cluster_Color = mycolr, TranscriptID = names(myclr)) # create a data frame of the cluster color each gene belongs to


if(ncol(heatmap.input.table) > 1){
    ## Make a heatmap without a column dendrogram
    col.breaks    <- seq(-3, 3, length.out = ncol(heatmap.input.table))
    heatmap       <- heatmap.2(heatmap.input.table, margin = c(15,5), col = prettycolors, dendrogram = 'row', trace = c("none"), Rowv=as.dendrogram(hr), Colv = NA, labRow = FALSE, key = TRUE, breaks = col.breaks, key.ylab = "Gene Count", key.xlab = "log2FoldChange", cexCol = 1.5, RowSideColors = mycolr)
    title(main = paste0("Clustering of ", nrow(heatmap.input.table)," Genes"), line = 0)
    par(cex.main=0.9)
}


if(ncol(heatmap.input.table) > 2) {
    k <- ifelse(ncol(heatmap.input.table < 5), 3, 5)
    myclc  <- cutree(hc, k = k) # create groupings for the column dendrogram
    mycolc <- c("Green", "Red", "Blue", "Orange", "Purple")
    mycolc <- mycolc[as.vector(myclc)]
    ## Make a heatmap of the logfold changes with column dendrogram.
    heatmap       <- heatmap.2(heatmap.input.table, margin = c(15,5), dendrogram = 'both', Rowv = as.dendrogram(hr), Colv = as.dendrogram(hc), col = prettycolors, trace = c("none"), labRow = FALSE, key = TRUE, breaks = col.breaks, main = paste0("Clustering of Timepoints on ", nrow(heatmap.input.table)," Genes"), key.ylab = "Gene Count", key.xlab = "log2FoldChange", cexCol = 1.5, RowSideColors = mycolr, ColSideColors = mycolc)
}}

```



```{r session2hpaControlAllReplicates, echo=FALSE}
writeLines(capture.output(sessionInfo()), "sessionInfo/2hpaAllSessionInfo.txt")
```

#[R-session information](sessionInfo/2hpaAllSessionInfo.txt)

</div>
<p>
<a href="http://stowers.org"><img src="images/Stowers-logo_001.jpg" style="width:200px;height:75px;"></a>
<a href="http://planaria.stowers.org/"><img src="http://smedgd.stowers.org/wp-content/uploads/2015/11/sllogo_whitebg_small.png"></a>
<a href="http://www.hhmi.org/"><img src="images/HHMI-logo-color_small.jpg"></a>
<a href="http://www.mbl.edu/"><img src="images/marine-biological-laboratory_small.jpg"></a>
</p>
<p><a href="http://www.stowers.org/privacy-policy">Privacy Policy</a></p>
<p><a href="http://www.stowers.org/terms">Terms of Use</a></p>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
$(document).ready(function () {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>