Commit aa182a42 authored by Kosmas Hench's avatar Kosmas Hench

pre submission

parent 9aee6225
......@@ -114,11 +114,11 @@ p2 <- ggplot(testdat,aes(x=sample,y=gene,fill=counts))+
viridis::scale_fill_viridis(name="Expression: ",option = 'C',
guide = guide_colorbar(direction = "horizontal",title.position = "top"))+
scale_color_manual(name="",values=c('#fb8620','#d93327','#1b519c','#666666'),guide=F)+
theme_minimal(base_size = 7)+
theme_minimal(base_size = 8)+
theme(axis.text.x = element_text(angle=90),
plot.margin = unit(c(1,1,50,1),'pt'),
axis.text.y = element_text(face = 'italic'),
legend.position = c(.05,-.28),panel.grid = element_blank(),legend.key.width = unit(20,'pt'))
legend.position = c(.02,-.4),panel.grid = element_blank(),legend.key.width = unit(20,'pt'))
legGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/legend-expression-cairo.svg"))))
......@@ -150,7 +150,7 @@ p3 <- ggplot(Cdf3,aes(x=0,y=Count))+
scale_y_continuous(expression(Count~(italic(rld(n)))),expand=c(0,0))+
scale_fill_manual('Gene',values = c('lightgray',viridis::viridis(9)),
labels=Flab)+
theme_minimal(base_size = 7)+
theme_minimal(base_size = 8)+
theme(legend.position = 'none',
axis.text.x = element_text(angle=90))
......
......@@ -180,7 +180,7 @@ S12c <- ggplot(data_both,aes(x=RHO,y=WEIGHTED_FST))+
annotate(geom = 'text',x=c(795),y=c(.55),label=an3,size=3,parse=TRUE,col=modclr)+
annotate(geom = 'text',x=c(745),y=c(.5),label=an1,size=3)+
annotate(geom = 'text',x=c(865),y=c(.5),label=c(an2),parse=TRUE,size=3)+
scale_x_continuous(name=expression(Recombination~rate~(italic("\u03C1"))),
scale_x_continuous(name=expression(Population~recombination~rate~(italic("\u03C1"))),
expand = c(.01,.01))+
scale_y_continuous(name=expression(Genetic~differentiation~(weighted~mean~italic(F[ST]))),
expand = c(.005,.005))+
......
This source diff could not be displayed because it is too large. You can view the blob instead.
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -214,11 +214,11 @@ p2 <- ggplot(testdat,aes(x=sample,y=gene,fill=counts))+
guide = guide_colorbar(direction = "horizontal",title.position = "top"))+
scale_color_manual(name="",values=c('#fb8620','#d93327','#1b519c','#666666'),guide=F)+
# general plot theme
theme_minimal(base_size = 13)+
theme_minimal(base_size = 8)+
theme(axis.text.x = element_text(angle=90),
plot.margin = unit(c(1,1,50,1),'pt'),
axis.text.y = element_text(face = 'italic'),
legend.position = c(.05,-.28),panel.grid = element_blank(),legend.key.width = unit(30,'pt'))
legend.position = c(.02,-.4),panel.grid = element_blank(),legend.key.width = unit(20,'pt'))
```
<center>
......@@ -278,7 +278,7 @@ p3 <- ggplot(Cdf3,aes(x=0,y=Count))+
scale_fill_manual('Gene',values = c('lightgray',viridis::viridis(9)),
labels=Flab)+
# general plot theme
theme_minimal(base_size = 13)+
theme_minimal(base_size = 8)+
theme(legend.position = 'none',
axis.text.x = element_text(angle=90))
```
......@@ -302,7 +302,7 @@ S05 <- ggdraw()+
It is then exported using `ggsave()`.
```{r,eval=FALSE}
ggsave(plot = S05, filename = '../output/S05.pdf',width=12,height=6,device = cairo_pdf)
ggsave(plot = S05, filename = '../output/S05.pdf',width=183,height=90,units = 'mm',device = cairo_pdf)
```
<center>
......
......@@ -303,7 +303,7 @@ S12c <- ggplot(data_both,aes(x=RHO,y=WEIGHTED_FST))+
annotate(geom = 'text',x=c(795),y=c(.55),label=an3,size=3,parse=TRUE,col=modclr)+
annotate(geom = 'text',x=c(745),y=c(.5),label=an1,size=3)+
annotate(geom = 'text',x=c(865),y=c(.5),label=c(an2),parse=TRUE,size=3)+
scale_x_continuous(name=expression(Recombination~rate~(italic("\u03C1"))),
scale_x_continuous(name=expression(Population~recombination~rate~(italic("\u03C1"))),
expand = c(.01,.01))+
scale_y_continuous(name=expression(Genetic~differentiation~(weighted~mean~italic(F[ST]))),
expand = c(.005,.005))+
......
......@@ -114,7 +114,7 @@ p2 <- ggplot()+
arrow = arrow(length = unit(4,'pt'),type = 'closed'))+
geom_text(data=edgsB,aes(x=(x+xend)*.5,y=(y+yend)*.5,label=label,angle=angle),
vjust=-1)+
# geom_text(data=ptsB,aes(x=x,y=y,label=nr),color='white')+
#geom_text(data=ptsB,aes(x=x,y=y,label=nr),color='white')+
geom_text(data=plotList,
aes(x=x,y=y,label=label),color=clr2[4])+
scale_x_continuous(expand=c(.03,.03))+
......
---
title: "Script repository"
subtitle: "Supplement to Hench *et al.* 2018"
subtitle: "Supplement to 'Association between vision and pigmentation genes during genomic divergence'"
author: "Kosmas Hench"
date: "`r Sys.Date()`"
documentclass: book
......@@ -8,7 +8,7 @@ bibliography: [book.bib]
biblio-style: apalike
link-citations: yes
github-repo: k-hench/bookdown
description: "Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018."
description: "Scripts used to produce Figures and Supplementary Figures of 'Association between vision and pigmentation genes during genomic divergence'."
---
# Intro
......
<!DOCTYPE html>
<html >
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<title>Script repository</title>
<meta name="description" content="Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018.">
<meta name="generator" content="bookdown 0.7 and GitBook 2.6.7">
<meta property="og:title" content="Script repository" />
<meta property="og:type" content="book" />
<meta property="og:description" content="Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018." />
<meta name="github-repo" content="k-hench/bookdown" />
<meta name="twitter:card" content="summary" />
<meta name="twitter:title" content="Script repository" />
<meta name="twitter:description" content="Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018." />
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-07-27">
<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">
<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-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" />
<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%; }
td.lineNumbers { text-align: right; padding-right: 4px; padding-left: 4px; color: #aaaaaa; border-right: 1px solid #aaaaaa; }
td.sourceCode { padding-left: 5px; }
code > span.kw { color: #007020; font-weight: bold; } /* Keyword */
code > span.dt { color: #902000; } /* DataType */
code > span.dv { color: #40a070; } /* DecVal */
code > span.bn { color: #40a070; } /* BaseN */
code > span.fl { color: #40a070; } /* Float */
code > span.ch { color: #4070a0; } /* Char */
code > span.st { color: #4070a0; } /* String */
code > span.co { color: #60a0b0; font-style: italic; } /* Comment */
code > span.ot { color: #007020; } /* Other */
code > span.al { color: #ff0000; font-weight: bold; } /* Alert */
code > span.fu { color: #06287e; } /* Function */
code > span.er { color: #ff0000; font-weight: bold; } /* Error */
code > span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
code > span.cn { color: #880000; } /* Constant */
code > span.sc { color: #4070a0; } /* SpecialChar */
code > span.vs { color: #4070a0; } /* VerbatimString */
code > span.ss { color: #bb6688; } /* SpecialString */
code > span.im { } /* Import */
code > span.va { color: #19177c; } /* Variable */
code > span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code > span.op { color: #666666; } /* Operator */
code > span.bu { } /* BuiltIn */
code > span.ex { } /* Extension */
code > span.pp { color: #bc7a00; } /* Preprocessor */
code > span.at { color: #7d9029; } /* Attribute */
code > span.do { color: #ba2121; font-style: italic; } /* Documentation */
code > span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code > span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
</style>
<link rel="stylesheet" href="style.css" type="text/css" />
</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><a href="../">Script repository</a></li>
<li class="divider"></li>
<li class="chapter" data-level="1" data-path=""><a href="#intro"><i class="fa fa-check"></i><b>1</b> Intro</a><ul>
<li class="chapter" data-level="1.1" data-path=""><a href="#data"><i class="fa fa-check"></i><b>1.1</b> Data</a></li>
<li class="chapter" data-level="1.2" data-path=""><a href="#figures"><i class="fa fa-check"></i><b>1.2</b> Figures</a></li>
<li class="chapter" data-level="1.3" data-path=""><a href="#background"><i class="fa fa-check"></i><b>1.3</b> Background</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </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="./">Script repository</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">Script repository</h1>
<h3 class="subtitle"><em>Supplement to Hench <em>et al.</em> 2018</em></h3>
<h4 class="author"><em>Kosmas Hench</em></h4>
<h4 class="date"><em>2018-07-27</em></h4>
</div>
<div id="intro" class="section level1">
<h1><span class="header-section-number">1</span> Intro</h1>
<p>This repository contains a <em>cleaned up</em> version of the scripts used in the Hench <em>et al.</em> 2018 paper. It documents the entire progression from raw data to the final manuscript figures.</p>
<p>A visual overview of the process is given in <a href="workflow.html">Workflow</a>.</p>
<div id="data" class="section level2">
<h2><span class="header-section-number">1.1</span> Data</h2>
<p>The raw data used within the study is stored at the <a href="https://www.ebi.ac.uk/ena">European Nucleotide Archive (ENA)</a>. It can be retrieved using the project accesion number PRJEB27858. This includes the raw data used for the genome assembly, the resequencing data used for the population genetic analysis as well as the RNA sequencing data.</p>
<p>External data that is used within the scripts can not be provided (eg. the stickleback reference genome) and needs to be accessed independently.</p>
</div>
<div id="figures" class="section level2">
<h2><span class="header-section-number">1.2</span> Figures</h2>
<p>A more detailed documentation exists for all the figures of the manuscript:</p>
<p><a href="figure-1.html">F1</a>, <a href="figure-2.html">F2</a> &amp; <a href="figure-3.html">F3</a></p>
<p>for the extended data figure:</p>
<p><a href="extendend-data-figure-1">E1</a></p>
<p>as well as for all the supplementary figures:</p>
<p><a href="supplementary-figure-01.html">S01</a>, <a href="supplementary-figure-02.html">S02</a>, <a href="supplementary-figure-03.html">S03</a>, <a href="supplementary-figure-05.html">S05</a>, <a href="supplementary-figure-06.html">S06</a>, <a href="supplementary-figure-07.html">S07</a>, <a href="supplementary-figure-08.html">S08</a>, <a href="supplementary-figure-09.html">S09</a>, <a href="supplementary-figure-10.html">S10</a>, <a href="supplementary-figure-11.html">S11</a>, <a href="supplementary-figure-12.html">S12</a>, <a href="supplementary-figure-13.html">S13</a>, <a href="supplementary-figure-14.html">S14</a> &amp; <a href="supplementary-figure-15.html">S15</a></p>
<p>The only exception to this is the supplementary figure S04. This figure is a byproduct of the anchoring step during the assembly and was produced by the <strong>Allmaps</strong> software. Afterwards, <strong>Inkscape</strong> was used to adjust the coloration and labels of the linkage maps.</p>
</div>
<div id="background" class="section level2">
<h2><span class="header-section-number">1.3</span> Background</h2>
<p>All scripts assume two variables to be set within the bash environment:</p>
<ul>
<li><code>$WORK</code> is assumed to point to the base folder of this repository</li>
<li><code>$SFTWR</code> is a folder that contains all the software dependencies that are used within the scripts</li>
</ul>
<p>The dependencies need to be downloaded and installed separately.</p>
<p>The scripts are organized/ numbered in chronological order. Multiple scripts with equal numbers (eg. 2.2.4.pca_bel.sh, 2.2.4.pca_hon.sh &amp; 2.2.4.pca_pan.sh) usually work on parallel branches of the process and can be executed in parallel. In contrast to this, scripts with higher numbers usually depend on the output of scripts with lower numbers and should therefore be executed afterwards.</p>
<p>Most of the scripts start with a comment block that defines the requested resources for the used computer cluster:</p>
<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash"><span class="co">#PBS -l elapstim_req=&lt;runtime&gt;</span>
<span class="co">#PBS -l memsz_job=&lt;memory&gt;</span>
<span class="co">#PBS -b &lt;threads&gt;</span>
<span class="co">#PBS -l cpunum_job=&lt;cores&gt;</span>
<span class="co">#PBS -N &lt;job-name&gt;</span>
<span class="co">#PBS -q &lt;job-que&gt;</span>
<span class="co">#PBS -o &lt;stdout-log&gt;.stdout</span>
<span class="co">#PBS -e &lt;stderr-log&gt;.stderr</span></code></pre></div>
</div>
</div>
</section>
</div>
</div>
</div>
</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/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>
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": true,
"twitter": true,
"google": false,
"linkedin": false,
"weibo": false,
"instapper": false,
"vk": false,
"all": ["facebook", "google", "twitter", "linkedin", "weibo", "instapaper"]
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"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
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......@@ -42,7 +42,7 @@ ptsB2 <- data.frame(stringsAsFactors = F, nr = 1:crLB2,
.84,1,2.1,3.5,1.25,1.5,2.5,
2.5,2.5,2.5,2.5,1.33,1.66,2,1.33,1.66,2,3.1,0,0,
1.33,2,
.55,.45,.45,.45,
.62,.45,.45,.45,
.25),
y=c(-1,-.5,0,.15,-1,.85,.15,-.5,.4,.85,.85,.85,
.3,
......@@ -51,7 +51,7 @@ ptsB2 <- data.frame(stringsAsFactors = F, nr = 1:crLB2,
.85,.85,.5,rep(.85,3),
-1,-.8,-.6,-.4,-1,-1,-1,-.6,-.6,-.6,.5,-1,-.2,
-.25,-.25,
-.4,-.05,.35,.85,
-.25,-.25,.35,.85,
-1),
decript=c('allGeno','dxy','pi','Hp2Ga','mac2',
'Circos','samples','pca','fst','fig1','fig2','fig3',
......@@ -61,8 +61,8 @@ ptsB2 <- data.frame(stringsAsFactors = F, nr = 1:crLB2,
'transform-ext','2dbin-ext','gffnames','LGmap','S8','selscan','selscan_slider',
'subsetFST','transformNH','NH','S13',
'fasteprr'),
type=c('class',rep('ind',6),rep('class',2),rep('ind',3),rep('class',2),rep('ind',2),'class',rep('ind',4),
rep('ind',4),rep('class',6),'ind','class','ind',rep("class",5),rep('ind',2)),
type=c('ind',rep('class',2),rep('ind',4),rep('class',2),rep('ind',3),rep('class',2),rep('ind',2),'class',rep('ind',4),
rep('ind',4),rep('class',6),'ind','class','ind',rep("class",5),'ind','class'),
label=c('txt',rep('txt',2),'txt','vcf','plot',rep('txt',3),
rep('plot',3),rep('txt',2),rep('plot',3),'txt',rep('plot',3),
rep('plot',4),rep('txt',8),'plot',rep('txt',5),'plot','txt'),
......@@ -76,7 +76,7 @@ edgB2 <- data.frame(stringsAsFactors = F,
32,28,28,31,31,33,
5,35,36,
9,37,38,39,8,
5,9,41),
5,9,41,5),
e=c(2,3,6,8,10,10,9,10,13,
26,29,14,
27,28,30,31,32,
......@@ -84,18 +84,18 @@ edgB2 <- data.frame(stringsAsFactors = F,
20,12,17,12,17,12,17,12,17,rep(21,5),
22:25,34,35,36,21,
37,38,39,40,40,
41,34,34),
41,34,34,38),
label=c('2.2.1.dxy','2.2.2. & 2.2.3.pi ','2.2.0.1.Circos',
'2.2.4.pca','pca','map','2.2.5.fst','',
'2.2.6.GxP','2.2.9.1.LDext','2.2.8.1.LD','GxP',
'2.2.9.2','2.2.9.3','2.2.8.2','2.2.8.3','2.2.7.gene_names',rep('',22),
'',"2.2.9.1 & 2","2.2.9.3 & 4","",
'2.10.1','2.10.2','2.10.3','','','2.2.11.fasteprr','',''),
'2.10.1','2.10.2','2.10.3','','','2.2.11.fasteprr','','',''),
type=c(rep('helper',2),rep('plot',1),'helper',rep('plot',2),'helper','plot',
rep('helper',8),'transform',rep('plot',23),"helper",rep('plot',2),rep('helper',3),rep('plot',2),
'helper',rep('plot',2)),
'helper',rep('plot',2),'helper'),
dir=c(rep(4,9),rep(1,2),1,rep(1,4),2,rep(4,5),rep(1,4),rep(4,2),2,2,1,1,4,2,2,rep(1,4),4,1,1,4,
3,4,4,4,4,2,2,4))
3,2,4,4,4,2,2,4,4))
# 3. Expression -----------------
crLB3 <- 7
......
......@@ -3,7 +3,7 @@ output: html_document
editor_options:
chunk_output_type: console
---
# Figure 4
# Figure 3
## Summary
......
......@@ -228,11 +228,11 @@ p2 <- ggplot(testdat,aes(x=sample,y=gene,fill=counts))+
guide = guide_colorbar(direction = "horizontal",title.position = "top"))+
scale_color_manual(name="",values=c('#fb8620','#d93327','#1b519c','#666666'),guide=F)+
# general plot theme
theme_minimal(base_size = 13)+
theme_minimal(base_size = 8)+
theme(axis.text.x = element_text(angle=90),
plot.margin = unit(c(1,1,50,1),'pt'),
axis.text.y = element_text(face = 'italic'),
legend.position = c(.05,-.28),panel.grid = element_blank(),legend.key.width = unit(30,'pt'))
legend.position = c(.02,-.4),panel.grid = element_blank(),legend.key.width = unit(20,'pt'))
```
<center>
......@@ -294,7 +294,7 @@ p3 <- ggplot(Cdf3,aes(x=0,y=Count))+
scale_fill_manual('Gene',values = c('lightgray',viridis::viridis(9)),
labels=Flab)+
# general plot theme
theme_minimal(base_size = 13)+
theme_minimal(base_size = 8)+
theme(legend.position = 'none',
axis.text.x = element_text(angle=90))
```
......@@ -321,7 +321,7 @@ It is then exported using `ggsave()`.
```r
ggsave(plot = S05, filename = '../output/S05.pdf',width=12,height=6,device = cairo_pdf)
ggsave(plot = S05, filename = '../output/S05.pdf',width=183,height=90,units = 'mm',device = cairo_pdf)
```
<center>
......
......@@ -314,7 +314,7 @@ S12c <- ggplot(data_both,aes(x=RHO,y=WEIGHTED_FST))+
annotate(geom = 'text',x=c(795),y=c(.55),label=an3,size=3,parse=TRUE,col=modclr)+
annotate(geom = 'text',x=c(745),y=c(.5),label=an1,size=3)+
annotate(geom = 'text',x=c(865),y=c(.5),label=c(an2),parse=TRUE,size=3)+
scale_x_continuous(name=expression(Recombination~rate~(italic("\u03C1"))),
scale_x_continuous(name=expression(Population~recombination~rate~(italic("\u03C1"))),
expand = c(.01,.01))+
scale_y_continuous(name=expression(Genetic~differentiation~(weighted~mean~italic(F[ST]))),
expand = c(.005,.005))+
......
......@@ -6,33 +6,33 @@
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<title>Script repository</title>
<meta name="description" content="Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018.">
<meta name="description" content="Scripts used to produce Figures and Supplementary Figures of ‘Association between vision and pigmentation genes during genomic divergence’.">
<meta name="generator" content="bookdown 0.7 and GitBook 2.6.7">
<meta property="og:title" content="Script repository" />
<meta property="og:type" content="book" />
<meta property="og:description" content="Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018." />
<meta property="og:description" content="Scripts used to produce Figures and Supplementary Figures of ‘Association between vision and pigmentation genes during genomic divergence’." />
<meta name="github-repo" content="k-hench/bookdown" />
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<meta name="author" content="Kosmas Hench">
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......@@ -129,12 +129,12 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="4.2.4" data-path="figure-2.html"><a href="figure-2.html#composing-the-final-figure"><i class="fa fa-check"></i><b>4.2.4</b> Composing the final figure</a></li>
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<li class="chapter" data-level="5" data-path="figure-4.html"><a href="figure-4.html"><i class="fa fa-check"></i><b>5</b> Figure 4</a><ul>
<li class="chapter" data-level="5.1" data-path="figure-4.html"><a href="figure-4.html#summary-2"><i class="fa fa-check"></i><b>5.1</b> Summary</a></li>
<li class="chapter" data-level="5.2" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.r"><i class="fa fa-check"></i><b>5.2</b> Details of <code>F3.R</code></a></li>
<li class="chapter" data-level="5.3" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.functions.r"><i class="fa fa-check"></i><b>5.3</b> Details of <code>F3.functions.R</code></a></li>
<li class="chapter" data-level="5.4" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.genomewide_box.r"><i class="fa fa-check"></i><b>5.4</b> Details of <code>F3.genomeWide_box.R</code></a></li>
<li class="chapter" data-level="5.5" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.peakarea_box.r"><i class="fa fa-check"></i><b>5.5</b> Details of <code>F3.peakArea_box.R</code></a></li>
<li class="chapter" data-level="5" data-path="figure-3.html"><a href="figure-3.html"><i class="fa fa-check"></i><b>5</b> Figure 3</a><ul>
<li class="chapter" data-level="5.1" data-path="figure-3.html"><a href="figure-3.html#summary-2"><i class="fa fa-check"></i><b>5.1</b> Summary</a></li>
<li class="chapter" data-level="5.2" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.r"><i class="fa fa-check"></i><b>5.2</b> Details of <code>F3.R</code></a></li>
<li class="chapter" data-level="5.3" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.functions.r"><i class="fa fa-check"></i><b>5.3</b> Details of <code>F3.functions.R</code></a></li>
<li class="chapter" data-level="5.4" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.genomewide_box.r"><i class="fa fa-check"></i><b>5.4</b> Details of <code>F3.genomeWide_box.R</code></a></li>
<li class="chapter" data-level="5.5" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.peakarea_box.r"><i class="fa fa-check"></i><b>5.5</b> Details of <code>F3.peakArea_box.R</code></a></li>
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<li class="chapter" data-level="6" data-path="extendend-data-figure-1.html"><a href="extendend-data-figure-1.html"><i class="fa fa-check"></i><b>6</b> Extendend Data Figure 1</a><ul>
<li class="chapter" data-level="6.1" data-path="extendend-data-figure-1.html"><a href="extendend-data-figure-1.html#summary-3"><i class="fa fa-check"></i><b>6.1</b> Summary</a></li>
......@@ -490,7 +490,7 @@ p4 &lt;-<span class="st"> </span><span class="kw">create_K_plot</span>(<span cla
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<meta name="twitter:description" content="Scripts used to produce Figures and Supplementary Figures of ‘Association between vision and pigmentation genes during genomic divergence’." />
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-07-27">
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......@@ -129,12 +129,12 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="4.2.4" data-path="figure-2.html"><a href="figure-2.html#composing-the-final-figure"><i class="fa fa-check"></i><b>4.2.4</b> Composing the final figure</a></li>
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<li class="chapter" data-level="5" data-path="figure-4.html"><a href="figure-4.html"><i class="fa fa-check"></i><b>5</b> Figure 4</a><ul>
<li class="chapter" data-level="5.1" data-path="figure-4.html"><a href="figure-4.html#summary-2"><i class="fa fa-check"></i><b>5.1</b> Summary</a></li>
<li class="chapter" data-level="5.2" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.r"><i class="fa fa-check"></i><b>5.2</b> Details of <code>F3.R</code></a></li>
<li class="chapter" data-level="5.3" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.functions.r"><i class="fa fa-check"></i><b>5.3</b> Details of <code>F3.functions.R</code></a></li>
<li class="chapter" data-level="5.4" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.genomewide_box.r"><i class="fa fa-check"></i><b>5.4</b> Details of <code>F3.genomeWide_box.R</code></a></li>
<li class="chapter" data-level="5.5" data-path="figure-4.html"><a href="figure-4.html#details-of-f3.peakarea_box.r"><i class="fa fa-check"></i><b>5.5</b> Details of <code>F3.peakArea_box.R</code></a></li>
<li class="chapter" data-level="5" data-path="figure-3.html"><a href="figure-3.html"><i class="fa fa-check"></i><b>5</b> Figure 3</a><ul>
<li class="chapter" data-level="5.1" data-path="figure-3.html"><a href="figure-3.html#summary-2"><i class="fa fa-check"></i><b>5.1</b> Summary</a></li>
<li class="chapter" data-level="5.2" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.r"><i class="fa fa-check"></i><b>5.2</b> Details of <code>F3.R</code></a></li>
<li class="chapter" data-level="5.3" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.functions.r"><i class="fa fa-check"></i><b>5.3</b> Details of <code>F3.functions.R</code></a></li>
<li class="chapter" data-level="5.4" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.genomewide_box.r"><i class="fa fa-check"></i><b>5.4</b> Details of <code>F3.genomeWide_box.R</code></a></li>
<li class="chapter" data-level="5.5" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.peakarea_box.r"><i class="fa fa-check"></i><b>5.5</b> Details of <code>F3.peakArea_box.R</code></a></li>
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<li class="chapter" data-level="6" data-path="extendend-data-figure-1.html"><a href="extendend-data-figure-1.html"><i class="fa fa-check"></i><b>6</b> Extendend Data Figure 1</a><ul>
<li class="chapter" data-level="6.1" data-path="extendend-data-figure-1.html"><a href="extendend-data-figure-1.html#summary-3"><i class="fa fa-check"></i><b>6.1</b> Summary</a></li>
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......@@ -6,26 +6,26 @@
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