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hamlets_ILD_vision_pigmentation
hamlets_ILD_vision_pigmentation
Commit aa182a42 authored by Kosmas Hench's avatar Kosmas Hench
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3_figures/F_scripts/S05.R
View file @ aa182a42
......@@ -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))
......
3_figures/F_scripts/S12.R
View file @ aa182a42
......@@ -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))+
......
3_figures/S01/circos-cairo.svg deleted 100644 → 0
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3_figures/S01/circos.svg deleted 100644 → 0
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3_figures/S05.Rmd
View file @ aa182a42
......@@ -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>
......
3_figures/S12.Rmd
View file @ aa182a42
......@@ -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))+
......
3_figures/Workflow.Rmd
View file @ aa182a42
......@@ -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))+
......
3_figures/index.Rmd
View file @ aa182a42
---
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
......
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3_figures/workflow/points_and_edges_analysis.R
View file @ aa182a42
......@@ -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
......
docs/F3.md
View file @ aa182a42
......@@ -3,7 +3,7 @@ output: html_document
editor_options:
chunk_output_type: console
---
# Figure 4
# Figure 3
## Summary
......
docs/S05.md
View file @ aa182a42
......@@ -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>
......
docs/S12.md
View file @ aa182a42
......@@ -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))+
......
docs/extendend-data-figure-1.html
View file @ aa182a42
......@@ -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" />
<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="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">
<meta name="date" content="2018-07-30">
<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="prev" href="figure-4.html">
<link rel="prev" href="figure-3.html">
<link rel="next" href="supplementary-figure-01.html">
<script src="libs/jquery-2.2.3/jquery.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
......@@ -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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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
</div>
</div>
</div>
<a href="figure-4.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
<a href="figure-3.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
<a href="supplementary-figure-01.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
</div>
</div>
......
docs/figure-1.html
View file @ aa182a42
......@@ -6,26 +6,26 @@
<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" />
<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="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">
<meta name="date" content="2018-07-30">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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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<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="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">
<meta name="date" content="2018-07-30">
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<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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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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<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" />
<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="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">
<meta name="date" content="2018-07-30">
<meta name="viewport" content="width=device-width, initial-scale=1">
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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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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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<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>
<h3 class="subtitle"><em>Supplement to ‘Association between vision and pigmentation genes during genomic divergence’</em></h3>
<h4 class="author"><em>Kosmas Hench</em></h4>
<h4 class="date"><em>2018-07-27</em></h4>
<h4 class="date"><em>2018-07-30</em></h4>
</div>
<div id="intro" class="section level1">
<h1><span class="header-section-number">1</span> Intro</h1>
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---
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: "2018-07-27"
date: "2018-07-30"
documentclass: book
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
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<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" />
<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="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">
<meta name="date" content="2018-07-30">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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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<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" />
<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="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">
<meta name="date" content="2018-07-30">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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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<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" />
<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="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">
<meta name="date" content="2018-07-30">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
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<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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