pre submission

aa182a42 · Kosmas Hench · 9aee6225 · aa182a42 · aa182a42 · aa182a42
Commit aa182a42 authored Jul 30, 2018 by Kosmas Hench
41 changed files
--- a/3_figures/F_scripts/Rplots.pdf
+++ b/3_figures/F_scripts/Rplots.pdf
--- a/3_figures/F_scripts/S05.R
+++ b/3_figures/F_scripts/S05.R
@@ -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))


--- a/3_figures/F_scripts/S12.R
+++ b/3_figures/F_scripts/S12.R
@@ -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))+

--- a/3_figures/S01/circos-cairo.svg
+++ b/3_figures/S01/circos-cairo.svg
--- a/3_figures/S01/circos.svg
+++ b/3_figures/S01/circos.svg
--- a/3_figures/S05.Rmd
+++ b/3_figures/S05.Rmd
@@ -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>

--- a/3_figures/S12.Rmd
+++ b/3_figures/S12.Rmd
@@ -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))+

--- a/3_figures/Workflow.Rmd
+++ b/3_figures/Workflow.Rmd
@@ -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))+

--- a/3_figures/index.Rmd
+++ b/3_figures/index.Rmd
 --- 
 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

--- a/3_figures/intro.html
+++ b/3_figures/intro.html
--- a/3_figures/workflow/points_and_edges_analysis.R
+++ b/3_figures/workflow/points_and_edges_analysis.R
@@ -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

--- a/docs/F3.md
+++ b/docs/F3.md
@@ -3,7 +3,7 @@ output: html_document
 editor_options: 
  chunk_output_type: console
 ---
-# Figure 4
+# Figure 3
  

 ## Summary

--- a/docs/S02_files/figure-html/s13SHOW-1.png
+++ b/docs/S02_files/figure-html/s13SHOW-1.png
--- a/docs/S05.md
+++ b/docs/S05.md
@@ -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>

--- a/docs/S05_files/figure-html/p2SHOW-1.png
+++ b/docs/S05_files/figure-html/p2SHOW-1.png
--- a/docs/S05_files/figure-html/s05SHOW-1.png
+++ b/docs/S05_files/figure-html/s05SHOW-1.png
--- a/docs/S12.md
+++ b/docs/S12.md
@@ -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))+

--- a/docs/S12_files/figure-html/s11SHOW-1.png
+++ b/docs/S12_files/figure-html/s11SHOW-1.png
--- a/docs/Workflow_files/figure-html/plot-1.png
+++ b/docs/Workflow_files/figure-html/plot-1.png
--- a/docs/extendend-data-figure-1.html
+++ b/docs/extendend-data-figure-1.html
@@ -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>

--- a/docs/figure-1.html
+++ b/docs/figure-1.html
@@ -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>
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-  <meta name="twitter:description" content="Scripts used to produce Figures and Supplementary Figures of Hench et al. 2018." />
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 <meta name="author" content="Kosmas Hench">


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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>
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-<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>
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+<a href="figure-3.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
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--- a/docs/figure-3.html
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@@ -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’.">
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  <meta property="og:title" content="Script repository" />
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-  <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’." />
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  <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>
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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>
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@@ -234,9 +234,9 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
            <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>

--- a/docs/index.md
+++ b/docs/index.md
 --- 
 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

--- a/docs/search_index.json
+++ b/docs/search_index.json
--- a/docs/supplementary-figure-01.html
+++ b/docs/supplementary-figure-01.html
@@ -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>

--- a/docs/supplementary-figure-02.html
+++ b/docs/supplementary-figure-02.html
@@ -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>
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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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 <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>
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