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hamlets_ILD_vision_pigmentation
hamlets_ILD_vision_pigmentation
Commit d7507191 authored by Kosmas Hench's avatar Kosmas Hench
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update fig 1 documentation

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3_figures/F1.Rmd
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3_figures/F1/F1.R
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......@@ -55,7 +55,6 @@ sampSize <- data %>% group_by(spec,loc) %>% summarise(n=length(id)) %>% filter(s
x=c(rep(-94.7,3)+xpos, # belize
rep(-78,3)+xpos, # panama
rep(-98.75,3)+xpos)) # honduras
ccc<-rgb(0,.4,.8)
uS <- readShapeSpatial('../../0_data/0_resources/F1_shps/F1.npu_distribution.shp');
uS_f <- fortify(uS,region="DN");
......@@ -69,6 +68,7 @@ hS_f <- clipPolys(hS_f, xlim=xlimW,ylim=ylimW, keepExtra=TRUE)
clrShps <- c("#ffc097","#b1d4f8")
cFILL <- rgb(.7,.7,.7)
ccc<-rgb(0,.4,.8)
p1 <- ggplot()+coord_map(projection = 'mercator',xlim=xlimW,ylim=ylimW)+
labs(y="Latitude",x="Longitude") +
......@@ -84,6 +84,31 @@ p1 <- ggplot()+coord_map(projection = 'mercator',xlim=xlimW,ylim=ylimW)+
geom_text(data = crvs[c(3,6,9),],aes(x= x, y = y, label=c('B','P','H')),size=3)+
geom_point(data=dataSum,aes(x=w,y=n),size=1.5,shape=21,fill='white')
fstdata <- read.csv('../../2_output/08_popGen/05_fst/genome_wide_weighted_mean_fst.txt',
sep='\t',skip = 1,head=F,col.names = c('pair','fst')) %>%
filter(!pair %in% c('NU','PN','PU')) %>%
arrange(fst) %>% mutate(x=row_number()) %>% rowwise() %>%
mutate(loc = substr(as.character(pair),2,2),
pop1 = substr(as.character(pair),1,1),
pop2 = substr(as.character(pair),3,3),
pairclass=paste(pop1,pop2,sep='-'))
clrP <- c('#fb8620','#1b519c','#d93327')
p5 <- ggplot(fstdata,aes(x=x,y=fst,fill=pairclass))+
geom_bar(stat='identity')+
annotation_custom(legPGrob,xmin =0.15,xmax =5,ymin =.008,ymax = .035)+
scale_fill_manual(values = clrP)+
scale_y_continuous(name=expression(italic("F"['ST'])),
expand = c(0,0))+
scale_x_continuous(expand = c(.01,0),breaks = 1:9,
labels = c('H','H','B','H','P','B','B','P','P'))+
theme_mapK+
theme(legend.position = 'none',
panel.grid.major.y = element_line(color=rgb(.9,.9,.9)),
axis.title.x = element_blank(),
axis.text.x = element_text(#face = 'bold',
size = 8));
clr<-c('#000000','#d45500','#000000')
fll<-c('#000000','#d45500','#ffffff')
eVclr <- c(rep('darkred',2),rep(cFILL,8))
......@@ -92,6 +117,22 @@ belPCA <- readRDS('../../2_output/08_popGen/04_pca/bel/belpca.Rds')
honPCA <- readRDS('../../2_output/08_popGen/04_pca/hon/honpca.Rds')
panPCA <- readRDS('../../2_output/08_popGen/04_pca/pan/panpca.Rds')
dataHON <- cbind(dataAll %>% filter(sample=='sample',loc=='hon')%>% select(id,spec),
honPCA$scores); names(dataHON)[3:12]<- paste('PC',1:10,sep='')
exp_varHON <- (honPCA$singular.values[1:10])^2/length(honPCA$maf)
xlabHON <- paste('PC1 (',sprintf("%.1f",exp_varHON[1]*100),'%)')# explained varinace)')
ylabHON <- paste('PC2 (',sprintf("%.1f",exp_varHON[2]*100),'%)')# explained varinace)')
p2 <- ggplot(dataHON,aes(x=PC1,y=PC2,col=spec,fill=spec))+geom_point(size=1.1,shape=21)+
scale_color_manual(values=clr,guide=F)+
scale_fill_manual(values=fll,guide=F)+theme_mapK+
theme(legend.position='bottom',
panel.border = element_rect(color=rgb(.9,.9,.9),fill=rgb(1,1,1,0)),
axis.title.y = element_text(vjust = -7),
axis.title.x = element_text(vjust = 6),
plot.margin = unit(rep(-10,4),'pt'))+#coord_equal()+
scale_x_continuous(name=xlabHON,breaks = c(-.2,.5))+
scale_y_continuous(name=ylabHON,breaks = c(-.4,.2))
dataBEL <- cbind(dataAll %>% filter(sample=='sample',loc=='bel') %>% select(id,spec),
belPCA$scores); names(dataBEL)[3:12]<- paste('PC',1:10,sep='')
......@@ -99,7 +140,7 @@ exp_varBEL <- (belPCA$singular.values[1:10])^2/length(belPCA$maf)
xlabBEL <- paste('PC1 (',sprintf("%.1f",exp_varBEL[1]*100),'%)')
ylabBEL <- paste('PC2 (',sprintf("%.1f",exp_varBEL[2]*100),'%)')
p2 <- ggplot(dataBEL,aes(x=PC1,y=PC2,col=spec,fill=spec))+geom_point(size=1.1,shape=21)+
p3 <- ggplot(dataBEL,aes(x=PC1,y=PC2,col=spec,fill=spec))+geom_point(size=1.1,shape=21)+
scale_color_manual(values=clr,guide=F)+
scale_fill_manual(values=fll,guide=F)+theme_mapK+
theme(legend.position='bottom',
......@@ -108,23 +149,8 @@ p2 <- ggplot(dataBEL,aes(x=PC1,y=PC2,col=spec,fill=spec))+geom_point(size=1.1,sh
axis.title.x = element_text(vjust = 6),
plot.margin = unit(rep(-10,4),'pt'))+
scale_x_continuous(name=xlabBEL,breaks = c(-.15,.25))+
scale_y_continuous(name=ylabBEL,breaks = c(-.3,.2));p2
scale_y_continuous(name=ylabBEL,breaks = c(-.3,.2))
dataHON <- cbind(dataAll %>% filter(sample=='sample',loc=='hon')%>% select(id,spec),
honPCA$scores); names(dataHON)[3:12]<- paste('PC',1:10,sep='')
exp_varHON <- (honPCA$singular.values[1:10])^2/length(honPCA$maf)
xlabHON <- paste('PC1 (',sprintf("%.1f",exp_varHON[1]*100),'%)')# explained varinace)')
ylabHON <- paste('PC2 (',sprintf("%.1f",exp_varHON[2]*100),'%)')# explained varinace)')
p3 <- ggplot(dataHON,aes(x=PC1,y=PC2,col=spec,fill=spec))+geom_point(size=1.1,shape=21)+
scale_color_manual(values=clr,guide=F)+
scale_fill_manual(values=fll,guide=F)+theme_mapK+
theme(legend.position='bottom',
panel.border = element_rect(color=rgb(.9,.9,.9),fill=rgb(1,1,1,0)),
axis.title.y = element_text(vjust = -7),
axis.title.x = element_text(vjust = 6),
plot.margin = unit(rep(-10,4),'pt'))+#coord_equal()+
scale_x_continuous(name=xlabHON,breaks = c(-.2,.5))+
scale_y_continuous(name=ylabHON,breaks = c(-.4,.2));p3
dataPAN <- cbind(dataAll %>% filter(sample=='sample',loc=='boc',spec!='gum')%>% select(id,spec),
panPCA$scores); names(dataPAN)[3:12]<- paste('PC',1:10,sep='')
......@@ -140,39 +166,13 @@ p4 <- ggplot(dataPAN,aes(x=PC1,y=PC2,col=spec,fill=spec))+geom_point(size=1.1,sh
axis.title.x = element_text(vjust = 6),
plot.margin = unit(rep(-10,4),'pt'))+
scale_x_continuous(name=xlabPAN,breaks = c(-.15,.2))+
scale_y_continuous(name=ylabPAN,breaks = c(-.2,.2));p4
fstdata <- read.csv('../../2_output/08_popGen/05_fst/genome_wide_weighted_mean_fst.txt',
sep='\t',skip = 1,head=F,col.names = c('pair','fst')) %>%
filter(!pair %in% c('NU','PN','PU')) %>%
arrange(fst) %>% mutate(x=row_number()) %>% rowwise() %>%
mutate(loc = substr(as.character(pair),2,2),
pop1 = substr(as.character(pair),1,1),
pop2 = substr(as.character(pair),3,3),
pairclass=paste(pop1,pop2,sep='-'))
clrP <- c('#fb8620','#1b519c','#d93327')
p5 <- ggplot(fstdata,aes(x=x,y=fst,fill=pairclass))+
geom_bar(stat='identity')+
annotation_custom(legPGrob,xmin =0.15,xmax =5,ymin =.008,ymax = .035)+
scale_fill_manual(values = clrP)+
scale_y_continuous(name=expression(italic("F"['ST'])),
expand = c(0,0))+
scale_x_continuous(expand = c(.01,0),breaks = 1:9,
labels = c('H','H','B','H','P','B','B','P','P'))+
theme_mapK+
theme(legend.position = 'none',
panel.grid.major.y = element_line(color=rgb(.9,.9,.9)),
axis.title.x = element_blank(),
axis.text.x = element_text(#face = 'bold',
size = 8));
scale_y_continuous(name=ylabPAN,breaks = c(-.2,.2))
hSC <- c(.07,.07)
yf <- c(0.07,0.035,0.00);xf<-c(0.07,0,0.07)
yS <- c(.485,.577,.805);xS<-c(.09,.417,.156)
ggdraw()+
F1 <- ggdraw()+
draw_plot(plot = p1,0,.38,.81,.64)+
draw_plot(plot = p5,0,.01,.24,.35)+
draw_plot(plot = p2,.25,.01,.23,.33)+
......@@ -197,12 +197,12 @@ ggdraw()+
draw_grob(belGrob, 0.2, 0.67, 0.042, 0.042)+
draw_grob(honGrob, 0.28, 0.61, 0.042, 0.042)+
draw_grob(belGrob, 0.285+.09, 0.37, 0.042, 0.042)+
draw_grob(honGrob, 0.535+.09, 0.37, 0.042, 0.042)+
draw_grob(honGrob, 0.285+.09, 0.37, 0.042, 0.042)+
draw_grob(belGrob, 0.535+.09, 0.37, 0.042, 0.042)+
draw_grob(panGrob, 0.785+.09, 0.37, 0.042, 0.042)+
draw_plot_label(x = c(.005,.005,.25),
y = c(.995,.42,.42),
label =letters[1:3])
ggsave('F1.pdf',width = 183,height = 145,units = 'mm',device = cairo_pdf)
ggsave(plot = F1,filename = '../output/F1.pdf',width = 183,height = 145,units = 'mm',device = cairo_pdf)
\ No newline at end of file
3_figures/_output.yml
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......@@ -3,7 +3,7 @@ bookdown::gitbook:
split_by: chapter
config:
toc:
collapse: subsection
collapse: subsubsection
before: |
<li><a href="./">Script repository</a></li>
after: |
......
3_figures/docs/F1.md
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3_figures/docs/f1.html
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3_figures/docs/index.html
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......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-05-29">
<meta name="date" content="2018-06-12">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -110,7 +110,15 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="2" data-path="workflow.html"><a href="workflow.html"><i class="fa fa-check"></i><b>2</b> Workflow</a><ul>
<li class="chapter" data-level="2.1" data-path="workflow.html"><a href="workflow.html#info"><i class="fa fa-check"></i><b>2.1</b> Info</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a><ul>
<li class="chapter" data-level="3.1" data-path="f1.html"><a href="f1.html#summary"><i class="fa fa-check"></i><b>3.1</b> Summary</a></li>
<li class="chapter" data-level="3.2" data-path="f1.html"><a href="f1.html#details-of-f1.r"><i class="fa fa-check"></i><b>3.2</b> Details of F1.R</a><ul>
<li class="chapter" data-level="3.2.1" data-path="f1.html"><a href="f1.html#fig.-1-a"><i class="fa fa-check"></i><b>3.2.1</b> Fig. 1 a)</a></li>
<li class="chapter" data-level="3.2.2" data-path="f1.html"><a href="f1.html#fig.-1-b"><i class="fa fa-check"></i><b>3.2.2</b> Fig. 1 b)</a></li>
<li class="chapter" data-level="3.2.3" data-path="f1.html"><a href="f1.html#fig.-1-c"><i class="fa fa-check"></i><b>3.2.3</b> Fig. 1 c)</a></li>
<li class="chapter" data-level="3.2.4" data-path="f1.html"><a href="f1.html#fig-1-complete"><i class="fa fa-check"></i><b>3.2.4</b> Fig 1 (complete)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="s01.html"><a href="s01.html"><i class="fa fa-check"></i><b>4</b> S01</a><ul>
<li class="chapter" data-level="4.1" data-path="s01.html"><a href="s01.html#preparation"><i class="fa fa-check"></i><b>4.1</b> Preparation</a></li>
<li class="chapter" data-level="4.2" data-path="s01.html"><a href="s01.html#content-of-circos_figure.r"><i class="fa fa-check"></i><b>4.2</b> Content of circos_figure.R</a></li>
......@@ -140,7 +148,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<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>2018-05-29</em></h4>
<h4 class="date"><em>2018-06-12</em></h4>
</div>
<div id="intro" class="section level1">
<h1><span class="header-section-number">1</span> Intro</h1>
......@@ -215,7 +223,7 @@ gitbook.start({
},
"download": null,
"toc": {
"collapse": "subsection"
"collapse": "subsubsection"
}
});
});
......
3_figures/docs/index.md
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......@@ -2,7 +2,7 @@
title: "Script repository"
subtitle: "Supplement to Hench *et al.* 2018"
author: "Kosmas Hench"
date: "2018-05-29"
date: "2018-06-12"
documentclass: book
bibliography: [book.bib]
biblio-style: apalike
......
3_figures/docs/s01.html
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......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-05-29">
<meta name="date" content="2018-06-12">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -110,7 +110,15 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="2" data-path="workflow.html"><a href="workflow.html"><i class="fa fa-check"></i><b>2</b> Workflow</a><ul>
<li class="chapter" data-level="2.1" data-path="workflow.html"><a href="workflow.html#info"><i class="fa fa-check"></i><b>2.1</b> Info</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a><ul>
<li class="chapter" data-level="3.1" data-path="f1.html"><a href="f1.html#summary"><i class="fa fa-check"></i><b>3.1</b> Summary</a></li>
<li class="chapter" data-level="3.2" data-path="f1.html"><a href="f1.html#details-of-f1.r"><i class="fa fa-check"></i><b>3.2</b> Details of F1.R</a><ul>
<li class="chapter" data-level="3.2.1" data-path="f1.html"><a href="f1.html#fig.-1-a"><i class="fa fa-check"></i><b>3.2.1</b> Fig. 1 a)</a></li>
<li class="chapter" data-level="3.2.2" data-path="f1.html"><a href="f1.html#fig.-1-b"><i class="fa fa-check"></i><b>3.2.2</b> Fig. 1 b)</a></li>
<li class="chapter" data-level="3.2.3" data-path="f1.html"><a href="f1.html#fig.-1-c"><i class="fa fa-check"></i><b>3.2.3</b> Fig. 1 c)</a></li>
<li class="chapter" data-level="3.2.4" data-path="f1.html"><a href="f1.html#fig-1-complete"><i class="fa fa-check"></i><b>3.2.4</b> Fig 1 (complete)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="s01.html"><a href="s01.html"><i class="fa fa-check"></i><b>4</b> S01</a><ul>
<li class="chapter" data-level="4.1" data-path="s01.html"><a href="s01.html#preparation"><i class="fa fa-check"></i><b>4.1</b> Preparation</a></li>
<li class="chapter" data-level="4.2" data-path="s01.html"><a href="s01.html#content-of-circos_figure.r"><i class="fa fa-check"></i><b>4.2</b> Content of circos_figure.R</a></li>
......@@ -238,7 +246,7 @@ gitbook.start({
},
"download": null,
"toc": {
"collapse": "subsection"
"collapse": "subsubsection"
}
});
});
......
3_figures/docs/s08.html
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......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-05-29">
<meta name="date" content="2018-06-12">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -110,7 +110,15 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="2" data-path="workflow.html"><a href="workflow.html"><i class="fa fa-check"></i><b>2</b> Workflow</a><ul>
<li class="chapter" data-level="2.1" data-path="workflow.html"><a href="workflow.html#info"><i class="fa fa-check"></i><b>2.1</b> Info</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a><ul>
<li class="chapter" data-level="3.1" data-path="f1.html"><a href="f1.html#summary"><i class="fa fa-check"></i><b>3.1</b> Summary</a></li>
<li class="chapter" data-level="3.2" data-path="f1.html"><a href="f1.html#details-of-f1.r"><i class="fa fa-check"></i><b>3.2</b> Details of F1.R</a><ul>
<li class="chapter" data-level="3.2.1" data-path="f1.html"><a href="f1.html#fig.-1-a"><i class="fa fa-check"></i><b>3.2.1</b> Fig. 1 a)</a></li>
<li class="chapter" data-level="3.2.2" data-path="f1.html"><a href="f1.html#fig.-1-b"><i class="fa fa-check"></i><b>3.2.2</b> Fig. 1 b)</a></li>
<li class="chapter" data-level="3.2.3" data-path="f1.html"><a href="f1.html#fig.-1-c"><i class="fa fa-check"></i><b>3.2.3</b> Fig. 1 c)</a></li>
<li class="chapter" data-level="3.2.4" data-path="f1.html"><a href="f1.html#fig-1-complete"><i class="fa fa-check"></i><b>3.2.4</b> Fig 1 (complete)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="s01.html"><a href="s01.html"><i class="fa fa-check"></i><b>4</b> S01</a><ul>
<li class="chapter" data-level="4.1" data-path="s01.html"><a href="s01.html#preparation"><i class="fa fa-check"></i><b>4.1</b> Preparation</a></li>
<li class="chapter" data-level="4.2" data-path="s01.html"><a href="s01.html#content-of-circos_figure.r"><i class="fa fa-check"></i><b>4.2</b> Content of circos_figure.R</a></li>
......@@ -182,7 +190,7 @@ gitbook.start({
},
"download": null,
"toc": {
"collapse": "subsection"
"collapse": "subsubsection"
}
});
});
......
3_figures/docs/search_index.json
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3_figures/docs/workflow.html
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......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-05-29">
<meta name="date" content="2018-06-12">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -110,7 +110,15 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="2" data-path="workflow.html"><a href="workflow.html"><i class="fa fa-check"></i><b>2</b> Workflow</a><ul>
<li class="chapter" data-level="2.1" data-path="workflow.html"><a href="workflow.html#info"><i class="fa fa-check"></i><b>2.1</b> Info</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a></li>
<li class="chapter" data-level="3" data-path="f1.html"><a href="f1.html"><i class="fa fa-check"></i><b>3</b> F1</a><ul>
<li class="chapter" data-level="3.1" data-path="f1.html"><a href="f1.html#summary"><i class="fa fa-check"></i><b>3.1</b> Summary</a></li>
<li class="chapter" data-level="3.2" data-path="f1.html"><a href="f1.html#details-of-f1.r"><i class="fa fa-check"></i><b>3.2</b> Details of F1.R</a><ul>
<li class="chapter" data-level="3.2.1" data-path="f1.html"><a href="f1.html#fig.-1-a"><i class="fa fa-check"></i><b>3.2.1</b> Fig. 1 a)</a></li>
<li class="chapter" data-level="3.2.2" data-path="f1.html"><a href="f1.html#fig.-1-b"><i class="fa fa-check"></i><b>3.2.2</b> Fig. 1 b)</a></li>
<li class="chapter" data-level="3.2.3" data-path="f1.html"><a href="f1.html#fig.-1-c"><i class="fa fa-check"></i><b>3.2.3</b> Fig. 1 c)</a></li>
<li class="chapter" data-level="3.2.4" data-path="f1.html"><a href="f1.html#fig-1-complete"><i class="fa fa-check"></i><b>3.2.4</b> Fig 1 (complete)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="s01.html"><a href="s01.html"><i class="fa fa-check"></i><b>4</b> S01</a><ul>
<li class="chapter" data-level="4.1" data-path="s01.html"><a href="s01.html#preparation"><i class="fa fa-check"></i><b>4.1</b> Preparation</a></li>
<li class="chapter" data-level="4.2" data-path="s01.html"><a href="s01.html#content-of-circos_figure.r"><i class="fa fa-check"></i><b>4.2</b> Content of circos_figure.R</a></li>
......@@ -188,7 +196,7 @@ gitbook.start({
},
"download": null,
"toc": {
"collapse": "subsection"
"collapse": "subsubsection"
}
});
});
......
3_figures/intro.html
View file @ d7507191
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-05-29">
<meta name="date" content="2018-06-12">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -131,17 +131,17 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<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>2018-05-29</em></h4>
<h4 class="date"><em>2018-06-12</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. A visual overview of the process is given in <a href="0_workflow_network/Workflow.html">Workflow</a>.</p>
<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. A visual overview of the process is given in <a href="workflow.html">Workflow</a>.</p>
<div id="figures" class="section level2">
<h2><span class="header-section-number">1.1</span> Figures</h2>
<p>A more detailed documentation exists for all the figures of the manuscript:</p>
<p><a href="">F1</a>, <a href="">F2</a>, <a href="">F3</a>, <a href="">F4</a> &amp; <a href="">F5</a></p>
<p>as well as for all the supplementary figures:</p>
<p><a href="3_figures/doc/S01.html">S01</a>, <a href="">S02</a>, <a href="">S04</a>, <a href="">S05</a>, <a href="">S06</a>, <a href="">S07</a>, <a href="">S08</a>, <a href="">S09</a>, <a href="">S10</a>, <a href="">S11</a> &amp; <a href="">S12</a></p>
<p><a href="s01.html">S01</a>, <a href="">S02</a>, <a href="">S04</a>, <a href="">S05</a>, <a href="">S06</a>, <a href="">S07</a>, <a href="">S08</a>, <a href="">S09</a>, <a href="">S10</a>, <a href="">S11</a> &amp; <a href="">S12</a></p>
<p>The only exception to this is the supplementary figure S03. 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">
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