Commit 961c6de3 authored by Kosmas Hench's avatar Kosmas Hench

update documentation (bookdown)

parent 7613949e
......@@ -132,4 +132,33 @@ plot_fun <- function(data,loc,sel,gl){
strip.text = element_blank())
return(p)
}
plotPCA <- function(pca,dataAll,locIN,introgression_candidates,clr,fll){
data <- cbind(dataAll %>% filter(sample=='sample',loc==locIN) %>%
select(id,spec),
pca$scores);
names(data)[3:12]<- paste('PC',1:10,sep='')
exp_var <- (pca$singular.values[1:10])^2/length(pca$maf)
xlab <- paste('PC1 (',sprintf("%.1f",exp_var[1]*100),'%)')# explained varinace)')
ylab <- paste('PC2 (',sprintf("%.1f",exp_var[2]*100),'%)')# explained varinace)')
p <- ggplot(data,aes(x=PC1,y=PC2,col=spec,fill=spec))+
geom_point(size=1.1,shape=21)+
geom_text_repel(inherit.aes = F,
data=(data %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2,col=spec,label=substr(id,1,5)),angle=30,size=2.5,nudge_y = .01)+
geom_point(inherit.aes = F,data=(data %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2),col=rgb(.5,.5,.5),size=2.5,shape=1)+
scale_color_manual(values=clr,guide=F)+
scale_fill_manual(values=fll,guide=F)+
theme_mapK+
theme(legend.position='bottom',
panel.border = element_rect(color=rgb(.9,.9,.9),fill=rgb(1,1,1,0)),
axis.title.y = element_text(vjust = -7),
axis.title.x = element_text(vjust = 6),
axis.text = element_blank(),
plot.margin = unit(c(10,5,10,30),'pt'))+#coord_equal()+
scale_x_continuous(name=xlab,breaks = c(-.2,.5),position = "top")+
scale_y_continuous(name=ylab,breaks = c(-.4,.2),position = "right");
return(p)
}
\ No newline at end of file
This diff is collapsed.
......@@ -5,8 +5,6 @@ library(grImport2)
library(tidyverse)
library(RColorBrewer)
library(cowplot)
#library(grConvert)
library(ggrepel)
source('../../0_data/0_scripts/S13.functions.R')
......@@ -53,77 +51,14 @@ panPCA <- readRDS('../../2_output/08_popGen/04_pca/pan/panpca.Rds')
introgression_candidates <- c('18161','18178','18180','18267','18274','18276',
'20554','20558','20559','20633','27678')
dataHON <- cbind(dataAll %>% filter(sample=='sample',loc=='hon')%>% select(id,spec),
honPCA$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)+
geom_text_repel(inherit.aes = F,
data=(dataHON %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2,col=spec,label=substr(id,1,5)),angle=30,size=2.5,nudge_y = .01)+
geom_point(inherit.aes = F,data=(dataHON %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2),col=rgb(.5,.5,.5),size=2.5,shape=1)+
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$scores); names(dataBEL)[3:12]<- paste('PC',1:10,sep='')
exp_varBEL <- (belPCA$singular.values[1:10])^2/length(belPCA$maf)
xlabBEL <- paste('PC1 (',sprintf("%.1f",exp_varBEL[1]*100),'%)')
ylabBEL <- paste('PC2 (',sprintf("%.1f",exp_varBEL[2]*100),'%)')
p1 <- ggplot(dataBEL,aes(x=PC1,y=PC2,col=spec,fill=spec))+
geom_point(size=1.1,shape=21)+
geom_text_repel(inherit.aes = F,data=(dataBEL %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2,col=spec,label=substr(id,1,5)),angle=30,size=2.5,nudge_y = .01)+
geom_point(inherit.aes = F,data=(dataBEL %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2),col=rgb(.5,.5,.5),size=2.5,shape=1)+
scale_color_manual(values=clr,guide=F)+
scale_fill_manual(values=fll,guide=F)+
theme_mapK+
theme(legend.position='bottom',
panel.border = element_rect(color=rgb(.9,.9,.9),fill=rgb(1,1,1,0)),
axis.title.y = element_text(vjust = -7),
axis.title.x = element_text(vjust = 6),
plot.margin = unit(rep(10,4),'pt'))+
scale_x_continuous(name=xlabBEL,breaks = c(-.15,.25))+
scale_y_continuous(name=ylabBEL,breaks = c(-.3,.2))
dataPAN <- cbind(dataAll %>% filter(sample=='sample',loc=='boc',spec!='gum')%>% select(id,spec),
panPCA$scores); names(dataPAN)[3:12]<- paste('PC',1:10,sep='')
exp_varPAN <- (panPCA$singular.values[1:10])^2/length(panPCA$maf)
xlabPAN <- paste('PC1 (',sprintf("%.1f",exp_varPAN[1]*100),'%)')
ylabPAN <- paste('PC2 (',sprintf("%.1f",exp_varPAN[2]*100),'%)')
p3 <- ggplot(dataPAN,aes(x=PC1,y=PC2,col=spec,fill=spec))+
geom_point(size=1.1,shape=21)+
geom_text_repel(inherit.aes = F,
data=(dataPAN %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2,col=spec,label=substr(id,1,5)),
angle=30,size=2.5,nudge_y = .01)+
geom_point(inherit.aes = F,data=(dataPAN %>% filter(gsub('[a-z,A-Z]','',id) %in% introgression_candidates)),
aes(x=PC1,y=PC2),col=rgb(.5,.5,.5),size=2.5,shape=1)+
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'))+
scale_x_continuous(name=xlabPAN,breaks = c(-.15,.2))+
scale_y_continuous(name=ylabPAN,breaks = c(-.2,.2))
p1 <- plotPCA(pca=belPCA, dataAll=dataAll, locIN='bel',
introgression_candidates=introgression_candidates, clr=clr, fll=fll)
p2 <- plotPCA(pca=honPCA, dataAll=dataAll, locIN='hon',
introgression_candidates=introgression_candidates, clr=clr, fll=fll)
p3 <- plotPCA(pca=panPCA, dataAll=(dataAll %>% filter(spec!='gum')), locIN='boc',
introgression_candidates=introgression_candidates, clr=clr, fll=fll)
cp1 <- plot_grid(pbel+theme(legend.position = 'none'),p1,
......@@ -142,7 +77,7 @@ yd <- .3025
labX <- .675
bclr <- rgb(.9,.9,.9)
boxes = data.frame(x=rep(labX-.015,3),y=c(ys,ys+yd+ysc,ys+(yd+ysc)*2))
ggdraw()+
S13 <- ggdraw()+
geom_rect(data = boxes, aes(xmin = x, xmax = x + .03, ymin = y, ymax = y + yd),
colour = NA, fill = c(rep(bclr,3)))+
draw_label('Belize', x = labX, y = boxes$y[3]+.13,
......@@ -158,5 +93,5 @@ ggdraw()+
draw_grob(honGrob, labX-.0225, boxes$y[2]+.84*yd, .045, .045)+
draw_grob(panGrob, labX-.0225, boxes$y[1]+.84*yd, .045, .045)
ggsave('../output/S13.pdf',width = 183,height = 235,units = 'mm',device = cairo_pdf)
ggsave(plot = S13,filename = '../output/S13.pdf',width = 183,height = 235,units = 'mm',device = cairo_pdf)
......@@ -25,7 +25,7 @@ rm Rplots.pdf
## Details of `S12.R`
In the following, the individual steps of the R script are documented.
Is an executable R script that depends on a variety of image manipulation and data managing and genomic data packages.
Is an executable R script that depends on a variety of image manipulation, data managing and genomic data packages.
It Furthermore depends on the R scripts `S07.functions.R` (located under `$WORK/0_data/0_scripts`).
......@@ -82,7 +82,7 @@ leg <- get_legend(plts[[1]]+theme(legend.text = element_text(size = 5),
legend.key.size = unit(7,'pt')))
```
Finally, the complete Figure 5 is put together.
Finally, the complete Supplementary Figure 12 is put together.
```{r finalPlot,results='hide', message=FALSE, warning=FALSE}
S12 <- ggdraw(pGr8)+
......
This diff is collapsed.
......@@ -66,7 +66,7 @@ plotList <- data.frame(x=c(0,.2,.66,.84,1,1.9,2.1,1.25,1.5,2.5,
status=c(rep(steps[5],15),steps[6],steps[5]))
```
<center>
```{r plot,fig.width=24, fig.height=17,echo=FALSE}
```{r plot,fig.width=26, fig.height=18,echo=FALSE}
# Assembly plot ------------------
p1 <- ggplot()+
coord_fixed(coord_ratio)+
......@@ -90,8 +90,12 @@ p1 <- ggplot()+
scale_linetype('Script\ntype')+
guides(colour = guide_legend(override.aes = list(size = 5,shape=21,fill=clr,color='black')),
shape= guide_legend(override.aes = list(size = 5,shape=c(21,22),fill='lightgray')))+
facet_grid(status~.,switch = 'y')+theme_void()+
facet_grid(status~.,switch = 'y')+#theme_void()+
theme(legend.position = 'bottom',
axis.text = element_blank(),
axis.title = element_blank(),
panel.grid = element_blank(),
strip.text = element_text(color='black'),
strip.background = element_rect(fill='lightgray'),
panel.background = element_rect(fill=rgb(.98,.98,.98)),
plot.margin = unit(rep(5,4),'pt'))
......@@ -120,9 +124,13 @@ p2 <- ggplot()+
scale_linetype('Script\ntype')+
guides(colour = guide_legend(override.aes = list(size = 5,shape=21,fill=clr2,color='black')),
shape= guide_legend(override.aes = list(size = 5,shape=c(21,22),fill='lightgray')))+
facet_grid(status~.)+theme_void()+
facet_grid(status~.)+#theme_void()+
theme(legend.position = 'bottom',
axis.text = element_blank(),
axis.title = element_blank(),
panel.grid = element_blank(),
strip.background = element_rect(fill='lightgray'),
strip.text = element_text(color='black'),
panel.background = element_rect(fill=rgb(.98,.98,.98)),
plot.margin = unit(rep(5,4),'pt'))
......
......@@ -2,7 +2,7 @@ book_filename: "Script repository Hench et al. 2018"
chapter_name: ""
repo: https://github.com/k-hench/bookdown
output_dir: docs
rmd_files: ["index.Rmd","Workflow.Rmd","F1.Rmd","F2.Rmd","F3.Rmd","F4.Rmd","F5.Rmd","S01.Rmd","S02.Rmd","S04.Rmd","S05.Rmd","S06.Rmd","S07.Rmd","S08.Rmd","S09.Rmd","S10.Rmd","S11.Rmd","S12.Rmd"]
rmd_files: ["index.Rmd","Workflow.Rmd","F1.Rmd","F2.Rmd","F3.Rmd","F4.Rmd","F5.Rmd","S01.Rmd","S02.Rmd","S04.Rmd","S05.Rmd","S06.Rmd","S07.Rmd","S08.Rmd","S09.Rmd","S10.Rmd","S11.Rmd","S12.Rmd","S13.Rmd"]
clean: [packages.bib, bookdown.bbl]
new_session: yes
delete_merged_file: True
......@@ -189,7 +189,8 @@ p1 <- ggplot()+
# genome wide Fst
geom_rect(data=gwFST,aes(xmin=570*10^6,xmax=573*10^6,ymin=0,ymax=gwFST*secScale))+
# layout of y axis and secondary y axis
scale_y_continuous(name = yl,breaks=0:4*0.2,labels = c(0,'',0.4,'',0.8),
scale_y_continuous(name = yl,limits=c(-.03,.83),
breaks=0:4*0.2,labels = c(0,'',0.4,'',0.8),
sec.axis = sec_axis(~./secScale,labels = c(0,'',.02,'',.04)))+
# layout of x axis
scale_x_continuous(expand = c(0,0),limits = c(0,577*10^6),
......@@ -220,6 +221,11 @@ p1 <- ggplot()+
```
<center>
```
## Warning: Removed 421 rows containing missing values (geom_point).
```
<img src="F2_files/figure-html/basePlotSHOW-1.png" width="672" />
</center>
......
......@@ -213,7 +213,7 @@ The first data track contains the gene models from the annotation file as well a
scale_color_manual(values=annoclr,breaks=c("x","y","z"),guide=F)+
scale_fill_manual(values=annoclr,guide=F)+
# axes labels and settings
scale_x_continuous(name=paste(searchLG,' (',muskID,', kb)'),expand=c(0,0),position = 'top')+
scale_x_continuous(name=paste0(searchLG,' (',muskID,', kb)'),expand=c(0,0),position = 'top')+
scale_y_continuous(breaks = seq(0,.75,length.out = 4))+
# plot format adjustments
theme(rect = element_blank(),
......
......@@ -436,7 +436,7 @@ Finally, the function returns the current base plot stored in `p1`.
Within this script, the ILD data of the genome wide subsets of SNPs is loaded and and plotted.
First we read in the global data set, then we loop over the individual population subsets and append the data to the global data set.
Since we're only interested in the distribution of r^2, we select only this column and create extra columns for the run ID, and the run type (global, subset by species, subset by location)
Since we're only interested in the distribution of r[2], we select only this column and create extra columns for the run ID, and the run type (global, subset by species, subset by location)
```r
......@@ -501,7 +501,7 @@ pBOX <- ggplot(BW,aes(x=run,y=R.2))+
# settting the axis and color labels
scale_x_discrete(labels = expression(Global,Panama,Belize,Honduas,
italic("H. nigricans"),italic("H. puella"),italic("H. unicolor")))+
scale_y_continuous('genome wide ')+
scale_y_continuous('genome wide ILD (r²)')+
scale_fill_manual('',values = clr[c(6,1)],labels=c('mean','median'))+
# formatting the legend
guides(shape = guide_legend(ncol = 1))+
......@@ -577,9 +577,9 @@ boxGenes <- ggplot(dataBoxGenes,aes(x=xS))+
# adding mean and median values
geom_point(data=BoxGenes_summary,aes(y=val,fill=type),shape=23,size=1)+
# set a fixed aspect ratio
coord_fixed(ylim=c(0,.06),ratio = 133)+
coord_fixed(ylim=c(0,.031),ratio = 133)+
# settting the axis and color labels
scale_y_continuous('peak area r²')+
scale_y_continuous('ILD around \ncandidate genes (r²)')+
scale_x_discrete(labels = expression(Global,Panama,Belize,Honduas,
italic("H. nigricans"),italic("H. puella"),italic("H. unicolor")))+
scale_fill_manual('',values = clr[c(6,1)],labels=c('mean','median'))+
......
......@@ -22,7 +22,7 @@ rm Rplots.pdf
## Details of `S12.R`
In the following, the individual steps of the R script are documented.
Is an executable R script that depends on a variety of image manipulation and data managing and genomic data packages.
Is an executable R script that depends on a variety of image manipulation, data managing and genomic data packages.
It Furthermore depends on the R scripts `S07.functions.R` (located under `$WORK/0_data/0_scripts`).
......@@ -83,7 +83,7 @@ leg <- get_legend(plts[[1]]+theme(legend.text = element_text(size = 5),
legend.key.size = unit(7,'pt')))
```
Finally, the complete Figure 5 is put together.
Finally, the complete Supplementary Figure 12 is put together.
```r
......
This diff is collapsed.
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......@@ -364,7 +369,8 @@ secScale &lt;-<span class="st"> </span><span class="dv">20</span></code></pre></
<span class="st"> </span><span class="co"># genome wide Fst</span>
<span class="st"> </span><span class="kw">geom_rect</span>(<span class="dt">data=</span>gwFST,<span class="kw">aes</span>(<span class="dt">xmin=</span><span class="dv">570</span><span class="op">*</span><span class="dv">10</span><span class="op">^</span><span class="dv">6</span>,<span class="dt">xmax=</span><span class="dv">573</span><span class="op">*</span><span class="dv">10</span><span class="op">^</span><span class="dv">6</span>,<span class="dt">ymin=</span><span class="dv">0</span>,<span class="dt">ymax=</span>gwFST<span class="op">*</span>secScale))<span class="op">+</span>
<span class="st"> </span><span class="co"># layout of y axis and secondary y axis</span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">name =</span> yl,<span class="dt">breaks=</span><span class="dv">0</span><span class="op">:</span><span class="dv">4</span><span class="op">*</span><span class="fl">0.2</span>,<span class="dt">labels =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="st">&#39;&#39;</span>,<span class="fl">0.4</span>,<span class="st">&#39;&#39;</span>,<span class="fl">0.8</span>),
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">name =</span> yl,<span class="dt">limits=</span><span class="kw">c</span>(<span class="op">-</span>.<span class="dv">03</span>,.<span class="dv">83</span>),
<span class="dt">breaks=</span><span class="dv">0</span><span class="op">:</span><span class="dv">4</span><span class="op">*</span><span class="fl">0.2</span>,<span class="dt">labels =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="st">&#39;&#39;</span>,<span class="fl">0.4</span>,<span class="st">&#39;&#39;</span>,<span class="fl">0.8</span>),
<span class="dt">sec.axis =</span> <span class="kw">sec_axis</span>(<span class="op">~</span>.<span class="op">/</span>secScale,<span class="dt">labels =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="st">&#39;&#39;</span>,.<span class="dv">02</span>,<span class="st">&#39;&#39;</span>,.<span class="dv">04</span>)))<span class="op">+</span>
<span class="st"> </span><span class="co"># layout of x axis</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">0</span>),<span class="dt">limits =</span> <span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">577</span><span class="op">*</span><span class="dv">10</span><span class="op">^</span><span class="dv">6</span>),
......@@ -393,6 +399,7 @@ secScale &lt;-<span class="st"> </span><span class="dv">20</span></code></pre></
<span class="st"> </span><span class="co"># separate the plots of the individual species pairs</span>
<span class="st"> </span><span class="kw">facet_grid</span>(RUN<span class="op">~</span>.)</code></pre></div>
<center>
<pre><code>## Warning: Removed 421 rows containing missing values (geom_point).</code></pre>
<img src="F2_files/figure-html/basePlotSHOW-1.png" width="672" />
</center>
<p>External images are loaded for annotation.</p>
......
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......@@ -368,7 +373,7 @@ p4 &lt;-<span class="st"> </span><span class="kw">create_K_plot</span>(<span cla
<span class="st"> </span><span class="kw">scale_color_manual</span>(<span class="dt">values=</span>annoclr,<span class="dt">breaks=</span><span class="kw">c</span>(<span class="st">&quot;x&quot;</span>,<span class="st">&quot;y&quot;</span>,<span class="st">&quot;z&quot;</span>),<span class="dt">guide=</span>F)<span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">scale_fill_manual</span>(<span class="dt">values=</span>annoclr,<span class="dt">guide=</span>F)<span class="op">+</span>
<span class="st"> </span><span class="co"># axes labels and settings</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">name=</span><span class="kw">paste</span>(searchLG,<span class="st">&#39; (&#39;</span>,muskID,<span class="st">&#39;, kb)&#39;</span>),<span class="dt">expand=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">0</span>),<span class="dt">position =</span> <span class="st">&#39;top&#39;</span>)<span class="op">+</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">name=</span><span class="kw">paste0</span>(searchLG,<span class="st">&#39; (&#39;</span>,muskID,<span class="st">&#39;, kb)&#39;</span>),<span class="dt">expand=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">0</span>),<span class="dt">position =</span> <span class="st">&#39;top&#39;</span>)<span class="op">+</span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">breaks =</span> <span class="kw">seq</span>(<span class="dv">0</span>,.<span class="dv">75</span>,<span class="dt">length.out =</span> <span class="dv">4</span>))<span class="op">+</span>
<span class="st"> </span><span class="co"># plot format adjustments</span>
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">rect =</span> <span class="kw">element_blank</span>(),
......
This diff is collapsed.
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......@@ -224,7 +229,7 @@ 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>2018-06-18</em></h4>
<h4 class="date"><em>2018-07-10</em></h4>
</div>
<div id="intro" class="section level1">
<h1><span class="header-section-number">1</span> Intro</h1>
......@@ -235,7 +240,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<p>A more detailed documentation exists for all the figures of the manuscript:</p>
<p><a href="figure-1.html">F1</a>, <a href="figure-2.html">F2</a>, <a href="figure-3.html">F3</a>, <a href="figure-4.html">F4</a> &amp; <a href="figure-5.html">F5</a></p>
<p>as well as for all the supplementary figures:</p>
<p><a href="supplementary-figure-01.html">S01</a>, <a href="supplementary-figure-02.html">S02</a>, <a href="supplementary-figure-04.html">S04</a>, <a href="supplementary-figure-05.html">S05</a>, <a href="supplementary-figure-06.html">S06</a>, <a href="supplementary-figure-07.html">S07</a>, <a href="supplementary-figure-08.html">S08</a>, <a href="supplementary-figure-09.html">S09</a>, <a href="supplementary-figure-10.html">S10</a>, <a href="supplementary-figure-11.html">S11</a> &amp; <a href="supplementary-figure-12.html">S12</a></p>
<p><a href="supplementary-figure-01.html">S01</a>, <a href="supplementary-figure-02.html">S02</a>, <a href="supplementary-figure-04.html">S04</a>, <a href="supplementary-figure-05.html">S05</a>, <a href="supplementary-figure-06.html">S06</a>, <a href="supplementary-figure-07.html">S07</a>, <a href="supplementary-figure-08.html">S08</a>, <a href="supplementary-figure-09.html">S09</a>, <a href="supplementary-figure-10.html">S10</a>, <a href="supplementary-figure-11.html">S11</a>, <a href="supplementary-figure-12.html">S12</a> &amp; <a href="supplementary-figure-13.html">S13</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">
......
......@@ -2,7 +2,7 @@
title: "Script repository"
subtitle: "Supplement to Hench *et al.* 2018"
author: "Kosmas Hench"
date: "2018-06-18"
date: "2018-07-10"
documentclass: book
bibliography: [book.bib]
biblio-style: apalike
......@@ -26,7 +26,7 @@ A more detailed documentation exists for all the figures of the manuscript:
as well as for all the supplementary figures:
[S01](supplementary-figure-01.html), [S02](supplementary-figure-02.html), [S04](supplementary-figure-04.html), [S05](supplementary-figure-05.html), [S06](supplementary-figure-06.html), [S07](supplementary-figure-07.html), [S08](supplementary-figure-08.html), [S09](supplementary-figure-09.html), [S10](supplementary-figure-10.html), [S11](supplementary-figure-11.html) & [S12](supplementary-figure-12.html)
[S01](supplementary-figure-01.html), [S02](supplementary-figure-02.html), [S04](supplementary-figure-04.html), [S05](supplementary-figure-05.html), [S06](supplementary-figure-06.html), [S07](supplementary-figure-07.html), [S08](supplementary-figure-08.html), [S09](supplementary-figure-09.html), [S10](supplementary-figure-10.html), [S11](supplementary-figure-11.html), [S12](supplementary-figure-12.html) & [S13](supplementary-figure-13.html)
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 **Allmaps** software. Afterwards, **Inkscape** was used to adjust the coloration and labels of the linkage maps.
......
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<li class="chapter" data-level="18.1" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#summary-14"><i class="fa fa-check"></i><b>18.1</b> Summary</a></li>
<li class="chapter" data-level="18.2" data-path="supplementary-figure-12.html"><a href="supplementary-figure-12.html#details-of-s12.r"><i class="fa fa-check"></i><b>18.2</b> Details of <code>S12.R</code></a></li>
</ul></li>
<li class="chapter" data-level="19" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html"><i class="fa fa-check"></i><b>19</b> Supplementary Figure 13</a><ul>
<li class="chapter" data-level="19.1" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#summary-15"><i class="fa fa-check"></i><b>19.1</b> Summary</a></li>
<li class="chapter" data-level="19.2" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.r"><i class="fa fa-check"></i><b>19.2</b> Details of <code>S13.R</code></a></li>
<li class="chapter" data-level="19.3" data-path="supplementary-figure-13.html"><a href="supplementary-figure-13.html#details-of-s13.functions.r"><i class="fa fa-check"></i><b>19.3</b> Details of <code>S13.functions.R</code></a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
<li> <image src="GL.svg" alt="Smiley face" style="width:100%; height:100px;"> </li>
......
......@@ -25,7 +25,7 @@
<meta name="author" content="Kosmas Hench">
<meta name="date" content="2018-06-18">
<meta name="date" content="2018-07-10">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
......@@ -199,6 +199,11 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf