update figure documentation

0_data/0_scripts/F4.functions.R

+se <-  function(x){
+  x2 <- x[!is.na(x)]
+  return(sd(x2)/sqrt(length(x2)))}
+
+trplot <- function(sel){
+  files <- c("global","boc","bel","hon","pue","nig","uni","nig-pue","nig-uni","pue-uni")
+  data <- read.csv(paste('../../2_output/08_popGen/07_LD/',files[sel],'-10000-bins.txt',sep=''),sep='\t')
+  message(files[sel])
+  
+  s1=17620000;s2=19910000;s3=21960000;s4=22320000;
+  e2=20660000;e3=22460000;
+  stp=20000;
+  l1=500000;l2=750000;l3=500000;l4=500000
+  scling <- c(-s1,-s2+(l1+stp),-s3+(l1+l2+2*stp),-s4+(l1+l2+l3+(stp*3)))
+  
+  dt <- data %>% mutate(miX = floor(Mx/10000),miY=floor(My/10000))
+  genes <- data.frame(start=c(17871610,20186151,22225149,22553187,22556763,22561894,22573388),
+                      end=c(17873915,20347811,22228342,22555052,22559742,22566321,22575503),
+                      sclr=c(1,2,3,4,4,4,4),
+                      LG=c("LG09","LG12-1","LG12-2","LG17","LG17","LG17","LG17"),
+                      name=c("sox10",'casz1',"hoxc13a","sws2a\u03B1","sws2a\u03B2","sws2b","lws"))
+  genes <- genes %>% mutate(Nx1 = (start+scling[sclr])/10000,Nx2 = (end+scling[sclr])/10000,
+                            labPOS = (Nx1+Nx2)/2) 
+  genes$labPOS[genes$name %in% c("sws2a\u03B1","sws2a\u03B2","sws2b","lws")] <- genes$labPOS[genes$name %in% c("sws2a\u03B1","sws2a\u03B2","sws2b","lws")]+c(-16,-1,12,20)
+  
+  GZrS <- 40000;GZrS2 <- 20000; #gene zoom offset
+  BS <- c(-5,5,-4,3,-8,8,-20,-10,-6,5,7,16,17,22)*10000 # Backshifter for gene zoom
+  GZdf <- data.frame(x=c(genes$start[1],genes$end[1],genes$end[1]+GZrS+BS[1],genes$start[1]+GZrS+BS[2],genes$start[1],
+                         genes$start[2],genes$end[2],genes$end[2]+GZrS+BS[3],genes$start[2]+GZrS+BS[4],genes$start[2],
+                         genes$start[3],genes$end[3],genes$end[3]+GZrS+BS[5],genes$start[3]+GZrS+BS[6],genes$start[3],
+                         genes$start[4],genes$end[4],genes$end[4]+GZrS+BS[7],genes$start[4]+GZrS+BS[8],genes$start[4],
+                         genes$start[5],genes$end[5],genes$end[5]+GZrS+BS[9],genes$start[5]+GZrS+BS[10],genes$start[5],
+                         genes$start[6],genes$end[6],genes$end[6]+GZrS+BS[11],genes$start[6]+GZrS+BS[12],genes$start[6],
+                         genes$start[7],genes$end[7],genes$end[7]+GZrS+BS[13],genes$start[7]+GZrS+BS[14],genes$start[7])+GZrS2,
+                     y=c(genes$start[1],genes$end[1],genes$end[1]-GZrS+BS[1],genes$start[1]-GZrS+BS[2],genes$start[1],
+                         genes$start[2],genes$end[2],genes$end[2]-GZrS+BS[3],genes$start[2]-GZrS+BS[4],genes$start[2],
+                         genes$start[3],genes$end[3],genes$end[3]-GZrS+BS[5],genes$start[3]-GZrS+BS[6],genes$start[3],
+                         genes$start[4],genes$end[4],genes$end[4]-GZrS+BS[7],genes$start[4]-GZrS+BS[8],genes$start[4],
+                         genes$start[5],genes$end[5],genes$end[5]-GZrS+BS[9],genes$start[5]-GZrS+BS[10],genes$start[5],
+                         genes$start[6],genes$end[6],genes$end[6]-GZrS+BS[11],genes$start[6]-GZrS+BS[12],genes$start[6],
+                         genes$start[7],genes$end[7],genes$end[7]-GZrS+BS[13],genes$start[7]-GZrS+BS[14],genes$start[7])-GZrS2,
+                     grp=rep(letters[1:7],each=5)) %>% 
+    mutate(sclr=rep(c(1,2,3,4,4,4,4),each=5),
+           Nx1 = (x+scling[sclr])/10000,
+           Nx2 = (y+scling[sclr])/10000)
+  
+  clr = c(viridis::inferno(5)[c(1,1:5)])
+  Gcol <- '#3bb33b'
+  Zcol = rgb(.94,.94,.94)
+  DG <- rgb(.4,.4,.4)
+  LGoffset <- 15
+  GLABoffset <- 8
+  if(sel %in% c(1,8)){
+    rS <- 100000 # width of grey annotation band
+    zmRange <- data.frame(x=c(s1,s1+l1,s1+l1+rS,s1+rS,s1,
+                              s2,s2+l2,s2+l2+rS,s2+rS,s2,
+                              s3,s3+l3,s3+l3+rS,s3+rS,s3,
+                              s4,s4+l4,s4+l4+rS,s4+rS,s4),
+                          y=c(s1,s1+l1,s1+l1-rS,s1-rS,s1,
+                              s2,s2+l2,s2+l2-rS,s2-rS,s2,
+                              s3,s3+l3,s3+l3-rS,s3-rS,s3,
+                              s4,s4+l4,s4+l4-rS,s4-rS,s4),
+                          grp=rep(letters[1:4],each=5)) %>% 
+      mutate(sclr=rep(1:4,each=5),
+             Nx1 = (x+scling[sclr])/10000-1,
+             Nx2 = (y+scling[sclr])/10000)
+    rS2 <- .75*rS
+    zmRange2 <- data.frame(x=c(s1,s1+l1,s1+l1+rS2,s1+rS2,s1,
+                               s2,s2+l2,s2+l2+rS2,s2+rS2,s2,
+                               s3,s3+l3,s3+l3+rS2,s3+rS2,s3,
+                               s4,s4+l4,s4+l4+rS2,s4+rS2,s4),
+                           y=c(s1,s1+l1,s1+l1-rS2,s1-rS2,s1,
+                               s2,s2+l2,s2+l2-rS2,s2-rS2,s2,
+                               s3,s3+l3,s3+l3-rS2,s3-rS2,s3,
+                               s4,s4+l4,s4+l4-rS2,s4-rS2,s4),
+                           grp=rep(letters[1:4],each=5)) %>% 
+      mutate(sclr=rep(1:4,each=5),
+             Nx1 = (x+scling[sclr])/10000-1,
+             Nx2 = (y+scling[sclr])/10000)
+    
+    rS3 <- .07*rS
+    zmRange3 <- data.frame(x=c(s1,s1+l1,s1+l1+rS3,s1+rS3,s1,
+                               s2,s2+l2,s2+l2+rS3,s2+rS3,s2,
+                               s3,s3+l3,s3+l3+rS3,s3+rS3,s3,
+                               s4,s4+l4,s4+l4+rS3,s4+rS3,s4),
+                           y=c(s1,s1+l1,s1+l1-rS3,s1-rS3,s1,
+                               s2,s2+l2,s2+l2-rS3,s2-rS3,s2,
+                               s3,s3+l3,s3+l3-rS3,s3-rS3,s3,
+                               s4,s4+l4,s4+l4-rS3,s4-rS3,s4),
+                           grp=rep(letters[1:4],each=5)) %>% 
+      mutate(sclr=rep(1:4,each=5),
+             Nx1 = (x+scling[sclr])/10000-1,
+             Nx2 = (y+scling[sclr])/10000)
+    
+    zmLab <- data.frame(x=c(s1+.5*l1,s2+.5*l2,s3+.5*l3,s4+.5*l4),
+                        label=c('LG09 (A)','LG12 (B)','LG12 (C)','LG17 (D)')) %>%  
+      mutate(sclr=1:4, Nx= (x+scling[sclr])/10000)
+    
+    zmEND <- data.frame(x=c(s1,s1+l1,
+                            s2,s2+l2,
+                            s3,s3+l3,
+                            s4,s4+l4)) %>% 
+      mutate(sclr=rep(1:4,each=2),
+             Nx = ((x+scling[sclr])/10000)+rep(c(2.5,-4),4),
+             label=round((x/1000000),2))
+    
+    textSCALE1 <- c(1.8,rep(NA,6),.7)
+    textSCALE2 <- c(2,rep(NA,6),1)
+    textSCALE3 <- c(3.5,rep(NA,6),1.75)
+    
+    p1 <- ggplot(dt %>% filter(!is.na(Mval)),aes(fill=Mval))+
+        coord_equal()+
+        geom_polygon(inherit.aes = F,data=zmRange,
+                     aes(x=Nx1+1,y=Nx2-1,group=grp),fill='lightgray')+
+        geom_polygon(inherit.aes = F,data=zmRange2,
+                     aes(x=Nx1+11,y=Nx2-11,group=grp),fill=DG)+
+        geom_polygon(inherit.aes = F,data=zmRange3,
+                     aes(x=Nx1+1.1,y=Nx2-1.1,group=grp),fill=DG)+
+        geom_polygon(inherit.aes = F,data=GZdf,
+                     aes(x=Nx1,y=Nx2,group=grp),fill=Zcol)+
+        geom_segment(inherit.aes = F,data=genes,
+                     aes(x=Nx1+1,y=Nx1-1,xend=Nx2+1,yend=Nx2-1),
+                     col=Gcol,size=1.5)+
+        geom_tile(aes(x=miX,y=miY))+
+        geom_text(inherit.aes = F,data=zmEND,
+                  aes(x=Nx+LGoffset,y=Nx-LGoffset,label=paste(label,'\n(Mb)')),
+                  angle=45,size=textSCALE1[sel])+
+        geom_text(inherit.aes = F,data=genes,
+                  aes(x=labPOS+GLABoffset,y=labPOS-GLABoffset,label=name),
+                  angle=-45,fontface='italic',size=textSCALE2[sel])+
+        geom_text(inherit.aes = F,data=zmLab,
+                  aes(x=Nx+LGoffset-.8,y=Nx-LGoffset+.8,label=label),
+                  angle=-45,fontface='bold',size=textSCALE3[sel],col='white')+
+        scale_x_continuous(expand=c(0,0))+
+        scale_y_continuous(expand=c(0,0),
+                           trans = 'reverse')+
+        scale_fill_gradientn(name=expression(bar(r^2)),colours=clr,
+                             values=rescale(c(1,.08,.03,.015,.01,0)),
+                             limits=c(0,1),guide = 'legend',breaks=c(0,.005,.01,.02,.03,.1,1))+
+        theme_void()+
+        theme(legend.position = c(.7,.75),legend.direction = 'vertical')
+  } else {
+    p1 <- ggplot(dt %>% filter(!is.na(Mval)),aes(fill=Mval))+
+      coord_equal()+
+      geom_segment(inherit.aes = F,data=genes,
+                   aes(x=Nx1+1.5,y=Nx1-1.5,xend=Nx2+1.5,yend=Nx2-1.5),
+                   col=Gcol,size=1)+
+      geom_tile(aes(x=miX,y=miY))+
+      scale_x_continuous(expand=c(0,0))+
+      scale_y_continuous(expand=c(0,0),
+                         trans = 'reverse')+
+      scale_fill_gradientn(name=expression(bar(r^2)),colours=clr,
+                           values=rescale(c(1,.08,.03,.015,.01,0)),
+                           limits=c(0,1),guide = 'legend',breaks=c(0,.005,.01,.02,.03,.1,1))+
+      theme_void()+
+      theme(legend.position = c(.7,.75),legend.direction = 'vertical')
+    
+  }
+  return(p1)
+}
\ No newline at end of file

0_data/0_scripts/F4.genomeWide_box.R

+BW <- read.csv('../../2_output/08_popGen/07_LD/subsets/glob_between.interchrom.hap.ld',sep='\t') %>% 
+  select(R.2) %>% 
+  mutate(type='Global',run='Global')
+
+for(j in 1:6){
+  flS <- c("boc","bel","hon","pue","nig","uni")
+  flL <- c("Panana","Belize","Honduras","H. puella","H. nigricans","H. unicolor")
+  flT <- c(rep('Geo',3),rep('Spec',3))
+  k <- flS[j]
+  q <- flL[j]
+  u <- flT[j]
+  print(j)
+  BW <- BW %>%
+    rbind(.,(read.csv(paste('../../2_output/08_popGen/07_LD/subsets/glob_between.',k,'.interchrom.hap.ld',sep=''),
+                      sep='\t') %>% 
+               select(R.2) %>% 
+               mutate(type=u,run=q)))
+}
+
+BW$run <- factor(BW$run,levels=c('Global',"Panana","Belize","Honduras",
+                                 "H. nigricans","H. puella","H. unicolor")) 
+
+dt2 <- BW %>% 
+  group_by(run) %>% 
+  summarise(meanR2=mean(R.2,na.rm = T),medR2=median(R.2,na.rm = T)) %>%
+  gather(key = 'type',value = 'val',2:3)
+
+BC <-rgb(.7,.7,.7)
+clr <-colorRampPalette(colors = c('white',BC,'black'))(8)
+
+pBOX <- ggplot(BW,aes(x=run,y=R.2))+
+  geom_boxplot(fill=BC,width=.7,outlier.size = .1)+
+  coord_fixed(ylim=c(0,.031),ratio = 250)+
+  geom_point(inherit.aes = F, data=dt2,aes(x=run,y=val,fill=type),shape=23,size=1)+
+  scale_x_discrete(labels = expression(Global,Panama,Belize,Honduas,
+                                       italic("H. nigricans"),italic("H. puella"),italic("H. unicolor")))+
+  scale_y_continuous('genome wide r²')+
+  scale_fill_manual('',values = clr[c(6,1)],labels=c('mean','median'))+
+  guides(shape = guide_legend(ncol = 1))+
+  theme(legend.position = c(-.4,1.27),
+        text = element_text(size=10),
+        axis.title.x = element_blank(),
+        axis.text.y = element_text(size=7),
+        axis.text.x = element_text(size=7,angle=45,hjust = 1),
+        panel.background = element_blank(),
+        plot.background = element_blank())
\ No newline at end of file

0_data/0_scripts/F4.peakArea_box.R

+dataBoxGenes <- data.frame(R.2=c(),run=c(),stringsAsFactors = F)
+
+for (file in dir("../../2_output/08_popGen/07_LD/",pattern = "interchrom.hap.ld.gz")) {
+  nm <- str_remove_all(file, "spotlight.") %>% str_remove_all(.,".interchrom.hap.ld.gz")
+  if(nm %in% c("global","uni","pue","nig","hon","bel","boc")){
+    dataBoxGenes <- read.csv(gzfile(paste('../../2_output/08_popGen/07_LD/',file,sep='')),sep='\t') %>% 
+      mutate(run = nm) %>% 
+      select(R.2,run) %>%
+      rbind(dataBoxGenes,.)
+  }
+}
+
+dataBoxGenes$xS <- factor(dataBoxGenes$run,
+                          levels = c("global","boc","bel","hon","nig","pue","uni"))
+
+BoxGenes_summary <- dataBoxGenes %>% 
+  group_by(xS) %>% 
+  summarise(run = run[1],
+            meanR2 = mean(R.2,na.rm = T),
+            medR2 = median(R.2,na.rm = T),
+            sdR2 = sd(R.2,na.rm=T),
+            seR2 = se(R.2),
+            nanr = sum(is.na(R.2)),
+            minR2 = min(R.2,na.rm = T),
+            maxR2 = max(R.2,na.rm = T),
+            lengthR2 = length(R.2)) %>%
+  select(xS,meanR2,medR2) %>%
+  gather(key = 'type',value = 'val',2:3)
+
+boxGenes <- ggplot(dataBoxGenes,aes(x=xS))+
+  geom_boxplot(aes(y=R.2),fill=BC,width=.7,outlier.size = .1) +
+  geom_point(data=BoxGenes_summary,aes(y=val,fill=type),shape=23,size=1)+
+  coord_fixed(ylim=c(0,.06),ratio = 133)+
+  scale_y_continuous('peak area 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'))+
+  guides(shape = guide_legend(ncol = 1))+
+  theme(legend.position = c(.35,1.27),
+        text = element_text(size=10),
+        axis.title.x = element_blank(),
+        axis.text.y = element_text(size=7),
+        axis.text.x = element_text(size=7,angle=45,hjust = 1),
+        panel.background = element_blank(),
+        plot.background = element_blank())
\ No newline at end of file

3_figures/F3.Rmd

 ---
 output: html_document
 editor_options: 
-chunk_output_type: console
+  chunk_output_type: console
 ---
 # Figure 3
   

3_figures/F5.Rmd

 ---
 output: html_document
 editor_options: 
-chunk_output_type: console
+  chunk_output_type: console
 ---
 # Figure 5
   
@@ -23,3 +23,87 @@ Rscript --vanilla F5.R
 rm Rplots.pdf
 
 ```
+## Details of F5.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.
+
+It Furthermore depends on the R scripts `F4.functions.R` (located under `$WORK/0_data/0_scripts`).
+
+This script is a modification of sript F4.R. It uses the same funtions and just differs in the data sets and settings 
+
+```{r head,results='hide',message=FALSE}
+library(tidyverse)
+library(scales)
+library(cowplot)
+library(grid)
+library(gridSVG)
+library(grImport2)
+source('../../0_data/0_scripts/F4.functions.R')
+```
+
+The script `F4.functions.R`contains a function (`trplot()`) that plots a single LD triangle as seen in Figure 5.
+The Details of this script are explained below.
+The output depends on the data set plotted (sub figure a contains additional annotations).
+
+We create an empty list that is then filled with the subplots using the `trplot()` function.
+
+```{r basePlot,results='hide',message=FALSE}
+plts <- list()
+
+for(k in 1:3){
+plts[[k]] <- trplot((8:10)[k])
+}
+```
+
+The basic plots are transformed into `grid obgects`.
+These are afterwards rotated by 45 degrees.
+
+```{r grobPlot,results='hide', message=FALSE, warning=FALSE}
+tN <- theme(legend.position = 'none')
+
+pG8 <- ggplotGrob(plts[[1]]+tN)
+pG9 <- ggplotGrob(plts[[2]]+tN)
+pG10 <- ggplotGrob(plts[[3]]+tN)
+pGr8 <- editGrob(pG8, vp=viewport(x=0.5, y=0.97, angle=45,width = .76), name="pG8")
+pGr9 <- editGrob(pG9, vp=viewport(x=0.5, y=0.62, angle=45,width = .7), name="pG9")
+pGr10 <- editGrob(pG10, vp=viewport(x=0.5, y=0.3, angle=45,width = .7), name="pG10")
+```
+
+Then, external annotations loaded and the legend ins extracted from the first plot.
+
+```{r annotatePlot,results='hide', message=FALSE, warning=FALSE}
+npGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/pue-nig-cairo.svg"))))
+puGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/uni-pue-cairo.svg"))))
+nuGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/nig-uni-cairo.svg"))))
+
+leg <- get_legend(plts[[1]]+theme(legend.text = element_text(size = 5),
+                                   legend.title =  element_text(size = 5),
+                                   legend.key.size = unit(7,'pt')))
+```
+
+Finally, the complete Figure 5 is put together.
+
+```{r finalPlot,results='hide', message=FALSE, warning=FALSE}
+F5 <- ggdraw(pGr8)+
+  draw_grob(pGr9,0,0,1,1)+
+  draw_grob(leg,-.65,.04,1,1)+
+  draw_grob(pGr10,0,0,1,1)+
+  draw_grob(npGrob, 0.7, 0.7, 0.28, 0.1)+
+  draw_grob(nuGrob, 0.7, 0.37, 0.28, 0.1)+
+  draw_grob(puGrob, 0.7, .04, 0.28, 0.1)
+```
+
+The final figure is then exported using `ggsave()`.
+
+```{r, eval=FALSE}
+#ggsave(plot = F5,filename = '../output/F5.pdf',width =  91.5,height = 145,units = 'mm',device = cairo_pdf)
+ggsave(plot = F5,filename = '../output/F5.png',width = 91.5,height = 145,units = 'mm',dpi = 150)
+```
+
+<center>
+```{r f5SHOW, echo=FALSE, fig.height=145*0.03937008, fig.width=91.5*0.03937008, warning=FALSE}
+F5
+```
+</center>
+---
\ No newline at end of file

3_figures/F_scripts/F5.R

+#!/usr/bin/env Rscript
+library(tidyverse)
+library(scales)
+library(cowplot)
+library(grid)
+library(gridSVG)
+library(grImport2)
+source('../../0_data/0_scripts/F4.functions.R')
+
+plts <- list()
+
+for(k in 1:3){
+plts[[k]] <- trplot((8:10)[k])
+}
+
+tN <- theme(legend.position = 'none')
+
+pG8 <- ggplotGrob(plts[[1]]+tN)
+pG9 <- ggplotGrob(plts[[2]]+tN)
+pG10 <- ggplotGrob(plts[[3]]+tN)
+pGr8 <- editGrob(pG8, vp=viewport(x=0.5, y=0.97, angle=45,width = .76), name="pG8")
+pGr9 <- editGrob(pG9, vp=viewport(x=0.5, y=0.62, angle=45,width = .7), name="pG9")
+pGr10 <- editGrob(pG10, vp=viewport(x=0.5, y=0.3, angle=45,width = .7), name="pG10")
+
+npGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/pue-nig-cairo.svg"))))
+puGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/uni-pue-cairo.svg"))))
+nuGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/nig-uni-cairo.svg"))))
+
+leg <- get_legend(plts[[1]]+theme(legend.text = element_text(size = 5),
+                                   legend.title =  element_text(size = 5),
+                                   legend.key.size = unit(7,'pt')))
+
+F5 <- ggdraw(pGr8)+
+  draw_grob(pGr9,0,0,1,1)+
+  draw_grob(leg,-.65,.04,1,1)+
+  draw_grob(pGr10,0,0,1,1)+
+  draw_grob(npGrob, 0.7, 0.7, 0.28, 0.1)+
+  draw_grob(nuGrob, 0.7, 0.37, 0.28, 0.1)+
+  draw_grob(puGrob, 0.7, .04, 0.28, 0.1)
+
+#ggsave(plot = F5,filename = '../output/F5.pdf',width =  91.5,height = 145,units = 'mm',device = cairo_pdf)
+ggsave(plot = F5,filename = '../output/F5.png',width = 91.5,height = 145,units = 'mm',dpi = 150)
\ No newline at end of file

3_figures/S01.Rmd

-# S01
+---
+output: html_document
+editor_options: 
+  chunk_output_type: console
+---
+# Supplement Figure S01
 
 This is the accessory documentation of Supplementary Figure 01.
 It explains the steps of script **2.2.0.1.maf2circos.sh** and documents progression from the whole genome alignment of the *de novo* *Hypoplectrus puella* genome assembly with the *Gasterosteus aculeatus* reference genome. 

3_figures/S08.Rmd

-# S08
+---
+output: html_document
+editor_options: 
+  chunk_output_type: console
+---
+# Supplement Figure S08
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)

3_figures/Workflow.Rmd

@@ -31,6 +31,12 @@ edgR <- function(pts,edg){
 ## Info
 
 In the following, I give an overview over the individual steps done in during *de novo* assembly of the barred hamlet (*Hypoplectrus puella*) genome. 
+
+Within the scheme, each arrow represents a script (or class of scripts) connecting individual setps of the assembly/ analysis.
+The respective scripts are store in the folders `$WORK/1_assembly_scripts` & `$WORK/2_reSeq-scripts`.
+
+For the final visualization (the green squares in panel 2.2.Popgen), additional documetation is provided in the following pages.
+
 ```{r data_prep,echo=FALSE}
 source('workflow/points_and_edges_assembly.R')
 source('workflow/points_and_edges_analysis.R')

3_figures/docs/F2.md

@@ -118,6 +118,8 @@ gwFST <- read.csv('../../2_output/08_popGen/05_fst/genome_wide_weighted_mean_fst
 gwFST$RUN <- factor(gwFST$run,levels=levels(data$RUN))
 ```
 
+### Computing 99.98 *F~ST~* percentiles
+
 The upper 99.98 *F~ST~* percintile is computed per run.
 Then windows above this threshold are indentified for each global run.
 
@@ -153,6 +155,8 @@ musks <- data2 %>% group_by(musk) %>% summarise(MUSKmin=min(xmin),
                                                      MUSKmin-1e+07,MUSKmax+1e+07))
 ```
 
+### Plotting
+
 For plotting, colors,labels and the scaling of the secondary axis are pre-defined.
 
 
@@ -234,6 +238,8 @@ yd <- .2195
 boxes = data.frame(x=rep(.9675,4),y=c(ys,ys+yd+ysc,ys+(yd+ysc)*2,ys+(yd+ysc)*3))
 ```
 
+### Composing the final figure
+
 And finally the base plot is combined with the external annotations.
 
 

3_figures/docs/F3.md

 ---
 output: html_document
 editor_options: 
-chunk_output_type: console
+  chunk_output_type: console
 ---
 # Figure 3
   

3_figures/docs/F5.md

 ---
 output: html_document
 editor_options: 
-chunk_output_type: console
+  chunk_output_type: console
 ---
 # Figure 5
   
@@ -20,3 +20,91 @@ Rscript --vanilla F5.R
 rm Rplots.pdf
 
 ```
+## Details of F5.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.
+
+It Furthermore depends on the R scripts `F4.functions.R` (located under `$WORK/0_data/0_scripts`).
+
+This script is a modification of sript F4.R. It uses the same funtions and just differs in the data sets and settings 
+
+
+```r
+library(tidyverse)
+library(scales)
+library(cowplot)
+library(grid)
+library(gridSVG)
+library(grImport2)
+source('../../0_data/0_scripts/F4.functions.R')
+```
+
+The script `F4.functions.R`contains a function (`trplot()`) that plots a single LD triangle as seen in Figure 5.
+The Details of this script are explained below.
+The output depends on the data set plotted (sub figure a contains additional annotations).
+
+We create an empty list that is then filled with the subplots using the `trplot()` function.
+
+
+```r
+plts <- list()
+
+for(k in 1:3){
+plts[[k]] <- trplot((8:10)[k])
+}
+```
+
+The basic plots are transformed into `grid obgects`.
+These are afterwards rotated by 45 degrees.
+
+
+```r
+tN <- theme(legend.position = 'none')
+
+pG8 <- ggplotGrob(plts[[1]]+tN)
+pG9 <- ggplotGrob(plts[[2]]+tN)
+pG10 <- ggplotGrob(plts[[3]]+tN)
+pGr8 <- editGrob(pG8, vp=viewport(x=0.5, y=0.97, angle=45,width = .76), name="pG8")
+pGr9 <- editGrob(pG9, vp=viewport(x=0.5, y=0.62, angle=45,width = .7), name="pG9")
+pGr10 <- editGrob(pG10, vp=viewport(x=0.5, y=0.3, angle=45,width = .7), name="pG10")
+```
+
+Then, external annotations loaded and the legend ins extracted from the first plot.
+
+
+```r
+npGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/pue-nig-cairo.svg"))))
+puGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/uni-pue-cairo.svg"))))
+nuGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/nig-uni-cairo.svg"))))
+
+leg <- get_legend(plts[[1]]+theme(legend.text = element_text(size = 5),
+                                   legend.title =  element_text(size = 5),
+                                   legend.key.size = unit(7,'pt')))
+```
+
+Finally, the complete Figure 5 is put together.
+
+
+```r
+F5 <- ggdraw(pGr8)+
+  draw_grob(pGr9,0,0,1,1)+
+  draw_grob(leg,-.65,.04,1,1)+
+  draw_grob(pGr10,0,0,1,1)+
+  draw_grob(npGrob, 0.7, 0.7, 0.28, 0.1)+
+  draw_grob(nuGrob, 0.7, 0.37, 0.28, 0.1)+
+  draw_grob(puGrob, 0.7, .04, 0.28, 0.1)
+```
+
+The final figure is then exported using `ggsave()`.
+
+
+```r
+#ggsave(plot = F5,filename = '../output/F5.pdf',width =  91.5,height = 145,units = 'mm',device = cairo_pdf)
+ggsave(plot = F5,filename = '../output/F5.png',width = 91.5,height = 145,units = 'mm',dpi = 150)
+```
+
+<center>
+<img src="F5_files/figure-html/f5SHOW-1.png" width="345.82678272" />
+</center>
+---

3_figures/docs/Workflow.md

@@ -5,6 +5,12 @@
 
 In the following, I give an overview over the individual steps done in during *de novo* assembly of the barred hamlet (*Hypoplectrus puella*) genome. 
 
+Within the scheme, each arrow represents a script (or class of scripts) connecting individual setps of the assembly/ analysis.
+The respective scripts are store in the folders `$WORK/1_assembly_scripts` & `$WORK/2_reSeq-scripts`.
+
+For the final visualization (the green squares in panel 2.2.Popgen), additional documetation is provided in the following pages.
+
+
 <center>
 <img src="Workflow_files/figure-html/plot-1.png" width="2304" />
 </center>

3_figures/docs/figure-1.html

@@ -25,7 +25,7 @@
 <meta name="author" content="Kosmas Hench">
 
 
-<meta name="date" content="2018-06-13">
+<meta name="date" content="2018-06-14">
 
   <meta name="viewport" content="width=device-width, initial-scale=1">
   <meta name="apple-mobile-web-app-capable" content="yes">
@@ -123,16 +123,26 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
 <li class="chapter" data-level="4.1" data-path="figure-2.html"><a href="figure-2.html#summary-1"><i class="fa fa-check"></i><b>4.1</b> Summary</a></li>
 <li class="chapter" data-level="4.2" data-path="figure-2.html"><a href="figure-2.html#details-of-f2.r"><i class="fa fa-check"></i><b>4.2</b> Details of F2.R</a><ul>
 <li class="chapter" data-level="4.2.1" data-path="figure-2.html"><a href="figure-2.html#reading-in-data"><i class="fa fa-check"></i><b>4.2.1</b> Reading in Data</a></li>
+<li class="chapter" data-level="4.2.2" data-path="figure-2.html"><a href="figure-2.html#computing-99.98-fst-percentiles"><i class="fa fa-check"></i><b>4.2.2</b> Computing 99.98 <em>F<sub>ST</sub></em> percentiles</a></li>
+<li class="chapter" data-level="4.2.3" data-path="figure-2.html"><a href="figure-2.html#plotting"><i class="fa fa-check"></i><b>4.2.3</b> Plotting</a></li>
+<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-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 F3.R</a></li>
+<li class="chapter" data-level="5.3" data-path="figure-3.html"><a href="figure-3.html#details-of-f3.plot_fun.r"><i class="fa fa-check"></i><b>5.3</b> Details of F3.plot_fun.R</a></li>
 </ul></li>
 <li class="chapter" data-level="6" data-path="figure-4.html"><a href="figure-4.html"><i class="fa fa-check"></i><b>6</b> Figure 4</a><ul>
 <li class="chapter" data-level="6.1" data-path="figure-4.html"><a href="figure-4.html#summary-3"><i class="fa fa-check"></i><b>6.1</b> Summary</a></li>
+<li class="chapter" data-level="6.2" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.r"><i class="fa fa-check"></i><b>6.2</b> Details of F4.R</a></li>
+<li class="chapter" data-level="6.3" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.functions.r"><i class="fa fa-check"></i><b>6.3</b> Details of F4.functions.R</a></li>
+<li class="chapter" data-level="6.4" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.genomewide_box.r"><i class="fa fa-check"></i><b>6.4</b> Details of F4.genomeWide_box.R</a></li>
+<li class="chapter" data-level="6.5" data-path="figure-4.html"><a href="figure-4.html#details-of-f4.peakarea_box.r"><i class="fa fa-check"></i><b>6.5</b> Details of F4.peakArea_box.R</a></li>
 </ul></li>
 <li class="chapter" data-level="7" data-path="figure-5.html"><a href="figure-5.html"><i class="fa fa-check"></i><b>7</b> Figure 5</a><ul>
 <li class="chapter" data-level="7.1" data-path="figure-5.html"><a href="figure-5.html#summary-4"><i class="fa fa-check"></i><b>7.1</b> Summary</a></li>
+<li class="chapter" data-level="7.2" data-path="figure-5.html"><a href="figure-5.html#details-of-f5.r"><i class="fa fa-check"></i><b>7.2</b> Details of F5.R</a></li>
 </ul></li>
 <li class="chapter" data-level="8" data-path="s01.html"><a href="s01.html"><i class="fa fa-check"></i><b>8</b> S01</a><ul>
 <li class="chapter" data-level="8.1" data-path="s01.html"><a href="s01.html#preparation"><i class="fa fa-check"></i><b>8.1</b> Preparation</a></li>
@@ -163,7 +173,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
 <h1><span class="header-section-number">3</span> Figure 1</h1>
 <div id="summary" class="section level2">
 <h2><span class="header-section-number">3.1</span> Summary</h2>
-<p>This is the accessory documentation of Figure 1. The Figure can be recreated by using runing the <strong>R</strong> script F1.R:</p>
+<p>This is the accessory documentation of Figure 1. The Figure can be recreated by runing the <strong>R</strong> script F1.R:</p>
 <div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash"><span class="bu">cd</span> <span class="va">$WORK</span>/3_figures/F_scripts
 
 <span class="ex">Rscript</span> --vanilla F1.R