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

update documentation (bookdown)

parent 7613949e

0_data/0_scripts/S13.functions.R

+29 −0
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@@ -133,3 +133,32 @@ plot_fun <- function(data,loc,sel,gl){ 


  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)

}
 
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3_figures/F_scripts/Rplots.pdf

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3_figures/F_scripts/S07bu.R

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#!/usr/bin/env Rscriptlibrary(ggplot2)

library(dplyr)

library(scales)

library(reshape2)

library(cowplot)

library(grid)

library(gridSVG)

library(grImport2)



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/08_LD_extended/',files[sel],'.ext-10000-bins.txt',sep=''),sep='\t')

  message(files[sel])

  

  s1=5760000;s2=1884000;s3=12860000;s4=17745000;s5=20149000;s6=22085000;s7=22445000;s8=13730000

  e2=2134000;e3=13110000;e5=20399000;e6=22335000

  stp=20000;lALL=250000

  

  scling <- c(-s1,

              -s2+(lALL+stp),

              -s3+((lALL+stp)*2),

              -s4+((lALL+stp)*3),

              -s5+((lALL+stp)*4),

              -s6+((lALL+stp)*5),

              -s7+((lALL+stp)*6),

              -s8+((lALL+stp)*7))

  

  dt <- data %>% mutate(miX = floor(Mx/10000),miY=floor(My/10000))

  genes <- data.frame(start=c(5884279,2009113,12992396,17871610,20186151,22228342,22553187,22556763,22561894,22573388,13862931),

                      end=c(5878614,2010303,12976894,17873915,20347811,22225149,22555052,22559742,22566321,22575503,13884003),

                      sclr=c(1,2,3,4,5,6,7,7,7,7,8),

                      LG=c("LG04","LG08","LG08","LG09","LG12","LG12","LG17","LG17","LG17","LG17","LG20"),

                      name=c("ednrb","foxd3","rorb","sox10","casz1","hoxc13a","sws2a\u03B2","sws2a\u03B1","sws2b","lws","invs"))

  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(-7,-3,5,9)

  

  GZrS <- 40000;GZrS2 <- 20000; #gene zoom offset

  BS <- c(-2,2,       # ednrb

          2,-2,       # foxd3

          -2.5,2.5,   # rorb

          2,-2,       # sox10

          -5,5,       # casz1

          -3,3,       # hoxc13a

          -11,-6,     # sws2a beta

          -.1,-5,     # sws2a alpha

          7,2,        # sws2b

          8,11,       # lws

          1,-1)*10000 # invs   ## Backshifter for gene zoom

  OPSoffset <- 2.5*10000 # correcting the zoom on lws & sws2abeta

  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$end[7]+GZrS+BS[13]-OPSoffset,genes$start[7]+GZrS+BS[14]-OPSoffset,genes$start[7],

                         genes$start[8],genes$end[8],genes$end[8]+GZrS+BS[15],genes$start[8]+GZrS+BS[16],genes$start[8],

                         genes$start[9],genes$end[9],genes$end[9]+GZrS+BS[17],genes$start[9]+GZrS+BS[18],genes$start[9],

                         genes$start[10],genes$end[10],genes$end[10]+GZrS+BS[19]-OPSoffset,genes$start[10]+GZrS+BS[20]-OPSoffset,genes$start[10],

                         genes$start[11],genes$end[11],genes$end[11]+GZrS+BS[21],genes$start[11]+GZrS+BS[22],genes$start[11])+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$end[7]-GZrS+BS[13]+OPSoffset,genes$start[7]-GZrS+BS[14]+OPSoffset,genes$start[7],

                         genes$start[8],genes$end[8],genes$end[8]-GZrS+BS[15],genes$start[8]-GZrS+BS[16],genes$start[8],

                         genes$start[9],genes$end[9],genes$end[9]-GZrS+BS[17],genes$start[9]-GZrS+BS[18],genes$start[9],

                         genes$start[10],genes$end[10],genes$end[10]-GZrS+BS[19]+OPSoffset,genes$start[10]-GZrS+BS[20]+OPSoffset,genes$start[10],

                         genes$start[11],genes$end[11],genes$end[11]-GZrS+BS[21],genes$start[11]-GZrS+BS[22],genes$start[11])-GZrS2,

                     grp=rep(letters[1:11],each=5)) %>% 

    mutate(sclr=rep(c(1,2,3,4,5,6,7,7,7,7,8),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)

  LGoffset <- 15

  GLABoffset <- 8

  if(sel %in% c(1,8)){

    rS <- 100000 # width of grey annotation band

    zmRange <- data.frame(x=c(s1,s1+lALL,s1+lALL+rS,s1+rS,s1,

                              s2,s2+lALL,s2+lALL+rS,s2+rS,s2,

                              s3,s3+lALL,s3+lALL+rS,s3+rS,s3,

                              s4,s4+lALL,s4+lALL+rS,s4+rS,s4,

                              s5,s5+lALL,s5+lALL+rS,s5+rS,s5,

                              s6,s6+lALL,s6+lALL+rS,s6+rS,s6,

                              s7,s7+lALL,s7+lALL+rS,s7+rS,s7,

                              s8,s8+lALL,s8+lALL+rS,s8+rS,s8),

                          y=c(s1,s1+lALL,s1+lALL-rS,s1-rS,s1,

                              s2,s2+lALL,s2+lALL-rS,s2-rS,s2,

                              s3,s3+lALL,s3+lALL-rS,s3-rS,s3,

                              s4,s4+lALL,s4+lALL-rS,s4-rS,s4,

                              s5,s5+lALL,s5+lALL-rS,s5-rS,s5,

                              s6,s6+lALL,s6+lALL-rS,s6-rS,s6,

                              s7,s7+lALL,s7+lALL-rS,s7-rS,s7,

                              s8,s8+lALL,s8+lALL-rS,s8-rS,s8),

                          grp=rep(letters[1:8],each=5)) %>% 

      mutate(sclr=rep(1:8,each=5),

             Nx1 = (x+scling[sclr])/10000-1,

             Nx2 = (y+scling[sclr])/10000)

    rS2 <- .75*rS

    zmRange2 <- data.frame(x=c(s1,s1+lALL,s1+lALL+rS2,s1+rS2,s1,

                               s2,s2+lALL,s2+lALL+rS2,s2+rS2,s2,

                               s3,s3+lALL,s3+lALL+rS2,s3+rS2,s3,

                               s4,s4+lALL,s4+lALL+rS2,s4+rS2,s4,

                               s5,s5+lALL,s5+lALL+rS2,s5+rS2,s5,

                               s6,s6+lALL,s6+lALL+rS2,s6+rS2,s6,

                               s7,s7+lALL,s7+lALL+rS2,s7+rS2,s7,

                               s8,s8+lALL,s8+lALL+rS2,s8+rS2,s8),

                           y=c(s1,s1+lALL,s1+lALL-rS2,s1-rS2,s1,

                               s2,s2+lALL,s2+lALL-rS2,s2-rS2,s2,

                               s3,s3+lALL,s3+lALL-rS2,s3-rS2,s3,

                               s4,s4+lALL,s4+lALL-rS2,s4-rS2,s4,

                               s5,s5+lALL,s5+lALL-rS2,s5-rS2,s5,

                               s6,s6+lALL,s6+lALL-rS2,s6-rS2,s6,

                               s7,s7+lALL,s7+lALL-rS2,s7-rS2,s7,

                               s8,s8+lALL,s8+lALL-rS2,s8-rS2,s8),

                           grp=rep(letters[1:8],each=5)) %>% 

      mutate(sclr=rep(1:8,each=5),

             Nx1 = (x+scling[sclr])/10000-1,

             Nx2 = (y+scling[sclr])/10000)

    

    

    

    rS3 <- .07*rS

    zmRange3 <- data.frame(x=c(s1,s1+lALL,s1+lALL+rS3,s1+rS3,s1,

                               s2,s2+lALL,s2+lALL+rS3,s2+rS3,s2,

                               s3,s3+lALL,s3+lALL+rS3,s3+rS3,s3,

                               s4,s4+lALL,s4+lALL+rS3,s4+rS3,s4,

                               s5,s5+lALL,s5+lALL+rS3,s5+rS3,s5,

                               s6,s6+lALL,s6+lALL+rS3,s6+rS3,s6,

                               s7,s7+lALL,s7+lALL+rS3,s7+rS3,s7,

                               s8,s8+lALL,s8+lALL+rS3,s8+rS3,s8),

                           y=c(s1,s1+lALL,s1+lALL-rS3,s1-rS3,s1,

                               s2,s2+lALL,s2+lALL-rS3,s2-rS3,s2,

                               s3,s3+lALL,s3+lALL-rS3,s3-rS3,s3,

                               s4,s4+lALL,s4+lALL-rS3,s4-rS3,s4,

                               s5,s5+lALL,s5+lALL-rS3,s5-rS3,s5,

                               s6,s6+lALL,s6+lALL-rS3,s6-rS3,s6,

                               s7,s7+lALL,s7+lALL-rS3,s7-rS3,s7,

                               s8,s8+lALL,s8+lALL-rS3,s8-rS3,s8),

                           grp=rep(letters[1:8],each=5)) %>% 

      mutate(sclr=rep(1:8,each=5),

             Nx1 = (x+scling[sclr])/10000-1,

             Nx2 = (y+scling[sclr])/10000)

    

    zmLab <- data.frame(x=c(s1+.5*lALL,s2+.5*lALL,s3+.5*lALL,s4+.5*lALL,

                            s5+.5*lALL,s6+.5*lALL,s7+.5*lALL,s8+.5*lALL),

                        label=c("LG4 (E)","LG08 (F)","LG08 (G)",'LG09 (A)','LG12 (B)','LG12 (C)','LG17 (D)',"LG20 (H)")) %>%  

      mutate(sclr=1:8, Nx= (x+scling[sclr])/10000)

    

    zmEND <- data.frame(x=c(s1,s1+lALL,

                            s2,s2+lALL,

                            s3,s3+lALL,

                            s4,s4+lALL,

                            s5,s5+lALL,

                            s6,s6+lALL,

                            s7,s7+lALL,

                            s8,s8+lALL)) %>% 

      mutate(sclr=rep(1:8,each=2),

             Nx = ((x+scling[sclr])/10000)+rep(c(2.5,-4),8),

             label=round((x/1000000),2))

    DG <- rgb(.4,.4,.4)

    gnShift <- c(rep(0,6),3.5,0,0,3.5,0)

    

    textSCALE1 <- c(1.8,rep(NA,6),.9)

    textSCALE2 <- c(2,rep(NA,6),1)

    textSCALE3 <- c(2.5,rep(NA,6),1.25)

    

    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=size=textSCALE1[sel])+

      geom_text(inherit.aes = F,data=genes,

                aes(x=labPOS+GLABoffset-gnShift,

                    y=labPOS-GLABoffset+gnShift,

                    label=name),

                angle=-45,fontface='italic',size=size=textSCALE2[sel])+

      geom_text(inherit.aes = F,data=zmLab,

                aes(x=Nx+LGoffset+5.5,y=Nx-LGoffset-5.5,label=label),

                angle=-45,fontface='bold',size=textSCALE3[sel],col='black')+

      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))+

      scale_color_manual(values=viridis_pal(option='A')(6))+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))+

      scale_color_manual(values=viridis_pal(option='A')(6))+theme_void()+

      theme(legend.position = c(.7,.75),legend.direction = 'vertical')

  }

  return(p1)

}



plts <- list()



for(k in 1:7){

  plts[[k]] <- trplot(k)

};



tN <- theme(legend.position = 'none')

pG1 <- ggplotGrob(plts[[1]]+tN)

pG2 <- ggplotGrob(plts[[2]]+tN)

pG3 <- ggplotGrob(plts[[3]]+tN)

pG4 <- ggplotGrob(plts[[4]]+tN)

pG5 <- ggplotGrob(plts[[6]]+tN)

pG6 <- ggplotGrob(plts[[5]]+tN)

pG7 <- ggplotGrob(plts[[7]]+tN)



pGr1 <- editGrob(pG1, vp=viewport(x=0.5, y=0.95, angle=45,width = .7), name="pG1")

pGr2 <- editGrob(pG2, vp=viewport(x=0.25, y=0.54, angle=45,width = .28), name="pG2")

pGr3 <- editGrob(pG3, vp=viewport(x=0.25, y=0.357, angle=45,width = .28), name="pG3")

pGr4 <- editGrob(pG4, vp=viewport(x=0.25, y=0.175, angle=45,width = .28), name="pG4")

pGr5 <- editGrob(pG5, vp=viewport(x=0.75, y=0.54, angle=45,width = .28), name="pG5")

pGr6 <- editGrob(pG6, vp=viewport(x=0.75, y=0.357, angle=45,width = .28), name="pG5")

pGr7 <- editGrob(pG7, vp=viewport(x=0.75, y=0.175, angle=45,width = .28), name="pG5")



pGRAD <- ggplot(data = data.frame(x=c(0,1,-1,0),

                                  y=c(0,15,15,0)),

                aes(x,y))+geom_polygon(fill='lightgray')+coord_equal()+theme_void()

nigGrob <- gTree(children=gList(pictureGrob(readPicture("img/nigricans-cairo.svg"))))

pueGrob <- gTree(children=gList(pictureGrob(readPicture("img/puella-cairo.svg"))))

uniGrob <- gTree(children=gList(pictureGrob(readPicture("img/unicolor-cairo.svg"))))



belGrob <- gTree(children=gList(pictureGrob(readPicture("img/belize-cairo.svg"))))

honGrob <- gTree(children=gList(pictureGrob(readPicture("img/honduras-cairo.svg"))))

panGrob <- gTree(children=gList(pictureGrob(readPicture("img/panama-cairo.svg"))))

globGrob <- gTree(children=gList(pictureGrob(readPicture("img/caribbean-cairo2.svg"))))



# library(tidyr)

# BW <- read.csv('subs/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)

#   # WI <- WI  %>%

#   #    rbind(.,(read.csv(paste('glob_within.',k,'.hap.ld',sep=''),sep='\t') %>% select(R.2) %>% mutate(type='wi',run=k)))

#   BW <- BW %>%

#     rbind(.,(read.csv(paste('subs/glob_between.',k,'.interchrom.hap.ld',sep=''),sep='\t') %>% select(R.2) %>% mutate(type=u,run=q)))

# }

# 

# 

# #dt <- rbind(WI,BW)

# BW$run <- factor(BW$run,levels=c('Global',"Panana","Belize","Honduras",

#                                  "H. nigricans","H. puella","H. unicolor")) 

# 

# dt2 <- BW %>% 

#   group_by(run) %>% 

#   summarise(mn=mean(R.2,na.rm = T),md=median(R.2,na.rm = T)) %>%

#   gather(key = 'type',value = 'val',2:3)

# 

# BC <-rgb(.7,.7,.7)#viridis_pal(option='A')(7)[6]

# clr <-colorRampPalette(colors = c('white',BC,'black'))(8)

# 

# pBOX <- ggplot(BW,aes(x=run,y=R.2))+#geom_violin(fill='#3bb33b')+

#   geom_boxplot(fill=BC,width=.7,outlier.size = .1)+

#   #  coord_cartesian(ylim=c(0,.031))+

#   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('r²')+

#   scale_fill_manual('',values = clr[c(1,6)],labels=c('median','mean'))+

#   # scale_color_manual('',values = clr[c(2,4)],labels=c('median','mean'))+

#   # scale_shape_manual(values=c(21,23))+

#   theme(legend.position = c(-.4,1.15),legend.direction = 'horizontal',

#         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());pBOX





leg <- get_legend(plts[[1]])

sY <- .035;

sX <- -.03;

ggdraw(pGr1)+

  #draw_plot(pBOX,-.1,.55,.45,.21)+

  draw_plot(pGRAD,.307,-.018,.16,.53)+

  draw_grob(pGr2,0,0,1,1)+

  draw_grob(leg,.15,-.08,1,1)+

  draw_grob(pGr3,0,0,1,1)+

  draw_grob(pGr4,0,0,1,1)+

  draw_grob(pGr5,0,0,1,1)+

  draw_grob(pGr6,0,0,1,1)+

  draw_grob(pGr7,0,0,1,1)+

  draw_grob(nigGrob, 0.85, 0.38, 0.12, 0.095)+

  draw_grob(pueGrob, 0.85, 0.2, 0.12, 0.095)+

  draw_grob(uniGrob, 0.85, 0, 0.12, 0.095)+

  draw_grob(panGrob, 0.35+sX+.01, 0.37+sY, 0.12, 0.045)+

  draw_grob(belGrob, 0.35+sX+.01, 0.19+sY, 0.12, 0.045)+

  draw_grob(honGrob, 0.35+sX, 0+sY, 0.14, 0.045)+

  draw_grob(globGrob, 0.7, .6, 0.14, 0.08)+

  draw_plot_label(letters[1:3],x = c(rep(0.01,2),.52),

                  y=c(.99,.57,.57), size = 14)



# draw_plot_label(letters[1:7],

#                  x = c(rep(0.01,4),rep(.52,3)),

#                 y=c(.99,rep(c(.57,.39,.2),2)),

#                  size = 14)+



#getwd()

#ggsave('ms_fig_4.pdf',width = 183,height = 210,units = 'mm',device = cairo_pdf)

ggsave('LDtriangle_extended.pdf',width = 183,height = 230,units = 'mm',device = cairo_pdf)

ggsave('LDtriangle_extended.png',width = 183,height = 230,units = 'mm',dpi = 300)



## ---------------- pairwise ----------------



pG8 <- ggplotGrob(plts[[8]]+tN)

pG9 <- ggplotGrob(plts[[9]]+tN)

pG10 <- ggplotGrob(plts[[10]]+tN)

pGr8 <- editGrob(pG8, vp=viewport(x=0.5, y=0.95, angle=45,width = .76), name="pG8")

pGr9 <- editGrob(pG9, vp=viewport(x=0.5, y=0.61, angle=45,width = .7), name="pG9")

pGr10 <- editGrob(pG10, vp=viewport(x=0.5, y=0.29, angle=45,width = .7), name="pG10")



npGrob <- gTree(children=gList(pictureGrob(readPicture("img/pue-nig-cairo.svg"))))

puGrob <- gTree(children=gList(pictureGrob(readPicture("img/uni-pue-cairo.svg"))))

nuGrob <- gTree(children=gList(pictureGrob(readPicture("img/nig-uni-cairo.svg"))))



leg2 <- get_legend(plts[[8]]+theme(legend.text = element_text(size = 5),

                                   legend.title =  element_text(size = 5),

                                   legend.key.size = unit(7,'pt')))





ggdraw(pGr8)+

  draw_grob(pGr9,0,0,1,1)+

  draw_grob(leg2,-.65,-.02,1,1)+

  draw_grob(pGr10,0,0,1,1)+

  draw_grob(npGrob, 0.7, 0.65, 0.28, 0.1)+

  draw_grob(nuGrob, 0.7, 0.34, 0.28, 0.1)+

  draw_grob(puGrob, 0.7, .01, 0.28, 0.1)





ggsave('LDtriangle_extended_pw.pdf',width =  91.5,height = 150,units = 'mm',device = cairo_pdf)

ggsave('LDtriangle_extended_pw.png',width = 91.5,height = 150,units = 'mm',dpi = 150)

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