Commit 5ddd61bf authored by Kosmas Hench's avatar Kosmas Hench
Browse files

update figure documentation

parent 4a40cb84

0_data/0_img/nig-uni-cairo.svg

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0_data/0_img/pue-nig-cairo.svg

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0_data/0_img/uni-pue-cairo.svg

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0_data/0_scripts/F4.functions.R

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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)

}
 
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0_data/0_scripts/F4.genomeWide_box.R

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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())
 
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