Commit a4fd034b authored by Kosmas Hench's avatar Kosmas Hench
Browse files

update suppl fig documentation

parent 5ddd61bf

0_data/0_resources/retina_samples_ID.txt

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ID	rID	population

28383	R28383	H. unicolor

28384	R28384	H. puella

28385	R28385	H. nigricans

28387	R28387	H. nigricans

28390	R28390	H. nigricans

28391	R28391	H. unicolor

28394	R28394	H. nigricans

28399	R28399	H. nigricans

AG9RX46	RAG9RX46	H. nigricans

AG9RX47	RAG9RX47	H. puella

AG9RX48	RAG9RX48	H. puella

AG9RX49	RAG9RX49	H. nigricans

AG9RX50	RAG9RX50	H. nigricans

AG9RX51	RAG9RX51	H. puella

AG9RX52	RAG9RX52	H. nigricans

AG9RX53	RAG9RX53	H. puella

AG9RX54	RAG9RX54	H. unicolor

AG9RX55	RAG9RX55	H. unicolor

PL17_01	RPL17_01	H. unicolor

PL17_02	RPL17_02	H. puella

PL17_04	RPL17_04	H. puella

PL17_16	RPL17_16	H. puella

PL17_17	RPL17_17	H. puella

PL17_18	RPL17_18	H. puella

28386	R28386

0_data/0_resources/retina_samples_ID_altVersion.csv

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ids	population

R28383	uni

R28384	pue

R28385	nig

R28387	nig

R28390	nig

R28391	uni

R28394	nig

R28399	nig

RAG9RX46	nig

RAG9RX47	pue

RAG9RX48	pue

RAG9RX49	nig

RAG9RX50	nig

RAG9RX51	pue

RAG9RX52	nig

RAG9RX53	pue

RAG9RX54	uni

RAG9RX55	uni

RPL17_01	uni

RPL17_02	pue

RPL17_04	pue

RPL17_16	pue

RPL17_17	pue

RPL17_18	pue

0_data/0_resources/seqSTART.csv

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0_data/0_resources/transcripts2genname.txt

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0_data/0_scripts/S07.functions.R

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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=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=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)

}
 
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