Commit 06738b06 authored by Kosmas Hench's avatar Kosmas Hench
Browse files

relabel -> new format

parent 79ce4b8c

0_data/0_scripts/E1.functions.R

deleted100644 → 0
+0 −30
Original line number Diff line number Diff line 
get_anno_df_single_line <- function(searchLG,gfffile,

                                    xrange,

                                    genes_of_interest,

                                    genes_of_sec_interest,

                                    anno_rown=3){

  gff_filter <- list(seqid=searchLG)

  data <- as.data.frame(readGFF(gfffile,filter=gff_filter)) %>% mutate(Parent=as.character(Parent))#%>%

  #rowwise() %>% mutate(Parent=ifelse(length(Parent)==0,ID,Parent))

  

  mRNAs <- data %>% filter(type=='mRNA',end>xrange[1],start<xrange[2]) %>% 

    ungroup() %>%  mutate(yl=row_number()%%anno_rown+2) %>% rowwise()%>%

    mutate(checkStart =ifelse(start<xrange[1],-Inf,start),

           checkEnd =ifelse(end>xrange[2],Inf,end),

           ps=ifelse(strand=='-',checkEnd,checkStart),

           pe=ifelse(strand=='-',checkStart,checkEnd),

           labelx=mean(c(sort(c(xrange[1],ps))[2],

                         sort(c(xrange[2],pe))[1])),

           window='bold(Gene)',

           clr=ifelse(Parentgenename %in% genes_of_interest,"y",

                      ifelse(Parentgenename %in% genes_of_sec_interest,"z","x"))) %>% 

    select(-Parent);

  names(mRNAs)[names(mRNAs)=='ID'] <- 'Parent'

  

  exons <- data %>% filter(type=='exon',end>xrange[1],start<xrange[2]) %>% 

    merge(.,mRNAs %>% select(Parent,yl,clr),by='Parent',all.x=T) %>% 

    mutate(ps=ifelse(strand=='-',end,start),

           pe=ifelse(strand=='-',start,end),

           window='bold(Gene)')

  return(list(mRNAs,exons))}

0_data/0_scripts/F3.functions.R

+28 −160
Original line number Diff line number Diff line 
se <-  function(x){

  x2 <- x[!is.na(x)]

  return(sd(x2)/sqrt(length(x2)))}

get_anno_df_single_line <- function(searchLG,gfffile,

                                    xrange,

                                    genes_of_interest,

                                    genes_of_sec_interest,

                                    anno_rown=3){

  gff_filter <- list(seqid=searchLG)

  data <- as.data.frame(readGFF(gfffile,filter=gff_filter)) %>% mutate(Parent=as.character(Parent))#%>%

  #rowwise() %>% mutate(Parent=ifelse(length(Parent)==0,ID,Parent))

  

  mRNAs <- data %>% filter(type=='mRNA',end>xrange[1],start<xrange[2]) %>% 

    ungroup() %>%  mutate(yl=row_number()%%anno_rown+2) %>% rowwise()%>%

    mutate(checkStart =ifelse(start<xrange[1],-Inf,start),

           checkEnd =ifelse(end>xrange[2],Inf,end),

           ps=ifelse(strand=='-',checkEnd,checkStart),

           pe=ifelse(strand=='-',checkStart,checkEnd),

           labelx=mean(c(sort(c(xrange[1],ps))[2],

                         sort(c(xrange[2],pe))[1])),

           window='bold(Gene)',

           clr=ifelse(Parentgenename %in% genes_of_interest,"y",

                      ifelse(Parentgenename %in% genes_of_sec_interest,"z","x"))) %>% 

    select(-Parent);

  names(mRNAs)[names(mRNAs)=='ID'] <- 'Parent'

  

  exons <- data %>% filter(type=='exon',end>xrange[1],start<xrange[2]) %>% 

    merge(.,mRNAs %>% select(Parent,yl,clr),by='Parent',all.x=T) %>% 

    mutate(ps=ifelse(strand=='-',end,start),

           pe=ifelse(strand=='-',start,end),

           window='bold(Gene)')

  return(list(mRNAs,exons))}

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(italic(r)^2)),colours=clr,

                             values=rescale(c(1,.5,.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(.9,.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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