Commit 89b22387 authored by Kosmas Hench's avatar Kosmas Hench
Browse files

incl linkage decay

parent eae8412e

0_data/0_scripts/F4.functions.R

+15 −8
Original line number Diff line number Diff line
@@ -134,10 +134,10 @@ trplot <- function(sel){ 
        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))+

      #  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')
@@ -151,14 +151,21 @@ trplot <- function(sel){ 
      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_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)

#  cs <- scale_fill_viridis_c(name=expression(bar(r^2)),begin = 0,end = 0.55,direction = -1)

  cs <- scale_fill_viridis_c(name=expression(bar(r^2)),

                             limits = c(0,0.55),values = c(0,.08,1),

                             option =  'B',direction = -1)

#  cs <- scale_fill_gradientn(name=expression(bar(r^2)),colours=clr,

#                             values=rescale(c(1,.08,.03,.015,.01,0)),

#                             limits=c(0,0.55))

  return(p1+cs)

}



run_one_sample_test <- function(pop,n,data){

0_data/0_scripts/S09.functions.R

+4 −7
Original line number Diff line number Diff line
@@ -188,9 +188,6 @@ trplot <- function(sel){ 
      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,.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 {
@@ -203,11 +200,11 @@ trplot <- function(sel){ 
      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)

  cs <- scale_fill_viridis_c(name=expression(bar(r^2)),

                             limits = c(0,0.55),values = c(0,.08,1),

                             option =  'B',direction = -1)

  return(p1+cs)

}
 
 No newline at end of file

0_data/0_scripts/S16.functions.R

+1 −1
Original line number Diff line number Diff line
@@ -138,7 +138,7 @@ trplot <- function(sel){ 
        scale_x_continuous(expand=c(0,0))+

        scale_y_continuous(expand=c(0,0),

                           trans = 'reverse')+

        scale_fill_viridis_c(name=expression(bar(italic(r)^2)))+

        scico::scale_fill_scico(name=expression(bar(italic(r)^2)),palette = 'lapaz',direction = -1)+

        theme_void()+

        theme(legend.position = c(.9,.75),

              legend.direction = 'vertical')

2_reSeq-scripts/2-2_popGen/2.2.8.1.linkage_decay.sh

0 → 100644
+30 −0
Original line number Diff line number Diff line 
#PBS -l elapstim_req=0:20:00

#PBS -l memsz_job=10gb

#PBS -b 1

#PBS -l cpunum_job=1

#PBS -N linkage_decay

#PBS -q clexpress

#PBS -o 2.2.8.1.linkage_decay.stdout

#PBS -e 2.2.8.1.linkage_decay.stderr



cd $WORK/2_output/08_popGen/07_LD

mkdir -p decay



cd decay



RANDOM=27678 #set seed

for k in {1..20};do

	LG=$(echo $(( (RANDOM % 24) + 1 )) | awk '$1<10{print "0"$1} $1>=10{print$1}')

	RN1=$(( ( RANDOM % 13684534 ) + 1))

	RN2=$(($RN2+15000))

	echo $RN2

	vcftools \

    --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \

    --chr LG$LG \

    --from-bp $RN1 \

    --to-bp  $RN2 \

    --hap-r2 \

    --out dist.$k.$RN1

done

gzip ./*.hap.ld

3_figures/F_scripts/F4.R

+2 −2
Original line number Diff line number Diff line
@@ -46,7 +46,7 @@ honGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/hond 
panGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/panama-cairo.svg"))))

globGrob <- gTree(children=gList(pictureGrob(readPicture("../../0_data/0_img/caribbean-cairo.svg"))))



leg <- get_legend(plts[[1]]+theme(legend.direction = 'horizontal')+ guides(fill = guide_legend(nrow=1)))

leg <- get_legend(plts[[1]]+theme(legend.direction = 'horizontal',legend.key.width = unit(60,'pt')))

sY <- .035;

sX <- -.03;

F4 <- ggdraw(pGr1)+
@@ -54,7 +54,7 @@ F4 <- ggdraw(pGr1)+ 
  draw_plot(boxGenes+theme(legend.position='none'),.65,.54,.45,.21)+

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

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

  draw_grob(leg,-.33,.22,1,1)+

  draw_grob(leg,-.25,.22,1,1)+

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

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

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