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hamlets_ILD_vision_pigmentation
hamlets_ILD_vision_pigmentation
Commit a5aeb3c5 authored by Kosmas Hench's avatar Kosmas Hench
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version: revision R1

parent 89b22387
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0_data/0_scripts/F3.plot_fun.R
View file @ a5aeb3c5
......@@ -81,24 +81,24 @@ create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchs
panel.border = element_blank()
);
if(muskID=='a'){
if(muskID=='A'){
p11$layers[[4]]$data$label <- c("italic(sox10)","italic(rnaseh2a)")
} else if(muskID=='b'){
} else if(muskID=='B'){
p11$layers[[4]]$data$label <- c("italic(casz1.3)","italic(casz1.2)","italic(casz1.1)")
} else if(muskID=='c'){
} else if(muskID=='C'){
p11$layers[[4]]$data$label <- c('italic(hoxc10a)',"italic(hoxc11a)","italic(hoxc12a)","italic(hoxc13a)","italic(calcoco1)")
}else if(muskID=='e'){
}else if(muskID=='E'){
p11$layers[[4]]$data$label <- c("italic(polr1d)","italic(ednrb)")
} else if(muskID=='f'){
} else if(muskID=='F'){
p11$layers[[4]]$data$label <- c("italic(foxd3)","italic(alg6)","italic(efcab7)")
} else if(muskID=='d'){
} else if(muskID=='D'){
p11$layers[[4]]$data$label <- c("italic(hcfc1)","italic(hcfc1[2])","italic(hcfc1[1])",'italic(paste(sws2a,"\u03B2"))',
'italic(paste(sws2a,"\u03B1"))',"italic(sw2b)","italic(lws)",
"italic(gnl3l)","italic(tfe3)","italic(mdfic2)","italic(cxxc1[3])",
"italic(cxxc1[1])",'italic(mbd1)','italic(ccdc120)')
}else if(muskID=='g'){
}else if(muskID=='G'){
p11$layers[[4]]$data$label <- c("italic(lgals3bpb)","italic(mpnd)","italic(sh3gl1)","italic(rorb)")
}else if(muskID=='h'){
}else if(muskID=='H'){
p11$layers[[4]]$data$label <- c("italic(alg2)","italic(sec61b)","italic(nr4a3)",
"italic(stx17)","italic(erp44)","italic(invs)")
}
......
0_data/0_scripts/S07.plot_fun.R → 0_data/0_scripts/S08.plot_fun.R
View file @ a5aeb3c5
create_K_plot <- function(searchLG,gfffile,xr,xr2,muskID){
source('../../0_data/0_scripts/S07.functions.R');
source('../../0_data/0_scripts/S08.functions.R');
source('../../0_data/0_scripts/F3.getFSTs.R')
highclr <- '#3bb33b'
......
0_data/0_scripts/S15.plot_fun.R
View file @ a5aeb3c5
create_K_plot <- function(searchLG,gfffile,xr,searchgene,secondary_genes,searchsnp,muskID){
source('../../0_data/0_scripts/F3.functions.R');
source('../../0_data/0_scripts/F3.getFSTs.R')
source('../../0_data/0_scripts/F3.getGxP.R')
source('../../0_data/0_scripts/F3.getDXY.R')
source('../../0_data/0_scripts/S15.getGxP.R')
source('../../0_data/0_scripts/S15.getPI.R')
source('../../0_data/0_scripts/S15.getPIpw.R')
source('../../0_data/0_scripts/S15.getIHH12.R')
......
0_data/0_scripts/S16.functions.R deleted 100644 → 0
View file @ 89b22387
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))
print(max(dt$Mval,na.rm=TRUE))
genes <- data.frame(start=c(17871610,20186151,22225149,22553187,22556763,22561894,22573388),
end=c(17873915,20347811,22228342,22555052,22559742,22566321,22575503),
sclr=c(1,2,3,4,4,4,4),
LG=c("LG09","LG12-1","LG12-2","LG17","LG17","LG17","LG17"),
name=c("sox10",'casz1',"hoxc13a","sws2a\u03B1","sws2a\u03B2","sws2b","lws"))
genes <- genes %>% mutate(Nx1 = (start+scling[sclr])/10000,Nx2 = (end+scling[sclr])/10000,
labPOS = (Nx1+Nx2)/2)
genes$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
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')+
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')
return(p1)
}
\ No newline at end of file
0_data/0_scripts/S16.genomeWide_box.R deleted 100644 → 0
View file @ 89b22387
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$run,levels=c('Global',"Panana","Belize","Honduras",
"H. nigricans","H. puella","H. unicolor"))
dt2 <- BW %>%
group_by(run) %>%
summarise(meanR2=mean(R.2,na.rm = T),medR2=median(R.2,na.rm = T)) %>%
gather(key = 'type',value = 'val',2:3)
BC <-rgb(.7,.7,.7)
clr <-colorRampPalette(colors = c('white',BC,'black'))(8)
pBOX <- ggplot(BW,aes(x=run,y=R.2))+
geom_boxplot(fill=BC,width=.7,outlier.size = .1)+
#coord_fixed(ylim=c(0,.031),ratio = 250)+
geom_point(inherit.aes = F, data=dt2,aes(x=run,y=val,fill=type),shape=23,size=1)+
ggtitle(expression(Genome~wide~ILD~(italic(r)^2)))+
scale_x_discrete(labels = expression(Global,Panama,Belize,Honduas,
italic("H. nigricans"),italic("H. puella"),italic("H. unicolor")))+
scale_y_continuous()+
scale_fill_manual('',values = clr[c(6,1)],labels=c('mean','median'))+
guides(shape = guide_legend(ncol = 1))+
theme(legend.position = c(-.4,1.27),
text = element_text(size=10),
axis.title.y = element_blank(),
axis.title.x = element_blank(),
axis.text.y = element_text(size=7),
axis.text.x = element_text(size=7,angle=45,hjust = 1),
panel.background = element_blank(),
plot.background = element_blank())
\ No newline at end of file
0_data/0_scripts/S16.peakArea_box.R deleted 100644 → 0
View file @ 89b22387
dataBoxGenes <- data.frame(R.2=c(),run=c(),stringsAsFactors = F)
for (file in dir("../../2_output/08_popGen/07_LD/",pattern = "interchrom.hap.ld.gz")) {
nm <- str_remove_all(file, "spotlight.") %>% str_remove_all(.,".interchrom.hap.ld.gz")
if(nm %in% c("global","uni","pue","nig","hon","bel","boc")){
dataBoxGenes <- read.csv(gzfile(paste('../../2_output/08_popGen/07_LD/',file,sep='')),sep='\t') %>%
mutate(run = nm) %>%
select(R.2,run) %>%
rbind(dataBoxGenes,.)
}
}
dataBoxGenes$xS <- factor(dataBoxGenes$run,
levels = c("global","boc","bel","hon","nig","pue","uni"))
BoxGenes_summary <- dataBoxGenes %>%
group_by(xS) %>%
summarise(run = run[1],