Plot hybrid Triangle

#-------------------------------------------------------------------------------

# This script performs hybrid index estimation with introgress (Gompert & Buerkle 2010).

#-------------------------------------------------------------------------------

# Install dependencies

install.packages("introgress",dependencies=TRUE)

library(introgress)


## produce triangle plots
#
## use prepare.data to produce introgress.data
introgress.data<-prepare.data(admix.gen=AdmixDataSim1,
                              loci.data=loci.data,
                              parental1="P1", parental2="P2",
                              pop.id=FALSE, ind.id=TRUE,
                              fixed=TRUE)

## estimate hybrid index
hi.index<-est.h(introgress.data=introgress.data,
                loci.data=loci.data, fixed=TRUE, p1.allele="P1",
                p2.allele="P2")

## Estimate interspecific heterozygosity
int.het<-calc.intersp.het(introgress.data=hybrid.index)

## make plot
triangle.plot(hi.index=hi.index, int.het=int.het, pdf=FALSE)

#######Plotting triange plot raw code

hi.index=hybrid.index
int.het=int.het 
hi.index<-hi.index[,2]
hi.index$Colour="black"
hi.index$Colour[hi.index$h>=0.5]="red"
hi.index$Colour[hi.index$h<=0.5]="blue"
# plot
plot(data$col_name1,data$col_name2, ylim=c(0,5), col=data$Colour, ylim=c(0,10))
plot(hi.index$h,int.het,xlab="Hybrid index",ylab="Interspecific heterozygosity",xlim=c(0,1),ylim=c(0,1),pch=19, col=hi.index$Colour, cex=1.5)
lines(c(0,0.5),c(0,1),lwd = 2)
lines(c(0.5,1),c(1,0),lwd = 2)

text(0.5,0.15,"Historical Introgression")
text(0.5,0.9,"F1")
text(0.5,0.52,"F2")
text(0.2,0.65,"Bx P1")
text(0.8,0.65,"Bx P2")
#Parental
text(0.1,0.02,"P1 S.cinereus")
text(0.9,0.02,"P2 S.ugyunak")