install.packages("BiocManager")
library(limma)


khao<-readLines("KhaoYai_woodpeckers.txt")
kaeng<-readLines("KaengKrachan_woodpeckers.txt")
doi<-readLines("Doi_woodpeckers.txt")
allpeckers<-union(khao,union(kaeng,doi))
in_all_three_parks<-intersect(doi,intersect(kaeng,khao))

data<-matrix(NA,nrow=length(allpeckers), ncol=3) 
colnames(data)<-c("kaeng","khao","doi") 
data<-as.data.frame(data) 
for (i in 1: length(allpeckers)){
ifelse (allpeckers[i] %in% kaeng,data$kaeng[i]<-1,data$kaeng[i]<-0) 
ifelse (allpeckers[i] %in% khao,data$khao[i]<-1,data$khao[i]<-0)
ifelse (allpeckers[i] %in% doi,data$doi[i]<-1,data$doi[i]<-0)
}
data
m2<-vennCounts(data) 
m2
vennDiagram(m2,names=c("Kaeng Krachan", "Khao Yai", "Doi Inthanon"), main="Woodpecker species", circle.col= c("coral","paleturquoise3","bisque3"),lwd=3) 
mtext ("Aves: Picidae")

X<-structure(vd1,class = "VennCounts")


######
plot(NULL,xlim=c(0,2),ylim=c(0,2),axes=F,xlab="",ylab="",main="Woodpecker overlap between three Thai N.P.s")
cx1<-0.7
cx2<-1.3
cx3<-1
cy1<-0.8
cy2<-0.8
cy3<-0.8+(((cx2-cx1)*3^0.5)/2)
theta<-seq(0,2*pi,0.01) 
radius<-0.5
x<-radius*cos(theta) 
y<-radius*sin(theta)
lines(x+cx1,y+cy1,lwd=3,col="blue")
lines(x+cx3,y+cy3,lwd=3,col="red")
lines(x+cx2,y+cy2,lwd=3,col=" darkgreen ")
text(0.7,0.22,"Kaeng Krachan N.P.",col="blue")
text(0.45,1.8,"Khao Yai N.P.",col="darkgreen")
text(cy3,0.22,"Doi Inthanon N.P.",col="red")
all<-intersect(intersect(kaeng,khao),doi)
text(1,1.04,length(all))

kk_ky_only<-length(intersect(kaeng,khao))-length(all)
kk_di_only<-length(intersect(kaeng,doi))-length(all)
di_ky_only<-length(intersect(doi,khao))-length(all)
text(1,0.65,kk_di_only)
text(0.75,1.1,kk_ky_only)
text(1.25,1.1,di_ky_only)
kk<-length(kaeng)-length(all)-kk_ky_only-kk_di_only
ky<-length(khao)-length(all)-di_ky_only-kk_ky_only
di<-length(doi)-length(all)-di_ky_only-kk_di_only
text(0.6,0.65,kk)
text(1.4,0.65,ky)
text(1,1.4,di)