R/coords.monmonier.R

In adegenet: Exploratory Analysis of Genetic and Genomic Data

coords.monmonier <- function(x){

if (!inherits(x, "monmonier")) stop("Use only with 'monmonier' objects")

xy.full <- x$xy
n.points <- nrow(xy.full)
k <- 1

#cn list to cn matrix
cn.matr <- matrix(data = 0, nrow = n.points, ncol = n.points)

for(i in 1:n.points){
	eval <- is.element(c(1:n.points), x$cn[[i]])
	cn.matr[i,which(eval == TRUE)] <- 1
	}

#halfway <- matrix(data = NA, nrow = (n.points^2-n.points)/2, ncol = 4)
halfway <- matrix(data = NA, nrow = sum(cn.matr)/2, ncol = 4)
colnames(halfway) <- c("x.hw","y.hw","first","second")

for(first in 1:(n.points-1)){
for(second in (first+1):n.points){
	if(cn.matr[first,second] == 1){
	halfway[k,] <- c(
		(xy.full[first,1]+xy.full[second,1])/2,
		(xy.full[first,2]+xy.full[second,2])/2,
		first, second)
	k <- k+1}
	}}

output=list()
for(run in 1:x$nrun){
	runname <- paste('run',run,sep='')
	output[[runname]] <- list(dir1=list(),dir2=list())

dir1.in <- x[[runname]]$dir1$path
output[[runname]]$dir1 <- matrix(data = NA, nrow = nrow(dir1.in), ncol = 4)
colnames(output[[runname]]$dir1) <- c("x.hw","y.hw","first","second")
rownames(output[[runname]]$dir1) <- rownames(x[[runname]]$dir1$path)
for(i in 1:nrow(dir1.in)){
	eval.x <- is.element(halfway[,1], dir1.in[i,1])
	eval.y <- is.element(halfway[,2], dir1.in[i,2])
	output[[runname]]$dir1[i,] <- halfway[which(eval.x == TRUE & eval.y == TRUE),]
	}

dir2.in <- x[[runname]]$dir2$path
output[[runname]]$dir2 <- matrix(data = NA, nrow = nrow(dir2.in), ncol = 4)
colnames(output[[runname]]$dir2) <- c("x.hw","y.hw","first","second")
rownames(output[[runname]]$dir2) <- rownames(x[[runname]]$dir2$path)
for(i in 1:nrow(dir2.in)){
	eval.x <- is.element(halfway[,1], dir2.in[i,1])
	eval.y <- is.element(halfway[,2], dir2.in[i,2])
	output[[runname]]$dir2[i,] <- halfway[which(eval.x == TRUE & eval.y == TRUE),]
	}
}

return(output)
}