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#### Pairwise DeltaD across loci
plotdiff1 = function(x, ncode) {
diveRsity::readGenepop
gp = ncode
fr = readGenepop(x, gp, bootstrap = FALSE)
af = fr$allele_freq
DeltaD = function(abun, struc) {
## Chao et al, 2017
n = sum(abun)
N = ncol(abun)
ga = rowSums(abun)
gp = ga[ga > 0]/n
G = sum(-gp * log(gp))
H = nrow(struc)
A = numeric(H - 1)
W = numeric(H - 1)
Diff = numeric(H - 1)
wi = colSums(abun)/n
W[H - 1] = -sum(wi[wi > 0] * log(wi[wi > 0]))
pi = sapply(1:N, function(k) abun[, k]/sum(abun[, k]))
Ai = sapply(1:N, function(k) -sum(pi[, k][pi[, k] > 0] * log(pi[, k][pi[, k] > 0])))
A[H - 1] = sum(wi * Ai)
if (H > 2) {
for (i in 2:(H - 1)) {
I = unique(struc[i, ])
NN = length(I)
ai = matrix(0, ncol = NN, nrow = nrow(abun))
c
for (j in 1:NN) {
II = which(struc[i, ] == I[j])
if (length(II) == 1) {
ai[, j] = abun[, II]
} else {
ai[, j] = rowSums(abun[, II])
}
}
pi = sapply(1:NN, function(k) ai[, k]/sum(ai[, k]))
wi = colSums(ai)/sum(ai)
W[i - 1] = -sum(wi * log(wi))
Ai = sapply(1:NN, function(k) -sum(pi[, k][pi[, k] > 0] * log(pi[, k][pi[, k] > 0])))
A[i - 1] = sum(wi * Ai)
}
}
Diff[1] = (G - A[1])/W[1]
if (H > 2) {
for (i in 2:(H - 1)) {
Diff[i] = (A[i - 1] - A[i])/(W[i] - W[i - 1])
}
}
Diff = Diff
out = matrix(c(Diff), ncol = 1)
return(out)
}
v1 = c("ecosystem", "region1", "pop1")
v2 = c("ecosystem", "region1", "pop2")
str = data.frame(v1, v2)
str = as.matrix(str)
npops = fr$npops
nloci = fr$nloci
Dmat = list()
for (l in 1:nloci) {
Dmat[[l]] = matrix(data = 0, nrow = npops, ncol = npops)
for (i in 1:npops) {
for (j in 1:npops) {
## for every loci has one differentiation value
Dmat[[l]][i, j] = DeltaD((af[[l]][, c(i, j)]), str)[2] ### select two pops from allelefrequency
}
}
}
pwdeltaD = lapply(Dmat, function(x) {
x[x != 0]
})
pwdeltaD <- do.call(cbind, lapply(pwdeltaD, as.vector))
pwdeltaD = unique(pwdeltaD)
Loci = c(1:fr$nloci)
reshape2::melt
pwd <- melt(pwdeltaD)
colnames(pwd) = c("pwpop", "Loci", "DeltaD")
ylab = c("Pairwise Genetic Differentiation Across Loci (Delta_D)")
requireNamespace("ggplot2")
p1 <- ggplot(pwd, aes(x = Loci, y = pwd$DeltaD, colour = factor(Loci))) + ylab(ylab) + ylim(-0.25, 1) + geom_jitter(size = 4,
alpha = 0.8) + scale_x_continuous("Loci", labels = as.character(pwd$Loci), breaks = pwd$Loci) + geom_hline(yintercept = mean(pwd$DeltaD),
linetype = "dashed", color = "red", size = 1) + geom_smooth(method = loess, se = FALSE, fullrange = TRUE)
p2 = boxplot(pwd$DeltaD ~ pwd$Loci, xlab = "Loci", ylab = "Diff1", main = "Pairwise Genetic Differentiation Across Loci (Delta_D)")
return(list(p1 = p1, p2 = p2))
}
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