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## The function to plot diversity (q=1,2,3)
qDplot = function(x, q, ncode) {
# q=1,2,3
D00 = qD(x, q = 0, ncode)
D11 = qD(x, q = 1, ncode)
D22 = qD(x, q = 2, ncode)
D0 = colMeans(D00)
D1 = colMeans(D11)
D2 = colMeans(D22)
if (q == 0) {
data = melt(D0)
data = data.frame("popname" = rownames(data), D0)
requireNamespace("ggplot2")
p = ggplot(data, aes(x = popname, y = D0, group = 1)) + geom_line(size = 1) + ylim(0, (max(D0) + 5)) + ylab(paste("Diversity q=",
q)) + xlab("Populations") + geom_point(size = 1) + theme(axis.text.x = element_text(angle = 30, hjust = 1))
} else if (q == 1) {
data = melt(D1)
data = data.frame("popname" = rownames(data), D1)
requireNamespace("ggplot2")
p = ggplot(data, aes(x = popname, y = D1, group = 1)) + geom_line(size = 1) + ylim(0, (max(D1) + 5)) + ylab(paste("Diversity q=",
q)) + xlab("Populations") + geom_point(size = 1) + theme(axis.text.x = element_text(angle = 30, hjust = 1))
} else if (q == 2) {
data = melt(D2)
data = data.frame("popname" = rownames(data), D2)
requireNamespace("ggplot2")
p = ggplot(data, aes(x = popname, y = D2, group = 1)) + geom_line(size = 1) + ylim(0, (max(D2) + 5)) + ylab(paste("Diversity q=",
q)) + xlab("Populations") + geom_point(size = 1) + theme(axis.text.x = element_text(angle = 30, hjust = 1))
} else if (q == "all") {
qtotal = cbind(D0, D1, D2)
rownames(qtotal) = gsub(",", "", rownames(qtotal))
reshape2::melt
data = melt(qtotal)
colnames(data) = c("Populations", "qD", "Diversity")
requireNamespace("ggplot2")
p = ggplot(data, aes(x = Populations, y = Diversity, group = qD, colour = qD)) + ylab("Diversity") + xlab("Populations") +
geom_line(size = 1) + ylim(0, (max(data$Diversity) + 5)) + geom_point(aes(shape = qD), size = 2) + theme(axis.text.x = element_text(angle = 30,
hjust = 1))
} else {
stop("none of the q is workable")
}
return(p)
}
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