当使用 haploNet 包在单倍型网络上绘制一些图时，我使用了 Internet 上可用的脚本来执行此操作。不过我觉得有什么地方不对。该脚本以 woodmouse 示例的形式提供。我使用的代码是：
x <- read.dna(file="Masto.fasta",format="fasta")
h <- haplotype(x)
net <- haploNet(h)
plot(net)
plot(net, size = attr(net, "freq"), fast = TRUE)
plot(net, size = attr(net, "freq"))
plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8
table(rownames(x))
ind.hap<-with(
stack(setNames(attr(h, "index"), rownames(h))),
table(hap=ind, pop=rownames(x)[values])
)
ind.hap
plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8, pie=ind.hap)
legend(50,50, colnames(ind.hap), col=rainbow(ncol(ind.hap)), pch=20)
legend(x=7,y=10,c("Baeti ero","Felege weyni","Golgole naele","Hagare selam","Ruba feleg","Ziway"),c("red","yellow","green","turquoise","blue","magenta"))
但是，在绘制 ind.hap 时，您会注意到某些行不在正确的位置。你可以在这里看到这个：
pop
hap Baetiero ETH022 ETH742 Felegeweyni Golgolenaele Rubafeleg
I …