I am trying to make a haplotype network out of the COI marker for a dataset of 291 Microtus sp. sequences. I am concerned because there seems to be a 1:1 haplotype to sequence ratio. Additionally, I am having trouble formatting my haplotype network. I would like it to show pie charts and possibly be linked with geography.

This is the code that I have so far:

#Align the Sequeces
stringset <- DNAStringSet(MicrotusMarker$nucleotides)
MicrotusAlignment <- DNAStringSet(muscle::muscle(stringset, gapopen = -10000))

#Determine the Haplotypes
MicrotusBin <- as.DNAbin(MicrotusAlignment)
MicrotusHaplotypes <- haplotype(MicrotusBin)
attr(MicrotusHaplotypes, "index")[[1]]
plot(sort(MicrotusHaplotypes))

#Haplotype Network
HaploNet <- haploNet(MicrotusHaplotypes, d = NULL, getProb = TRUE)
plot(HaploNet, size = attr(HaploNet,"freq"), scale.ratio = 10, cex = 2, pie = NULL)