I have 20 DNA sequences from 4 sampling location, 5 individual each location. I would like to make haplotype network using R studio. Based on the analysis, It was written that I have 8 haplotypes. However, I cannot give different color for each location, especially when there are sharing haplotype between locations.
Here is my script
library("ape")
library("pegas")
read.dna("FIKS YA.fasta", format="fasta") -> Naso
Naso
NasoHaps <- haplotype(Naso)
NasoHaps
NasoNet <- haploNet(NasoHaps)
pop <- rep(paste0("pop", 1:4), each = 5)
region <- rep(c("regA", "regB", "regC", "regD"), each = 5)
table(region, pop)
h <- haplotype(Naso)
h
d <- dist.dna(NasoHaps, "N")
nt <- rmst(d, quiet = TRUE)
nt
plot(nt)
This is the output
Could anyone help me how to distinguish each haplotype based on the sampling locations and give them different color based on sampling locations? please note: these instructions are ambiguos
pop <- rep(paste0("pop", 1:4), each = 5)
region <- rep(c("regA", "regB", "regC", "regD"), each = 5)
•
written
by
amirandi1808 •
1 answer
Hi amirandi, I write some R code using your variable names to answer your question. First, we need a hap.pie file which is used to set the location and colors for each pie.
> hap.pies <- with(
> stack(setNames(attr(NasoHaps,'index'),1:length(attr(NasoHaps,'index')))),
> table(hap=as.numeric(as.character(ind)),pop=samples[values,region]) )
here let me explain the codes, hap.pies is what we need to set the location or other information for haplotypes.
> attr(NasoHaps,index)
hap file generated by haplotype(Naso) contains the haplotype and related fasta sequences. The format is like: index1(haplotype 1) : sequence 1; sequence 2. sample file is a file where you put the region information for each fasta sequence( the order of sample file is the same as fasta file). it contains two columns: sequence id and region;
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