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emmanuelparadis / pegas

Population and Evolutionary Genetics Analysis System
GNU General Public License v2.0
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Known haplotype frequencies #70

Closed Timzladen closed 2 years ago

Timzladen commented 2 years ago

Hi Emmanuel, I have a set of sequences derived from metabarcoding that I want to use to reconstruct a haplotype network. However, I encountered a problem, since the sequences all return unique haplotypes when processed with the haplotype function. Now this is not a surprise, since my set was denoised and clustered essentially producing 97% OTUs. But I would still like to see the representation of each OTU in a pie chart format with the haplonet function. However, I don't see to find a way to introduce the individual OTU frequencies into the picture. Some OTUs are way more abundant than others and I would like to compare the metabarcoding haplotype network to a haplotype network I have generated with specimens I collected in the field. Essentially, I would like to join a phylogenetic tree and a heatmap of occurrences in different samples into a haplotype network.

So can you recommend me a way to introduce the haplotype frequencies as prior knowledge for haplonet generation?

emmanuelparadis commented 2 years ago

Hi Tim, Did you see the option pie in plot.haploNet? You may have a look at the function haploFreq too (although I'm not sure). See also vignette("PlotHaploNet") where there some additional info on plotting haplotypes. Emmanuel