[R-sig-genetics] How to avoid overlapping pies when plotting haplotype networks when using the packages 'pegas' and 'ape' in R

[Steen Wilhelm Knudsen]

Dear All subscribers of the R-sig-genetics Archives,

I have a question to plotting haplotype networks using the packages 'pegas' and 'ape' in R.
I often end up with overlapping pies for haplotypes, and appear unable to work around it by adjusting the 'scale.ratio' when making the plot.
I could abstain from using the frequency of the haplotypes as determining the size of the pies. But I would prefer to keep this setting, so that the diagram ends up having circles that reflects the sample size. Instead I would like to know if I can adjust the length of the lines between the pies, and perhaps determine where the pies are to be positioned in the plot.
My understanding of the lines between the pies is that these lines are adjusted in length to reflect the number of differences between the haplotypes. This is fine, but seems to prevent me from avoiding the pies being overlaid. I am happy to have incorrect lengths for the connecting lines, and can instead just use the option that adds a number on such a connecting line, a number that  informs how many differences there are between the haplotypes being connected by the line.
I have had a go with the 'replot' function, but for some reason I can only select the same pie over and over again. Also, I would prefer to do the entire plotting by code alone. One of my motivations from switching away from 'Network', 'popart' and 'TCS' was to avoid all the clicking and moving around with pies.

I have placed my input file here
https://github.com/monis4567/Mnemiopsis_leidyi_in_NE_Atlantic/blob/main/suppmat01_inp_files/algn_Mnelei_18s_10.aligned.fasta.fas

My R code for making a haplotype network with this input file can be found here
https://github.com/monis4567/Mnemiopsis_leidyi_in_NE_Atlantic/blob/main/suppmat03_Rcodes/Rcode_example02_make_haplonet_v01.R



Can anyone suggest me how I can adjust this code to get haplotype networks where pies do not overlap, or how I can adjust the length of the connecting lines, to avoid the pies overlapping. Or suggest me a different solution that can sort out my problem, but preferably let me solve the issue of presenting a diagram that is possible to read while performing all the coding in R, and not having to adjust the plot manually afterwards?

Thanks in advance for your time and help,

Steen Knudsen
Natural History Museum of Denmark



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