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

[Emmanuel Paradis]

Dear Steen,

There is no simple way to handle your problem. One possibility is to use the package 'network' which has a nicer algorithm to calculate the layout of nodes than pegas has. The good thing is that 'network' returns the coordinates which can then be input into plot.haploNet (see ?replot for something similar in pegas). Here's a possible solution:

## net3 is from your script
library(network)
xy <- plot(as.network(net3))
xy <- list(x = xy[, 1], y = xy[, 2])
size <- round(sqrt(attr(net3, "freq")))
plot(net3, size = size, xy = xy, pie = ind.hap3, legend = TRUE, threshold = 0)

Note the layout returned by network is random, so you can repeat the 2nd line above several times if you want, but it seems a single try is enough!

The second trick is to change the scale of the pie sizes using a square root transformation. I'm afraid that when the sizes of symbols are too contrasted, plot.haploNet() is really at a pain! I'll try to have a look at it if this can be improved.

In the last command, you'll still need to click on the plot to show where to draw the legend, but R will print the coordinates so these may be included in the script (or more simply you can delete the 'legend = TRUE' of you don't want the legend).

Note that you did a TCS network (has done by pegas::haploNet) which has a lot of alternative links (hence the 'threshold = 0' option). You may try an RMST network which has much less alternatives links:

d3 <- dist.dna(h3, "N", p = TRUE)
rmst3 <- rmst(d3)

Plotting can be done with:

xybis <- plot(as.network(rmst3))
xybis <- list(x = xybis[, 1], y = xybis[, 2])
plot(rmst3, size = sz, xy = xybis, pie = ind.hap3, legend = TRUE, threshold = 0)

Note that, if this is useful for you, you can use 'xy = xy' in the last command so that the layout of haplotypes will be identical with the two networks.

You may also look in more details this help page in network:

?network.layout.fruchtermanreingold

It explains how the change the parameters of the layout calculations.

HTH

Best,

Emmanuel

----- Le 2 Juin 22, à 9:07, Steen Wilhelm Knudsen swknudsen using snm.ku.dk a écrit :

> 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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