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I'm working in R. From a dataset of about 150 sequences I want to draw an haplotype network.

I used haploNet function in the "pegas" library. The problem is that I obtain a network with a lot of "2" labels (labels within a grey square indicating 2). I don't know exactly what is it.

In addition I have several overlapping circles.

Do you have any suggestions?

CafféSospeso
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  • Can you insert the network so we can see it? Can you provide a reproducible data set (using dput())? – lawyeR May 18 '15 at 18:19
  • I don't Know what is it dput() but I can put the script. – CafféSospeso May 18 '15 at 18:43
  • I cannot put a picture in the question, I need at least 10 reputations.. – CafféSospeso May 18 '15 at 18:54
  • With your "dataset", which is probably a data frame, you can reproduce it quickly so people on StackOverflow can see the problem. if you data frame is called "sequences" you might want to reduce it -- since even a small part should show the problem, and enter dput(sequences) in the console. Copy the result and paste it into your question. Then add the code that uses the data frame and the haploNet function so others can create the plot on their own (after installing pegas), – lawyeR May 18 '15 at 19:52
  • There is a related question [here](http://stackoverflow.com/questions/33347752/how-to-plot-a-network-without-background-connection-or-labels-r-pegas) – hugot Oct 27 '15 at 15:32

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