Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. Example: network of alleles Network  in black and white of groups of alleles I just feel like there's got to be a better, more time effective way to do this.

  • $\begingroup$ Can you post a picture as an example? $\endgroup$
    – benn
    Apr 17 '18 at 18:04
  • $\begingroup$ imgur.com/a/MYuB5 . Here's a couple dumbed down examples of our current network figures. $\endgroup$
    – Ryan Fahy
    Apr 17 '18 at 18:12
  • $\begingroup$ You might want to take a look at Rgraphviz from bioconductor. $\endgroup$
    – benn
    Apr 17 '18 at 19:32
  • $\begingroup$ I haven't tried it, but this looks kinda cool: briatte.github.io/ggnet $\endgroup$ Apr 17 '18 at 20:39
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    $\begingroup$ What kind of data do you have? In which format? That would help to create an example of answers $\endgroup$
    – llrs
    Apr 18 '18 at 9:22

This is a haplotype map, where each node is proportional to the frequency of a given allele. The formal tool to do this is Network 5 found here. The problem with manaul haplotype maps is the area of the node should be proportional to the frequency, if this is not accurate it could be perceived to be misleading.

The approach for looking at each parsimonious state along a branch is a phylogenetics method which is performed via MacClade 4.0 ... requires an old Mac though.

  • $\begingroup$ What do network edges represent? $\endgroup$
    – Colin D
    May 10 '21 at 3:35

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