Conversion among phylogenetic network objects

as.networx convert splits objects into a networx object. And most important there exists a generic plot function to plot phylogenetic network or split graphs.

Usage

as.networx(x, ...)

# S3 method for splits
as.networx(x, planar = FALSE, coord = "none", ...)

# S3 method for phylo
as.networx(x, ...)

Arguments

x: an object of class "splits" or "phylo"
...: Further arguments passed to or from other methods.
planar: logical whether to produce a planar graph from only cyclic splits (may excludes splits).
coord: add coordinates of the nodes, allows to reproduce the plot.

Details

A networx object hold the information for a phylogenetic network and extends the phylo object. Therefore some generic function for phylo objects will also work for networx objects. The argument planar = TRUE will create a planar split graph based on a cyclic ordering. These objects can be nicely plotted in "2D".

Note

The internal representation is likely to change.

References

Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W. (2017), Intertwining phylogenetic trees and networks. Methods Ecol Evol. 8, 1212--1220. doi:10.1111/2041-210X.12760

Author

Klaus Schliep klaus.schliep@gmail.com

Examples


set.seed(1)
tree1 <- rtree(20, rooted=FALSE)
sp <- as.splits(rNNI(tree1, n=10))
net <- as.networx(sp)
plot(net)

if (FALSE) {
# also see example in consensusNet
example(consensusNet)
}