phangorn (version 2.12.1)

as.networx: Conversion among phylogenetic network objects

Description

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, ...)

Value

an object of class networx.

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.

Author

Klaus Schliep

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".

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

See Also

consensusNet, neighborNet, splitsNetwork, hadamard, distanceHadamard, plot.networx, evonet, as.phylo

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)
}