as.networx: Conversion among phylogenetic network objects

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

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 class 'splits'
as.networx(x, planar = FALSE, coord = "none", ...)

## S3 method for class '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".

Value

an object of class networx.

Note

The internal representation is likely to change.

Author(s)

Klaus Schliep [e-mail]

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)
## Not run: 
# also see example in consensusNet
example(consensusNet)

## End(Not run)

KlausVigo/phangorn documentation built on Feb. 14, 2025, 8:24 a.m.