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". The argument "coord" allows to create coordinates, with options are "none", "equal angle", "3D", "2D" and "outline" (Bagci et al. 2021).

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

Bagci, C., Bryant, D., Cetinkaya, B. and Huson, D.H. (2021), Microbial Phylogenetic Context Using Phylogenetic Outlines. Genome Biology and Evolution. Volume 13. Issue 9. evab213

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)

spl <- allCircularSplits(5)
plot(as.networx(spl))
plot(as.networx(spl, coord="outline"))
## Not run: 
# also see example in consensusNet
example(consensusNet)

## End(Not run)

KlausVigo/phangorn documentation built on June 9, 2025, 5:44 a.m.