R: Conversion among phylogenetic network 0bjects

as.networx {phangorn} | R Documentation

## Conversion among phylogenetic network 0bjects

### 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 = c("none", "2D", "3D"), ...)

    ## 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"`.

### Note

The internal representation is likely to change.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### 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)

[Package phangorn version 2.6.2 Index]