phangorn: as.networx – R documentation

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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 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

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)

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release