Conversion among phylogenetic network objects

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.

Value

an object of class networx.

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).

Note

The internal representation is likely to change.

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

Author

Klaus Schliep klaus.schliep@gmail.com

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"))

if (FALSE) { # \dontrun{
# also see example in consensusNet
example(consensusNet)
} # }