# as.networx

0th

Percentile

##### Conversion among phylogenetic network 0bjects

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.

Keywords
plot
##### Usage
as.networx(x, ...)# S3 method for splits
as.networx(x, planar = FALSE, coord = c("none", "2D",
"3D"), ...)# S3 method for 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.

##### 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

consensusNet, neighborNet, splitsNetwork, hadamard, distanceHadamard, plot.networx, evonet, as.phylo

##### Aliases
• as.networx
• networx
• as.networx.splits
• as.networx.phylo
##### Examples
# NOT RUN {
set.seed(1)
tree1 <- rtree(20, rooted=FALSE)
sp <- as.splits(rNNI(tree1, n=10))
net <- as.networx(sp)
plot(net, "2D")
# }
# NOT RUN {
# also see example in consensusNet
example(consensusNet)
# }
# NOT RUN {
# }

Documentation reproduced from package phangorn, version 2.5.5, License: GPL (>= 2)

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