as.networx

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Phylogenetic networks

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, ...)

# S3 method for networx plot(x, type = "3D", use.edge.length = TRUE, show.tip.label = TRUE, show.edge.label = FALSE, edge.label = NULL, show.node.label = FALSE, node.label = NULL, show.nodes = FALSE, tip.color = "black", edge.color = "black", edge.width = 3, edge.lty = 1, split.color = NULL, split.width = NULL, split.lty = NULL, font = 3, cex = par("cex"), cex.node.label = cex, cex.edge.label = cex, col.node.label = tip.color, col.edge.label = tip.color, font.node.label = font, font.edge.label = font, ...)

Arguments
x

an object of class "splits" (as.networx) or "networx" (plot)

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.

type

"3D" to plot using rgl or "2D" in the normal device.

use.edge.length

a logical indicating whether to use the edge weights of the network to draw the branches (the default) or not.

show.tip.label

a logical indicating whether to show the tip labels on the graph (defaults to TRUE, i.e. the labels are shown).

show.edge.label

a logical indicating whether to show the tip labels on the graph.

edge.label

an additional vector of edge labels (normally not needed).

show.node.label

a logical indicating whether to show the node labels (see example).

node.label

an additional vector of node labels (normally not needed).

show.nodes

a logical indicating whether to show the nodes (see example).

tip.color

the colors used for the tip labels.

edge.color

the colors used to draw edges.

edge.width

the width used to draw edges.

edge.lty

a vector of line types.

split.color

the colors used to draw edges.

split.width

the width used to draw edges.

split.lty

a vector of line types.

font

an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic).

cex

a numeric value giving the factor scaling of the labels.

cex.node.label

a numeric value giving the factor scaling of the node labels.

cex.edge.label

a numeric value giving the factor scaling of the edge labels.

col.node.label

the colors used for the node labels.

col.edge.label

the colors used for the edge labels.

font.node.label

the font used for the node labels.

font.edge.label

the font used for the edge labels.

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". So far not all parameters behave the same on the the rgl "3D" and basic graphic "2D" device.

Often it is easier and safer to supply vectors of graphical parameters for splits (e.g. splits.color) than for edges. These overwrite values edge.color.

Note

The internal representation is likely to change.

References

Dress, A.W.M. and Huson, D.H. (2004) Constructing Splits Graphs IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 1(3), 109--115

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, layout_with_kk, evonet, as.igraph, densiTree

Aliases
  • as.networx
  • networx
  • as.networx.splits
  • as.networx.phylo
  • plot.networx
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 2.4.0, License: GPL (>= 2)

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