phangorn (version 1.7-4)

plot.networx: Plot phylogenetic networks

Description

plot.networx plot phylogenetic network or split graphs.

Usage

## S3 method for class 'networx':
plot(x, type = "3D", show.tip.label = TRUE, show.edge.label=FALSE, show.nodes = FALSE, tip.color = "blue", edge.color = "grey", edge.width = 3, font = 3, cex = 1, ...)

Arguments

x

an object of class "networx"

type

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

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.

show.nodes

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

tip.color

the colours used for the tip labels.

edge.color

the colours used to draw edges.

edge.width

the width used to draw edges.

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.

...

Further arguments passed to or from other methods.

References

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

See Also

consensusNet, hadamard, distanceHadamard, layout.kamada.kawai

Examples

see example in consensusNet 
example(consensusNet)