phangorn (version 2.12.1)

plot.networx: plot phylogenetic networks

Description

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

Usage

# S3 method for networx
plot(x, type = "equal angle", 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, underscore = FALSE, angle = 0, digits = 3,
  ...)

Value

plot.networx returns invisibly a list with paramters of the plot.

Arguments

x

an object of class "networx"

type

"3D" to plot using rgl or "equal angle" and "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.

underscore

a logical specifying whether the underscores in tip labels should be written as spaces (the default) or left as are (if TRUE).

angle

rotate the plot.

digits

if edge labels are numerical a positive integer indicating how many significant digits are to be used.

...

Further arguments passed to or from other methods.

Author

Klaus Schliep

Details

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.

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, as.networx, evonet, as.phylo, densiTree, nodelabels

Examples

set.seed(1)
tree1 <- rtree(20, rooted=FALSE)
sp <- as.splits(rNNI(tree1, n=10))
net <- as.networx(sp)
plot(net)
plot(net, direction="axial")
if (FALSE) {
# also see example in consensusNet
example(consensusNet)
}