phangorn (version 2.1.1)

plot.networx: Phylogenetic networks

Description

as.networx convert splits objects into a networx object. plot.networx plot phylogenetic network or split graphs.

Usage

as.networx(x, ...)
"as.networx"(x, planar = FALSE, coord = c("none", "2D", "3D"), ...)
"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)

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.

...

Further arguments passed to or from other methods.

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 = FALSE 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). 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

See Also

consensusNet, neighborNet, splitsNetwork, hadamard, distanceHadamard, layout_with_kk, evonet, as.igraph, densiTree

Examples

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)
# ## End(Not run)