R: plot phylogenetic networks

plot.networx {phangorn} | R Documentation

## 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 class '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, ...)

### Arguments

`x` | an object of class `"networx"`
`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

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.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### 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)
    ## Not run:
    # also see example in consensusNet
    example(consensusNet)

    ## End(Not run)

[Package phangorn version 2.6.2 Index]