Computes a consensusNetwork from a list of trees Computes a networx
object from a collection of splits.
Source: R/consensusNet.R
consensusNet.Rd
Computes a consensusNetwork, i.e. an object of class networx
from a
list of trees, i.e. an class of class multiPhylo
. Computes a
networx
object from a collection of splits.
Arguments
- obj
An object of class multiPhylo.
- prob
the proportion a split has to be present in all trees to be represented in the network.
- ...
Further arguments passed to or from other methods.
Value
consensusNet
returns an object of class networx. This is
just an intermediate to plot phylogenetic networks with igraph.
References
Holland B.R., Huber K.T., Moulton V., Lockhart P.J. (2004) Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution, 21, 1459--61
Author
Klaus Schliep klaus.schliep@gmail.com
Examples
data(Laurasiatherian)
set.seed(1)
bs <- bootstrap.phyDat(Laurasiatherian, FUN = function(x)nj(dist.hamming(x)),
bs=50)
cnet <- consensusNet(bs, .3)
plot(cnet, angle=-60, direction="axial")
if (FALSE) {
library(rgl)
open3d()
plot(cnet, type = "3D", show.tip.label=FALSE, show.nodes=TRUE)
plot(cnet, type = "equal angle", show.edge.label=TRUE)
tmpfile <- normalizePath(system.file(
"extdata/trees/RAxML_bootstrap.woodmouse", package="phangorn"))
trees <- read.tree(tmpfile)
cnet_woodmouse <- consensusNet(trees, .3)
plot(cnet_woodmouse, type = "equal angle", show.edge.label=TRUE)
}