BMhyd (version 1.2-8)

PlotNetwork: Phylogenetic Network Plot

Description

This function plots the phylogenetic network with required number of taxa . The hybrids with gene flow direction.

Usage

PlotNetwork(phy, flow, col.non="black", col.hybrid="red", col.donor="blue", 
	name.padding=1.5, cex=1, xlab="", bty="n", head.length=0.2, edge.width=2, 
	col.tree="darkgray", col.arrow="red", arrow.width=1, ...)

Arguments

phy

a class of phylo tree

flow

a flow structure of gene flow

col.non

color of non hybrid taxa

col.hybrid

color of hybrid taxa

col.donor

color of the donor

name.padding

the size that allowed for the plot in the x axis

cex

number indicating the amount by which plotting text and symbols should be scaled relative to the default. 1=default, 1.5 is 50 percent larger, 0.5 is 50 percent smaller, etc.

xlab

X axis label using font and character expansion par("font.lab") and color par("col.lab").

bty

the type of box to be drawn around the legend. The allowed values are "o" (the default) and "n".

head.length

length of the head.

edge.width

width of the edges.

col.tree

color of the tree.

col.arrow

color of gene flow arrow.

arrow.width

width of the arrow.

...

other arugments

Value

plot of the network that involves the phylogeny and the gene flow direction.

Details

This function generates plots for network models. It first draws the phylogetic tree for the given species. Then uses the gene flow data to draw the arrow from the donor species to recipient species. The hybrid taxa are shown in read with the gene flow direction from the donor species (colored in blue).

References

Jhwueng D.C. and O'Meara B.C. 2015. Trait evolution on phylogenetic networks. Submitted.

Examples

	#set the number of non hybrid species
	ntax.nonhybrid<-10
	#set the number of hybrid species
	ntax.hybrid<-3
	#simulate the network with desired species
	network<-SimulateNetwork(ntax.nonhybrid=ntax.nonhybrid, ntax.hybrid=ntax.hybrid,
	flow.proportion=0.5, origin.type='clade', birth = 1, death = 0.5, sample.f = 0.5, 
	tree.height = 1, allow.ghost=FALSE)
	#plot the network
	PlotNetwork(network$phy,network$flow)