phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Value Author(s) See Also Examples

This function is intented to plot reticulate phylogenetic data (e.g. hyplotype ot genotype networks, "minimum spanning trees"). It is in an eraly state of development - use with care!

plotNetwork(m, freq, spread = 180, rotate = 0, mirror = FALSE, 
    freqmode = 2, loc = NULL, locorder = "lat", cex = 1, 
    col = "r", piecolrev = FALSE, contrast = 0, border = NA, 
    xshift = 0, yshift = 0, replace.names = FALSE, stp = NA, 
    modify = NULL)

`m`	A binary matrix of node connection: 1 means there is an edge between node[m] and node[n]; 0 means no edge.
`freq`	A named vector of haplotype frequencies; if omitted the frequency of each haplotype is taken to be 1.
`spread`
`rotate`	A numeric vector of length one: the angle of clock-wise rotation of the whole plot.
`mirror`	Logical: if `TRUE`, the whole plot is mirrored through X-axis.
`freqmode`	Currently not implemented.
`loc`	Currently not implemented.
`locorder`	Currently not implemented.
`cex`
`col`
`piecolrev`
`contrast`
`border`
`xshift`
`yshift`
`replace.names`	Logical: if `TRUE`, the names of the haplotypes are replaced by consecutive capital letters.
`stp`	Currently not implemented.
`modify`	Currently not implemented.

Currently no value implemented.

Christoph Heibl

mst, plot.mst

data(woodmouse)
mst <- mst(dist.dna(woodmouse))
plotNetwork(mst, mirror = TRUE)
plotNetwork(mst, replace.names = TRUE)

# include information about frequency of haplotypes
# -------------------------------------------------
freq <- c(1, 1, 7, 2, 2, 3, 3, 1, 1, 4, 1, 1, 1, 1, 2)
names(freq) <- rownames(mst)
plotNetwork(mst, freq = freq, replace.names = TRUE)