plot.pml: Plot phylogeny of a pml object

In phangorn: Phylogenetic Reconstruction and Analysis

Plot phylogeny of a pml object

Description

plot.pml is a wrapper around plot.phylo with different default values for unrooted, ultrametric and tip dated phylogenies.

Usage

## S3 method for class 'pml'
plot(x, type = "phylogram", direction = "rightwards", ...)

Arguments

x	an object of class pml or phyDat.
type	a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial", "tidy", or any unambiguous abbreviation of these.
direction	a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards".
...	further parameters to be passed to plot.phylo.

Value

plot.pml returns invisibly a list with arguments dexcribing the plot. For further details see the plot.phylo.

Author(s)

Klaus Schliep [e-mail]

See Also

plot.phylo, axisPhylo, add.scale.bar

Examples

fdir <- system.file("extdata/trees", package = "phangorn")
tmp <- read.csv(file.path(fdir,"H3N2_NA_20.csv"))
H3N2 <- read.phyDat(file.path(fdir,"H3N2_NA_20.fasta"), format="fasta")
dates <- setNames(tmp$numdate_given, tmp$name)

fit_td <- pml_bb(H3N2, model="JC", method="tipdated", tip.dates=dates,
                 rearrangement="none", control = pml.control(trace = 0))
plot(fit_td, show.tip.label = FALSE)
# Same as:
# root_time <- max(dates) - max(node.depth.edgelength(fit_td$tree))
# plot(fit_td$tree, show.tip.label = FALSE)
# axisPhylo(root.time = root_time, backward = FALSE)
plot(fit_td, show.tip.label = FALSE, direction="up")

fit_unrooted <- pml_bb(H3N2, model="JC", rearrangement="none",
                       control = pml.control(trace = 0))
plot(fit_unrooted, cex=.5)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.