plot.pml: Plot phylogeny of a pml object

In KlausVigo/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", ...,
  adj = NULL, digits = 2, method = "FBP")

Arguments

x	an object of class pml.
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.
adj	one or two numeric values specifying the horizontal and vertical justification of the text or symbols of the support values.
digits	integer indicating the number of decimal places.
method	either "FBP" the classical bootstrap (default), "TBE" (transfer bootstrap) or "MCC" for assigning clade credibilities.

Value

plot.pml returns the pml object x.

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)

KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.