ape: plotTreeTime – R documentation

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ape

plotTreeTime

Plot Tree With Time Axis

Description

This function plots a non-ultrametric tree where the tips are not contemporary together with their dates on the x-axis.

Usage

plotTreeTime(phy, tip.dates, show.tip.label = FALSE, y.lim = NULL,
             color = TRUE, ...)

Arguments

`phy`	an object of class `"phylo"`.
`tip.dates`	a vector of the same length than the number of tips in `phy` (see details).
`show.tip.label`	a logical value; see `plot.phylo`.
`y.lim`	by default, one fifth of the plot is left below the tree; use this option to change this behaviour.
`color`	a logical value specifying whether to use colors for the lines linking the tips to the time axis. If `FALSE`, a grey scale is used.
`...`	other arguments to be passed to `plot.phylo`.

Details

The vector tip.dates may be numeric or of class “Date”. In either case, the time axis is set accordingly. The length of this vector must be equal to the number of tips of the tree: the dates are matched to the tips numbers. Missing values are allowed.

Value

NULL

Author(s)

Emmanuel Paradis

Examples

dates <- as.Date(.leap.seconds)
tr <- rtree(length(dates))
plotTreeTime(tr, dates)

## handling NA's:
dates[11:26] <- NA
plotTreeTime(tr, dates)

## dates can be on an arbitrary scale, e.g., [-1, 1]:
plotTreeTime(tr, runif(Ntip(tr), -1, 1))

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24