R: Plot Tree With Time Axis

plotTreeTime {ape} | R Documentation

## 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, ...)

### 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.
`...` | 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

### See Also

`plot.phylo`, `estimate.dates`

### 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))

[Package ape version 4.1 Index]