ape: trex – R documentation

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trex

Tree Explorer With Multiple Devices

Description

This function requires a plotted tree: the user is invited to click close to a node and the corresponding subtree (or clade) is plotted on a new window.

Usage

trex(phy, title = TRUE, subbg = "lightyellow3",
     return.tree = FALSE, ...)

Arguments

`phy`	an object of class `"phylo"`.
`title`	a logical or a character string (see details).
`subbg`	a character string giving the background colour for the subtree.
`return.tree`	a logical: if `TRUE`, the subtree is returned after being plotted and the operation is stopped.
`...`	further arguments to pass to `plot.phylo`.

Details

This function works with a tree (freshly) plotted on an interactive graphical device (i.e., not a file). After calling trex, the user clicks close to a node of the tree, then the clade from this node is plotted on a new window. The user can click as many times on the main tree: the clades are plotted successively on the same new window. The process is stopped by a right-click. If the user clicks too close to the tips, a message “Try again!” is printed.

Each time trex is called, the subtree is plotted on a new window without closing or deleting those possibly already plotted. They may be distinguished with the options title and/or subbg.

In all cases, the device where phy is plotted is the active window after the operation. It should not be closed during the whole process.

If title = TRUE, a default title is printed on the new window using the node label, or the node number if there are no node labels in the tree. If title = FALSE, no title is printed. If title is a character string, it is used for the title.

Value

an object of class "phylo" if return.tree = TRUE

Author(s)

Emmanuel Paradis

Examples

## Not run: 
tr <- rcoal(1000)
plot(tr, show.tip.label = FALSE)
trex(tr) # left-click as many times as you want, then right-click
tr <- makeNodeLabel(tr)
trex(tr, subbg = "lightgreen") # id.

## generate a random colour with control on the darkness:
rRGB <- function(a, b)
    rgb(runif(1, a, b), runif(1, a, b), runif(1, a, b))

### with a random pale background:
trex(tr, subbg = rRGB(0.8, 1))
## the above can be called many times...
graphics.off() # close all graphical devices

## End(Not run)

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