R: Tree Explorer With Multiple Devices

trex {ape} | R Documentation

## 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

### See Also

`plot.phylo`, `identify.phylo`

### 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)

[Package ape version 5.4 Index]