ape (version 3.0-3)

identify.phylo: Graphical Identification of Nodes and Tips

Description

This function allows to identify a clade on a plotted tree by clicking on the plot with the mouse. The tree, specified in the argument x, must be plotted beforehand.

Usage

## S3 method for class 'phylo':
identify(x, nodes = TRUE, tips = FALSE,
                  labels = FALSE, quiet = FALSE, ...)

Arguments

Value

A list with one or two vectors named "tips" and/or "nodes" with the identification of the tips and/or of the nodes.

Details

By default, the clade is identified by its number as found in the `edge' matrix of the tree. If tips = TRUE, the tips descending from the identified node are returned, possibly together with the node. If labels = TRUE, the labels are returned (if the tree has no node labels, then the node numbered is returned).

The node is identified by the shortest distance where the click occurs. If the click occurs close to a tip, the function returns its information.

See Also

plot.phylo, nodelabels, identify for the generic function

Examples

Run this code
tr <- rtree(20)
f <- function(col) {
    o <- identify(tr)
    nodelabels(node=o$nodes, pch = 19, col = col)
}
plot(tr)
f("red") # click close to a node
f("green")

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