ape: identify.phylo – R documentation

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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

`x`	an object of class `"phylo"`.
`nodes`	a logical specifying whether to identify the node.
`tips`	a logical specifying whether to return the tip information.
`labels`	a logical specifying whether to return the labels; by default only the numbers are returned.
`quiet`	a logical controlling whether to print a message inviting the user to click on the tree.
`...`	further arguments to be passed to or from other methods.

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.

Value

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

Note

This function does not add anything on the plot, but it can be wrapped with, e.g., nodelabels (see example), or its results can be sent to, e.g., drop.tip.

Author(s)

Emmanuel Paradis

Examples

## Not run: 
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")

## 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