define.links: Define links between landmarks

In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

Define links between landmarks

Description

An interactive function to define which landmarks should be linked to aid visualization.

Usage

define.links(spec, ptsize = 1, links = NULL)

Arguments

spec	Name of specimen, as an object matrix containing 2D or 3D landmark coordinates
ptsize	Numeric Size to plot the landmarks
links	Optional An existing links matrix to add on to

Details

Function takes a matrix of digitized landmark coordinates (e.g. from mshape) and allows the user to define pairs of landmarks to be linked, for visualization purposes. The output is a matrix to be used by plotAllSpecimens & plotRefToTarget option 'links='.

Note to RStudio users: if the 'zoom' of your RStudio window is set to something other than 100 sometimes the function can fail to identify the selected points ('warning: no point within 0.25 inches'). In these cases, set your zoom to 100

Selection

In the plot window select two landmarks that will be linked. In the console, the user will be prompted to continue linking landmarks to build the wireframe or end the session (typing y or n respectively). For 2D data in plot window, use LEFT mouse button to select landmarks.

Notes for geomorph 4.1

Starting with geomorph version 4.1, interactive module selection in 3D is no longer supported, as RGL is not supported under MacOS Tahoe. Only AUTO mode is available.

Value

Function returns a matrix of which landmarks will be links to be used by plotAllSpecimens & plotRefToTarget option 'links='.

Author(s)

Dean Adams and Emma Sherratt

See Also

plotAllSpecimens

plotRefToTarget

geomorph documentation built on July 5, 2026, 5:07 p.m.