geomorph (version 1.1-1)

plotTangentSpace: Plot specimens in tangent space

Description

Function plots a set of Procrustes-aligned specimens in tangent space along their principal axes

Usage

plotTangentSpace(A, axis1 = 1, axis2 = 2,
    warpgrids = TRUE, label = FALSE)

Arguments

A

An array (p x k x n) containing landmark coordinates for a set of specimens

warpgrids

A logical value indicating whether deformation grids for shapes along PC1 should be displayed

axis1

A value indicating which PC axis should be displayed as the X-axis (default = PC1)

axis2

A value indicating which PC axis should be displayed as the X-axis (default = PC2)

label

A logical value indicating whether labels for each specimen should be displayed

Details

The function performs a principal compoments analysis of shape variation and plots two dimensions of tangent space for a set of Procrustes-aligned specimens (default is PC1 vs. PC2). The percent variation along each PC-axis is returned. Additionally (and optionally), deformation grids can be requested, which display the shape of specimens at the ends of the range of variability along PC1. The function returns a table summarizing the percent variation explained by each pc axis, and the set of principal component scores for all specimens.

Examples

data(plethodon)
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment
ref<-mshape(Y.gpa$coords)

plotTangentSpace(Y.gpa$coords)