geomorph (version 2.1.6)

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, mesh = NULL,
  label = NULL, groups = NULL, verbose = FALSE)

Arguments

A

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

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 Y-axis (default = PC2)

warpgrids

A logical value indicating whether deformation grids for shapes along X-axis should be displayed

mesh

A mesh3d object to be warped to represent shape deformation along X-axis (when {warpgrids=TRUE}) as described in plotRefToTarget.

label

An optional vector indicating labels for each specimen are to be displayed (or if TRUE, numerical addresses are given)

groups

An optional factor vector specifying group identity for each specimen

verbose

A logical value indicating whether the output is basic or verbose (see Value below)

Value

• Function returns a table summarizing the percent variation explained by each pc axis (equivalent to summary() of prcomp) (default, verbose = FALSE). If verbose=TRUE, function returns a list containing the following components:
• pc.summary
  A PC summary table as above
• pc.scores
  The set of principal component scores for all specimens.
• pc.shapes
  A list with four components of the shape coordinates of the extreme ends of axis1 and axis2 is returned, which can be used by warpRefMesh.

Details

The function performs a principal components 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, {warpgrids=T}), deformation grids can be requested, which display the shape of specimens at the ends of the range of variability along PC1. If groups are provided, specimens from each group are plotted using distinct colors based on the order in which the groups are found in the dataset, and using R's standard color palette: black, red, green, blue, cyan, magenta, yellow, and gray. NOTE: to change the colors of the groups, simply substitute a vector of the desired colors for each specimen (see example below).

Examples

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

gp <- as.factor(paste(plethodon$species, plethodon$site)) # group must be a factor
plotTangentSpace(Y.gpa$coords, groups = gp)

## To plot residual shapes from an allometry regression (note: must add mean back in!)
plotTangentSpace(arrayspecs(resid(lm(two.d.array(Y.gpa$coords)~Y.gpa$Csize))+
         predict(lm(two.d.array(Y.gpa$coords)~1)),12,2))

##To change colors of groups
col.gp <- rainbow(length(levels(gp)))
   names(col.gp) <- levels(gp)
col.gp <- col.gp[match(gp, names(col.gp))] # col.gp must not be a factor

plotTangentSpace(Y.gpa$coords, groups = col.gp)

## To make a quick legend [not run]
#plot.new(); legend(0,1, legend= levels(gp), pch=19, col = levels(as.factor(col.gp)))