geomorph (version 2.1.6)

plotGMPhyloMorphoSpace: Plot phylogenetic tree and specimens in tangent space

Description

Function plots a phylogenetic tree and a set of Procrustes-aligned specimens in tangent space

Usage

plotGMPhyloMorphoSpace(phy, A, labels = TRUE, ancStates = TRUE,
  plot.param = list())

Arguments

phy

A phylogenetic tree of {class phylo} - see read.tree in library ape

A

A matrix (n x [p x k]) or 3D array (p x k x n) containing GPA-aligned coordinates for a set of specimens

labels

A logical value indicating whether taxa labels (tips and ancestors) should be included

ancStates

A logical value indicating whether ancestral state values should be returned

plot.param

A list of plotting parameters for the tips (t.bg, t.pch, t.cex), nodes (n.bg, n.pch, n.cex), branches (l.col, lwd), and taxa labels (txt.cex, txt.adj, txt.col)

Value

• Function returns estimated ancestral states if {ancStates=TRUE}

Details

The function creates a plot of the first two dimensions of tangent space for a set of Procrustes-aligned specimens. The phylogenetic tree for these specimens is superimposed in this plot revealing how shape evolves (e.g., Rohlf 2002; Klingenberg and Gidaszewski 2010). The plot also displays the ancestral states for each node of the phylogenetic tree (obtained from fastAnc), whose values can optionally be returned.

References

Klingenberg, C. P., and N. A. Gidaszewski. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst. Biol. 59:245-261. Rohlf, F. J. 2002. Geometric morphometrics and phylogeny. Pp. 175'193 in N. Macleod, and P. Forey, eds. Morphology, shape, and phylogeny. Taylor & Francis, London.

Examples

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

plotGMPhyloMorphoSpace(plethspecies$phy,Y.gpa$coords)
plotGMPhyloMorphoSpace(plethspecies$phy,Y.gpa$coords,
                 plot.param=list(t.bg="blue",txt.col="red",n.cex=1))