geomorph (version 3.0.4)

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, tip.labels = TRUE, node.labels = TRUE,
  ancStates = TRUE, xaxis = 1, yaxis = 2, zaxis = NULL,
  plot.param = list(), shadow = FALSE)

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

tip.labels

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

node.labels

A logical value indicating whether node labels (ancestors) should be included

ancStates

Either a logical value indicating whether ancestral state values should be returned, or a matrix of ancestral states (i.e. calculated with fastAnc or ace)

xaxis

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

yaxis

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

zaxis

Optional, a numeric value indicating which PC axis should be displayed as the Z-axis (e.g. PC3) or if zaxis="time", internal nodes are plotted along the Z-axis relative to time

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), taxa labels (txt.cex, txt.adj, txt.col) and node labels (n.txt.cex, n.txt.adj, n.txt.col)

shadow

A logical value indicating whether a 2D phylomorphospace should be plotted at the base when zaxis="time"

Value

Function returns estimated ancestral states if ancStates=TRUE

Details

The function creates a plot of the principal dimensions of tangent space for a set of Procrustes-aligned specimens. Default is a plot of PC axis 1 and 2. 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 (analogous to from fastAnc from phytools), whose values can optionally be returned. If a tree with branch lengths scaled by time is used, with the option zaxis = "time", the function plots a 3D phylomorphospace, with internal nodes positioned along the Z-axis scaled to time (a.k.a. Chronophylomorphospace, Sakamoto & Ruta 2012).

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.

Sakamoto, M. and Ruta, M. 2012. Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity. PLoSONE 7(7): e39752.

Examples

# NOT RUN {
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))
#NOTE: 3D plot also available: plotGMPhyloMorphoSpace(plethspecies$phy,Y.gpa$coords, zaxis= "time",
#                 plot.param=list(n.cex=2, n.bg="blue"), shadow=TRUE)
# }