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Last data update: 2014.03.03

R: Plot phylogenetic tree and specimens in tangent space

plotGMPhyloMorphoSpace

R Documentation

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`	A logical value indicating whether ancestral state values should be returned
`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"

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 (analagous to 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).

Value

Function returns estimated ancestral states if ancStates=TRUE

Author(s)

Dean Adams & Emma Sherratt

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

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)