Claddis (version 0.3.4)

ChronoPhyloMorphospacePlot: Chronophylomorphospace Plot

Description

Plots a 3D chronophylomorphospace.

Usage

ChronoPhyloMorphospacePlot(pcoa_data, x_axis = 1, y_axis = 2,
  shadow = TRUE)

Arguments

pcoa_data

Principal coordinate data in the format output by MorphMatrix2PCoA that includes a tree and ancestral states.

x_axis

Which ordination axis to plot as the x-axis.

y_axis

Which ordination axis to plot as the y-axis.

shadow

Whether or not to plot a shadow (2D plot) on the bottom face of the 3D plot (defaults to TRUE).

Details

Creates a movable three-dimensional (two ordination axes plus time) plot of a phylomorphospace.

Intended to mimic the data visualisation of Sakamoto and Ruta (2012; their Video S1).

References

Sakamoto, M. and Ruta, M. 2012. Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity. PLoS ONE, 7, e39752.

Examples

# NOT RUN {
require(rgl)

# Set random seed:
set.seed(4)

# Generate a random tree for the Michaux 1989 data set:
Tree <- rtree(nrow(Michaux1989$Matrix_1$Matrix))

# Set root time so latest tip terminates at the present:
Tree$root.time <- max(diag(vcv(Tree)))

# Add taxon names to the tree:
Tree$tip.label <- rownames(Michaux1989$Matrix_1$Matrix)

# Perform a phylogenetic Principal Coordinates Analysis:
pcoa_data <- MorphMatrix2PCoA(Michaux1989, Tree = Tree)

# Plot a chronophylomorphospace:
ChronoPhyloMorphospacePlot(pcoa_data)

# }