Claddis (version 0.3.4)

MorphospacePlot: Plot Morphopace

Description

Plots a morphospace using the output from MorphMatrix2PCoA.

Usage

MorphospacePlot(pcoa_input, x_axis = 1, y_axis = 2, z_axis = NULL,
  plot_taxon_names = FALSE, plot_internal_nodes = FALSE,
  plot_root = TRUE, root_colour = "grey")

Arguments

pcoa_input

The main input in the format output from MorphMatrix2PCoA.

x_axis

Which ordination axis to plot as the x-axis (defaults to 1).

y_axis

Which ordination axis to plot as the y-axis (defaults to 2).

z_axis

Which ordination axis to plot as the z-axis (defaults to NULL, i.e., is not plotted).

plot_taxon_names

Optional to plot the names of the taxa (defaults to FALSE).

plot_internal_nodes

Optional to plot the internal nodes of the tree (if included in pcoa_input) (defaults to FALSE).

plot_root

Optional to plot the root separately (defaults to FALSE).

root_colour

If plotting the root separately (previous option) sets the root colour.

Details

Uses output from MorphMatrix2PCoA as input.

Allows plotting of a third axis using the technique of Matthew Wills (Wills et al. 1994; their Figures 4 and 8; Wills 1998; his Figure 4), where black and white indicate positive and negative values respectovely, and the size of points there magnitudes.

References

Wills, M. A., 1998. Cambrian and Recent disparity: the picture from priapulids. Paleobiology, 24, 177-199.

Wills, M. A., Briggs, D. E. G. and Fortey, R. A., 1994. Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods. Paleobiology, 20, 93-130.

Examples

# NOT RUN {
# Set random seed:
set.seed(4)

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

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

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

# Plot the results:
MorphospacePlot(pcoa_input, plot_taxon_names = TRUE)

# }