Create treespace ordination including extra columns.

This function will take list of rwty.chains objects and produce a matrix of ordinations in treespace based on Robinson-Foulds Distance. The points can be colored and sized by extra columns listed in the `ext_columns` argument. This function is modified from the `RWTY` package.

custom_plots(CombinedTrees, StratFile, ext_columns = c("MIG", "Bayes"))

Arguments

CombinedTrees	A list of all the parsimony and Bayesian trees you'd like to plot
StratFile	The logfile containing your stratigraphic congrunence values. Should contain a column to indicate if the tree is Bayesian or not.
ext_columns	Any extra columns you'd like to color your plot by
n.points	The number of points on each plot
fill.color	The name of any column in your parameter file that you would like to use as a fill colour for the points of the plot.

Value

A matrix of ordinations in treespace.