MorphSim (version 0.1.0)

plotMorphoGrid: Plots morphological matrix

Description

This function plots the full morphological matrix assocaited with the character data at the tips of a tree. Requires a morpho object as input.

Usage

plotMorphoGrid(
  data = NULL,
  timetree = FALSE,
  seq = "tips",
  num.trait = "all",
  col = c("lavender", "white", "lightskyblue1", "pink", "gold2", "forestgreen", "coral")
)

Value

No return value, called for its side effect of producing a plot.

Arguments

data

A morpho object

timetree

TRUE or FALSE Indicate whether you want to plot a time tree or not. default FALSE, uses distance tree if FALSE

seq

the sequence data to plot: "tips", "nodes", "SA", or "recon"

num.trait

default is set to "all" which plots all traits in black font. If you want to focus on a specific trait set it here, e.g. num.trait = 1 and this trait will be highlighted

col

A vector of colors that should be the same length or longer than the number of different character states (k). if not specified, the traits from 0 to 6 can be differentiated

Examples

data(morpho_data)
# plot the character matrix
plotMorphoGrid(data = morpho_data, seq = "tips", num.trait = "all")