Claddis (version 0.6.3)

plot_changes_on_tree: Plots character changes on branches

Description

Plots character changes in boxes on branches.

Usage

plot_changes_on_tree(character_changes, time_tree, label_size = 0.5)

Value

A plot of character changes on a tree.

Arguments

character_changes

A matrix of character changes.

time_tree

Tree on which character changes occur.

label_size

The size of the text for the barnch labels. Default is 0.5.

Author

Graeme T. Lloyd

Details

Takes the character_changes output from test_rates and plots it on the tree used to generate it.

Examples

# Set random seed:
set.seed(17)

# Get first MPT for the Michaux data set:
time_tree <- ape::read.tree(text = paste0("(Ancilla:31.6,(Turrancilla:102.7,",
  "(Ancillista:1,Amalda:63.5):1):1);"))

# Set root time for tree:
time_tree$root.time <- 103.7

# Get discrete character rates (includes changes):
out <- test_rates(time_tree, michaux_1989,
  seq(time_tree$root.time, 0, length.out = 3),
  branch_partitions = list(list(1)), alpha = 0.01
)

# Plot character changes on the tree:
plot_changes_on_tree(
  out$inferred_character_changes,
  time_tree
)