find_common_subtrees {GeRnika} | R Documentation |
Plots the common subtrees between two phylogenetic trees and prints the information about their similarities and their differences.
find_common_subtrees(phylotree_1, phylotree_2, labels = FALSE)
phylotree_1 |
A |
phylotree_2 |
A |
labels |
A boolean, if |
A plot of the common subtrees between two phylogenetic trees and the information about the distance between them based on their independent and common edges.
# Load the predefined B matrices of the package
B_mats <- GeRnika::B_mats
B_real <- B_mats[[2]]$B_real
B_opt <- B_mats[[2]]$B_opt
# Generate the tags for the genes of
# the phyogenetic tree
tags <- LETTERS[1:nrow(B_real)]
# Instantiate two Phylotree class objects on
# the basis of the B matrices using tags
phylotree_real <- B_to_phylotree(
B = B_real,
labels = tags)
phylotree_opt <- B_to_phylotree(
B = B_opt,
labels = tags)
# find the set of common subtrees between both
# phylogenetic trees
find_common_subtrees(
phylotree_1 = phylotree_real,
phylotree_2 = phylotree_opt)
# find the set of common subtrees between both
# phylogenetic trees using tags
find_common_subtrees(
phylotree_1 = phylotree_real,
phylotree_2 = phylotree_opt,
labels = TRUE)