find_common_subtrees {GeRnika} | R Documentation |
Find the set of common subtrees between two phylogenetic trees
Description
Plots the common subtrees between two phylogenetic trees and prints the information about their similarities and their differences.
Usage
find_common_subtrees(phylotree_1, phylotree_2, labels = FALSE)
Arguments
phylotree_1 |
A |
phylotree_2 |
A |
labels |
A boolean, if |
Value
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.
Examples
# Load the predefined B matrices of the package
B_mats <- GeRnika::B_mats
B_real <- B_mats[[2]]$B_real
B_alg1 <- B_mats[[2]]$B_alg1
# 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_alg1 <- B_to_phylotree(
B = B_alg1,
labels = tags)
# find the set of common subtrees between both
# phylogenetic trees
find_common_subtrees(
phylotree_1 = phylotree_real,
phylotree_2 = phylotree_alg1)
# find the set of common subtrees between both
# phylogenetic trees using tags
find_common_subtrees(
phylotree_1 = phylotree_real,
phylotree_2 = phylotree_alg1,
labels = TRUE)
[Package GeRnika version 1.1.0 Index]