find_common_subtrees: Find the set of common subtrees between two phylogenetic...

In GeRnika: Simulation, Visualization and Comparison of Tumor Evolution Data

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 class object.
phylotree_2	A Phylotree class object.
labels	A boolean, if TRUE the rendered graph will be plotted with the tags of the genes in the phylogenetic trees instead of their gene index. FALSE by default.

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)

GeRnika documentation built on April 3, 2025, 7:48 p.m.