In sams25/rcombinator_old: Tools to Simulate the Evolution of Genetic Sequences

knitr::opts_chunk$set(echo = TRUE)

Setup

Load the package

library(rcombinator)

Create the sequences and the Kimura-80 model matrix for point mutations.

sequences <- get_random_sequence(sequence_length = 500, num_sequences = 6)
transition_matrix <- get_k80_matrix(time_jump = 10^6)

Simulation

Let the sequences evolve.

seq_data <- simulate_point_mutation_markov(sequences, num_jumps = 50, transition_matrix)

Collect the data.

library(magrittr)

pairwise_dist_data <- pairwise_distances(seq_data)
pairwise_dist_data <- pairwise_dist_data %>%
  tidyr::unite(seq1, seq2, col="comparing", sep=" and ")

Plot the data.

library(ggplot2)

p <- ggplot(data = pairwise_dist_data,
            aes(x=time, y=seq_dist, colour=comparing))
p <- p + geom_step()
p <- p + labs(x = "time (in 1M years)", y = "sequence distance",
           title = "Comparing sequence distances over time using the K80 model for mutations")
print(p)