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 set the parameters for the simulation.

num_sequences <- 2
sequence_length <- 50
sequences <- get_random_sequence(sequence_length, num_sequences)
num_jumps <- 10
time_jump <- 10^6
transition_matrix <- get_k80_matrix(time_jump)
burst_threshold <- 0.2
burst_mean <- 2
flip_probability <- 0.3

Simulation

Let the sequences evolve, and collect the data.

A <- simulate_recombination_cheap(sequences,
                      num_jumps,
                      transition_matrix,
                      burst_threshold,
                      burst_mean,
                      flip_probability)

library(magrittr)
library(tidyr)
A <- A %>%
  unite(seq1, seq2, col="comparing", sep=" and ")

Plot the data.

library(ggplot2)

p1 <- ggplot(data = A,
            aes(x=time, y=seq_dist, colour=comparing))
p1 <- p1 + geom_step()
p1 <- p1 + labs(x = "time (in 1M years)", y = "sequence distance",
         title = "Comparing sequence distances over time with recombination")
print(p1)