full_pipeline_new.R

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

library(rcombinator)
devtools::reload(".")
setwd("./output_with_new_pipeline/")

sequence_length <- 5000
num_initial_sequences <- 2
timestep <- c(100 * 10^3)
final_time <- 500 * 10^6
burst_probability <- 0.1
burst_mean <- 1
max_copy_number <- 20
recombination_mean <- 2
dist_method <- "ape"
num_seq_dumps <- 0
num_summary_dumps <- 100
num_pairmatrix_dumps <- 0

plot_title <- paste0("Sequence length: ", sequence_length,
                   "\nInitial number of sequences: ", num_initial_sequences,
                   "\nTimestep (years): ", timestep,
                   "\nFinal time (years): ", final_time,
                   "\nBurst mean: ", burst_mean,
                   "\nBurst probability: ", burst_probability,
                   "\nMaximum copy number: ", max_copy_number,
                   "\nDistance method: ", dist_method,
                   "\n")

save_file <- paste(sequence_length, num_initial_sequences,
                  timestep, final_time,
                  burst_probability, burst_mean, max_copy_number,
                  dist_method, sep="_")

z <- full_pipeline_comparison(
        sequence_length, num_initial_sequences,
        timestep, final_time,
        burst_probability, burst_mean, max_copy_number,
        recombination_mean,
        dist_method,
        num_seq_dumps, num_summary_dumps, num_pairmatrix_dumps)

compare_all(norecomb=z$norecomb, recomb=z$recomb, plot_title, save_file)