R/compare_all_old.R

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

compare_all_old <- function()
{
  clean_pairmatrix <- function(cumbersome_df)
  {
    cumbersome_df$pairmatrix <- sapply(cumbersome_df$pairmatrix, as.vector)
    return(tidyr::unnest(cumbersome_df))
  }

  data_recomb$pairmatrix_dump_data <- clean_pairmatrix(data_recomb$pairmatrix_dump_data)
  data_no_recomb$pairmatrix_dump_data <- clean_pairmatrix(data_no_recomb$pairmatrix_dump_data)

  # TODO: check if nrows > 0

  p <- ggplot2::ggplot()
  p <- p + ggplot2::geom_point(data=data_no_recomb$pairmatrix_dump_data,
                              ggplot2::aes(x=time, y=pairmatrix),
                              alpha = 0.05,
                              color="#FF6666")
  p <- p + ggplot2::geom_line(data=data_no_recomb$summary_dump_data,
                              ggplot2::aes(x=time, y=med_pair_dist),
                              color="#660000")
  p <- p + ggplot2::geom_point(data=data_recomb$pairmatrix_dump_data,
                              ggplot2::aes(x=time, y=pairmatrix),
                              alpha = 0.05,
                              color="#99CCFF")
  p <- p + ggplot2::geom_line(data=data_recomb$summary_dump_data,
                              ggplot2::aes(x=time, y=med_pair_dist),
                              color="#000033")
  p <- p + ggplot2::labs(x = paste("Time (in years)"),
                         y = paste("Sequence distances"),
                         title = paste0("Median pairwise distances\n",
                                 "Red - without recombination, Blue - with recombination"))
  print(p)
  ggplot2::ggsave(paste0(save_file, "_pairwise_median_dist.png"), scale = 3)
}