R/utils.R

In INRA-LPGP/PoolSex-vis: Visualization of results from PSASS

convert_to_mb <- function(x, n = 0) {
    round(x / 10^6, n)
}


convert_to_kb <- function(x, n = 0) {
    round(x / 10^3, n)
}


# Generate a nice scale for any interval
generate_x_scale <- function(region, scaffold_name) {

    # Size of the region
    S <- (region[2] - region[1]) / 10
    if (S <= 0) stop(paste0("Error: the size of the region has to be > 0 (value: ", S * 10, ")"))

    # Find the order of magnitude of the region's size
    N <- floor(log(S, 10))
    N10 <- 10 ^ N

    # Generate a scale of 10 round values within the region
    scale <- seq(N10 * floor(region[1] / N10), N10 * ceiling(region[2] / N10), N10 * round(S / N10, 1))

    # Adjust the labels based on the size of the values (megabp or kilop)
    if (region[1] < 10 ^ 6 & region[2] < 10 ^ 6) {
        scale_labels <- round(scale / 10 ^ 3, 3 - N)
        bp_unit <- "K"
    } else {
        scale_labels <- round(scale / 10 ^ 6, 6 - N)
        bp_unit <- "M"
    }

    output <- ggplot2::scale_x_continuous(name = paste0("Position on ", scaffold_name, " (", bp_unit, "bp)"),
                                          expand = c(0.01, 0.01),
                                          breaks = scale,
                                          labels = scale_labels,
                                          limits = c(min(scale[1], region[1]), max(tail(scale, 1), region[2])))

    return(output)
}