R/plot_compare_indels.R

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

#' Compare two indel mutation profiles
#'
#' Plots two indel mutation profiles and their difference, reports the residual
#' sum of squares (RSS).
#'
#' @param profile1 First mutation profile
#' @param profile2 Second mutation profile
#' @param profile_names Character vector with names of the mutations profiles
#' used for plotting, default = c("profile 1", "profile 2")
#' @param profile_ymax Maximum value of y-axis (relative contribution) for
#' profile plotting. This can only be used to increase the y axis.
#' If bars fall outside this limit, the maximum value is
#' automatically increased. default = 0.2.
#' @param diff_ylim Y-axis limits for profile difference plot,
#' default = c(-0.1, 0.1)
#'
#' @return A ggplot2 object
#' @export
#' @family Indels
#' @seealso \code{\link{plot_compare_profiles}},
#' \code{\link{plot_compare_dbs}},
#' \code{\link{plot_compare_mbs}}
#' @examples
#'
#' ## Get the indel counts
#' ## See 'count_indel_contexts()' for more info on how to do this.
#' indel_counts <- readRDS(system.file("states/blood_indel_counts.rds",
#'   package = "MutationalPatterns"
#' ))
#'
#' ## Get indel refit info.
#' ## See 'fit_to_signatures()' for more info on how to do this.
#' fit_res <- readRDS(system.file("states/indel_refit.rds",
#'   package = "MutationalPatterns"
#' ))
#'
#' ## Compare the reconstructed profile of sample 1 with the original profile
#' ## The same thing could be done with a reconstructed profile from NMF.
#' plot_compare_indels(indel_counts[, 1], fit_res$reconstructed[, 1])
#'
#' ## You could also compare regular mutation profiles with eachother.
#' plot_compare_indels(
#'   indel_counts[, 1],
#'   indel_counts[, 2]
#' )
#'
#' ## Or change the names of the profiles
#' plot_compare_indels(indel_counts[, 1],
#'   indel_counts[, 2],
#'   profile_names = c("Original", "Reconstructed")
#' )
#'
#' ## You can also change the y limits.
#' ## This can be done separately for the profiles and the different facets.
#' plot_compare_indels(indel_counts[, 1],
#'   indel_counts[, 2],
#'   profile_ymax = 0.3,
#'   diff_ylim = c(-0.03, 0.03)
#' )
plot_compare_indels <- function(profile1, profile2,
                                profile_names = c("profile 1", "profile 2"),
                                profile_ymax = 0.2,
                                diff_ylim = c(-0.1, 0.1)) {
  # These variables use non standard evaluation.
  # To avoid R CMD check complaints we initialize them to NULL.
  count <- muttype <- muttype_sub <- muttype_total <- value <- NULL


  # Create a comparison of the profiles.
  comp <- .create_profile_comparison(profile1, profile2, profile_names)

  # Separate muttype and muttype_sub. Then make data long
  counts <- comp$matrix %>%
    as.data.frame() %>%
    tibble::rownames_to_column("muttype_total") %>%
    tidyr::separate(muttype_total, c("muttype", "muttype_sub"), sep = "_(?=[0-9])") %>%
    dplyr::mutate(muttype = factor(muttype, levels = unique(muttype))) %>%
    tidyr::gather(key = "sample", value = "count", -muttype, -muttype_sub) %>%
    dplyr::mutate(sample = factor(sample, levels = unique(sample)))

  # Add dummy non_visible data points to force y axis limits per facet
  df_blank <- .create_dummy_limits(counts[, c("muttype", "muttype_sub")], profile_names, profile_ymax, diff_ylim)

  # Set facet names
  facet_labs_x <- c("1: C", "1: T", "1: C", "1: T", 2, 3, 4, "5+", 2, 3, 4, "5+", 2, 3, 4, "5+")
  names(facet_labs_x) <- levels(counts$muttype)


  # Create plot
  fig <- ggplot(counts, aes(x = muttype_sub, y = count, fill = muttype)) +
    geom_bar(stat = "identity") +
    geom_blank(data = df_blank, aes(x = muttype_sub, y = value)) +
    facet_grid(sample ~ muttype,
      scales = "free",
      space = "free_x",
      labeller = labeller(muttype = facet_labs_x)
    ) +
    scale_fill_manual(values = INDEL_COLORS) +
    labs(fill = "Mutation type", title = comp$title, y = "Relative contribution", x = "") +
    theme_minimal() +
    theme(panel.grid.major.x = element_blank(), strip.background = element_rect(fill = "cadetblue"))

  return(fig)
}