R/plot_sample_counts.R

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

#' @import ggplot2
#' @importFrom rlang .data
#' @import dplyr
#' @import tidyr
#' @import tidyverse
NULL

#' Plot distribution of sample counts
#'
#' Displays the proportion of counts for each mutation type across one
#' or more samples.
#'
#' @param musica A \code{\linkS4class{musica}} object.
#' @param sample_names Names of the samples to plot.
#' @param modality Name of table used for plotting counts. Default
#' \code{"SBS96"}.
#' @param text_size Size of axis text. Default \code{10}.
#' @param show_x_labels If \code{TRUE}, the labels for the mutation types
#' on the x-axis will be shown. Default \code{TRUE}.
#' @param show_y_labels If \code{TRUE}, the y-axis ticks and labels will be
#' shown. Default \code{TRUE}.
#' @param same_scale If \code{TRUE}, the scale of the y-axis for each
#' sample will be the same. If \code{FALSE}, then the scale of the y-axis
#' will be adjusted for each sample. Default \code{TRUE}.
#' @param annotation Vector of annotations to be displayed in the top right
#' corner of each sample. Vector length must be equivalent to the number of
#' samples. Default \code{NULL}.
#' @param table_name Use modality instead
#' @return Generates a ggplot object
#' @examples
#' data(musica_sbs96)
#' plot_sample_counts(musica_sbs96,
#'   sample_names =
#'     sample_names(musica_sbs96)[1]
#' )
#' @export
plot_sample_counts <- function(musica, sample_names, modality = "SBS96",
                               text_size = 10,
                               show_x_labels = TRUE, show_y_labels = TRUE,
                               same_scale = TRUE, annotation = NULL,
                               table_name = NULL) {
  if (!is.null(table_name)) {
    warning("table_name argument deprecated. Use modality instead.")
    modality <- table_name
  }

  # check if valid modality
  if (!(modality %in% names(extract_count_tables(musica)))) {
    stop(
      modality, " is not a valid modality. Current modalities are: ",
      paste(names(extract_count_tables(musica)), collapse = ", ")
    )
  }

  # Extract counts for specific samples
  tab <- .extract_count_table(musica, modality)
  ix <- match(sample_names, colnames(tab))
  if (all(is.na(ix))) {
    stop(
      "The values in 'sample_names' did not match any sample IDs in table '",
      modality, "'."
    )
  } else if (anyNA(ix)) {
    warning(
      "The following samples in 'sample_names' were not found  in ",
      "table '", modality,
      "' and will ", "be exlcuded from the plot: ",
      paste(sample_names[is.na(ix)], collapse = ", ")
    )
    ix <- ix[!is.na(ix)]
  }
  sample_counts <- tab[, ix, drop = FALSE]

  result <- methods::new("result_model",
    signatures = sample_counts, exposures = matrix(),
    modality = modality
  )
  g <- .plot_result_model_signatures(result, musica,
    percent = FALSE, text_size = text_size,
    show_x_labels = show_x_labels, show_y_labels = show_y_labels,
    same_scale = same_scale, annotation = annotation
  )
  return(g)
}