R/boxplot_tbl.R

In kevinwang09/top: Cross Platform Omics Prediction

#' @title Make a simple boxplot plotting tbl
#' @description Make a simple boxplot plotting tbl
#' @param x a matrix or data.frame
#' @param index summarisation index, "1" for rows or "2" (default) for columns.
#' @importFrom tibble tibble
#' @importFrom forcats as_factor
#' @return A tibble
#' @export
#' @examples
#' data(cpop_data_binary, package = 'CPOP')
#' ## Loading example matrix
#' x1 = cpop_data_binary$x1
#' set.seed(1)
#' boxplot_tbl(x = x1, index = 1)
#' boxplot_tbl(x = x1, index = 2)
boxplot_tbl = function(x, index = 2){
  means = apply(x, index, base::mean, na.rm = TRUE)
  medians = apply(x, index, stats::median, na.rm = TRUE)
  q1 = apply(x, index, stats::quantile, 0.25, na.rm = TRUE)
  q3 = apply(x, index, stats::quantile, 0.75, na.rm = TRUE)
  n_na = apply(is.na(x), index, sum)

  object = dimnames(x)[[index]]

  if(is.null(object)){
    n = dim(x)[index]
    digits = ceiling(log10(n + 1L))
    fmt = paste0("%0", digits, "d")
    object = sprintf(fmt, seq_len(n))
  }

  object = forcats::as_factor(object)


  tbl = tibble::tibble(
    object = object,
    means = means,
    medians = medians,
    q1 = q1,
    q3 = q3,
    n_na = n_na)

  return(tbl)
}