R/add_significance.R

In rstatix: Pipe-Friendly Framework for Basic Statistical Tests

#' @include utilities.R
NULL
#' Add P-value Significance Symbols
#' @description Add p-value significance symbols into a data frame.
#' @param data a data frame containing a p-value column.
#' @param p.col column name containing p-values.
#' @param output.col the output column name to hold the adjusted p-values.
#' @param cutpoints numeric vector used for intervals.
#' @param symbols character vector, one shorter than cutpoints, used as
#'   significance symbols.
#'
#' @return a data frame
#'
#' @examples
#' # Perform pairwise comparisons and adjust p-values
#' ToothGrowth %>%
#'  t_test(len ~ dose) %>%
#'  adjust_pvalue() %>%
#'  add_significance("p.adj")
#'
#' @rdname add_significance
#' @export
add_significance <- function(
  data, p.col = NULL, output.col = NULL,
  cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05,  1),
  symbols = c("****", "***", "**", "*",  "ns")
)
{
  .attributes <- get_test_attributes(data)
  if(is.null(p.col))
    p.col <- data %>% p_detect("p.adj")
  if(is.null(p.col))
    p.col <- data %>% p_detect("p")
  if(is.null(p.col))
    return(data)
  else if(!(p.col %in% colnames(data)))
    stop("The column ", p.col, " does not exist in the data")
  if(is.null(output.col))
    output.col <- paste0(p.col, ".signif")
  .p.values <- data %>% pull(!!p.col)
  if(all(is.na(.p.values))) {
    .p.signif <- rep("", length(.p.values))
  }
  else{
    .p.signif <- .p.values %>%
    stats::symnum(cutpoints = cutpoints, symbols = symbols, na = "") %>%
    as.character()
  }
  data %>%
    keep_only_tbl_df_classes() %>%
    mutate(!!output.col := .p.signif) %>%
    set_test_attributes(.attributes)
}