R/ggecdf.R

In YTLogos/ggpubr: 'ggplot2' Based Publication Ready Plots

#' @include utilities.R ggpar.R
NULL
#' Empirical cumulative density function
#' @description Empirical Cumulative Density Function (ECDF).
#' @inheritParams ggboxplot
#' @param x variable to be drawn.
#' @param color line and point color.
#' @param linetype line type. See \code{\link{show_line_types}}.
#' @param size line and point size.
#' @param ... other arguments to be passed to
#'   \code{\link[ggplot2]{stat_ecdf}} and \code{\link{ggpar}}.
#' @details The plot can be easily customized using the function ggpar(). Read
#'   ?ggpar for changing: \itemize{ \item main title and axis labels: main,
#'   xlab, ylab \item axis limits: xlim, ylim (e.g.: ylim = c(0, 30)) \item axis
#'   scales: xscale, yscale (e.g.: yscale = "log2") \item color palettes:
#'   palette = "Dark2" or palette = c("gray", "blue", "red") \item legend title,
#'   labels and position: legend = "right" \item plot orientation : orientation
#'   = c("vertical", "horizontal", "reverse") }
#' @seealso \code{\link{ggpar}}
#'
#' @examples
#' # Create some data format
#' set.seed(1234)
#' wdata = data.frame(
#'    sex = factor(rep(c("F", "M"), each=200)),
#'    weight = c(rnorm(200, 55), rnorm(200, 58)))
#'
#' head(wdata, 4)
#'
#' # Basic ECDF plot
#' ggecdf(wdata, x = "weight")
#'
#' # Change colors and linetype by groups ("sex")
#' # Use custom palette
#' ggecdf(wdata, x = "weight",
#'    color = "sex", linetype = "sex",
#'    palette = c("#00AFBB", "#E7B800"))
#'
#' @export
ggecdf <- function(data, x,  combine = FALSE, merge = FALSE,
                   color = "black",  palette = NULL,
                   size = NULL, linetype = "solid",
                   title = NULL, xlab = NULL, ylab = NULL,
                   facet.by = NULL, panel.labs = NULL, short.panel.labs = TRUE,
                   ggtheme = theme_pubr(),
                   ...){


  # Default options
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
  .opts <- list(
    combine = combine, merge = merge,
    color = color, palette = palette,
    linetype = linetype, size = size,
    title = title, xlab = xlab, ylab = ylab,
    facet.by = facet.by, panel.labs = panel.labs, short.panel.labs = short.panel.labs,
    ggtheme = ggtheme, ...)
  if(!missing(data)) .opts$data <- data
  if(!missing(x)) .opts$x <- x

  # User options
  #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
  .user.opts <- as.list(match.call(expand.dots = TRUE))
  .user.opts[[1]] <- NULL # Remove the function name
  # keep only user arguments
  for(opt.name in names(.opts)){
    if(is.null(.user.opts[[opt.name]]))
      .opts[[opt.name]] <- NULL
  }
  .opts$fun <- ggecdf_core
  .opts$y <- "..ecdf.."
  if(missing(ggtheme) & (!is.null(facet.by) | combine))
    .opts$ggtheme <- theme_pubr(border = TRUE)
  p <- do.call(.plotter, .opts)

  if(.is_list(p) & length(p) == 1) p <- p[[1]]
  return(p)

}

ggecdf_core <- function(data, x, y = "..ecdf..",
                      color = "black",  palette = NULL,
                      size = NULL, linetype = "solid",
                      title = NULL, xlab = NULL, ylab = NULL,
                      ggtheme = theme_classic(),
                      ...)
{

  p <- ggplot(data, aes_string(x))

  p <- p +
      geom_exec(stat_ecdf, data = data,
                 color = color,  size = size,
                 linetype = linetype)+
    labs(y = paste0("F(", x, ")"))
  p <- ggpar(p, palette = palette, ggtheme = ggtheme,
             title = title, xlab = xlab, ylab = ylab,...)
  p
}