R/vioplot_ext.R

In faridcher/futils: Farid utility functions

#these must be loaded after the vioplot loaded not before
# add ylab and na.action support
#' @export
vioplot <- function(x,...) UseMethod("vioplot",x)

#' @export
vioplot.list <- function(x,...){
  n <- names(x)
  names(x)[1] <- 'x'
  do.call(vioplot,
          c(x,list(names=n,...)))
}

#' @export
vioplot.default <- function (x, ..., range = 1.5, h = NULL, ylim = NULL, names = NULL,
                             horizontal = FALSE, col = "magenta", border = "black", lty = 1,
                             lwd = 1, rectCol = "black", colMed = "white", pchMed = 19,
                             at, add = FALSE, wex = 1, drawRect = TRUE)
{
  datas <- list(x, ...)
  n <- length(datas)
  if (missing(at))
    at <- 1:n
  upper <- vector(mode = "numeric", length = n)
  lower <- vector(mode = "numeric", length = n)
  q1 <- vector(mode = "numeric", length = n)
  q3 <- vector(mode = "numeric", length = n)
  med <- vector(mode = "numeric", length = n)
  base <- vector(mode = "list", length = n)
  height <- vector(mode = "list", length = n)
  baserange <- c(Inf, -Inf)
  args <- list(display = "none")
  if (!(is.null(h)))
    args <- c(args, h = h)
  for (i in 1:n) {
    data <- datas[[i]]
    data.min <- min(data)
    data.max <- max(data)
    q1[i] <- quantile(data, 0.25)
    q3[i] <- quantile(data, 0.75)
    med[i] <- median(data)
    iqd <- q3[i] - q1[i]
    upper[i] <- min(q3[i] + range * iqd, data.max)
    lower[i] <- max(q1[i] - range * iqd, data.min)
    est.xlim <- c(min(lower[i], data.min), max(upper[i],
                                               data.max))
    smout <- do.call(sm::sm.density, c(list(data, xlim = est.xlim),
                                     args))
    hscale <- 0.4/max(smout$estimate) * wex
    base[[i]] <- smout$eval.points
    height[[i]] <- smout$estimate * hscale
    t <- range(base[[i]])
    baserange[1] <- min(baserange[1], t[1])
    baserange[2] <- max(baserange[2], t[2])
  }
  if (!add) {
    xlim <- if (n == 1)
      at + c(-0.5, 0.5)
    else range(at) + min(diff(at))/2 * c(-1, 1)
    if (is.null(ylim)) {
      ylim <- baserange
    }
  }
  if (is.null(names)) {
    label <- 1:n
  }
  else {
    label <- names
  }
  boxwidth <- 0.05 * wex
  if (!add)
    plot.new()
  if (!horizontal) {
    if (!add) {
      plot.window(xlim = xlim, ylim = ylim)
      axis(2)
      axis(1, at = at, label = label)
    }
    box()
    for (i in 1:n) {
      polygon(c(at[i] - height[[i]], rev(at[i] + height[[i]])),
              c(base[[i]], rev(base[[i]])), col = col, border = border,
              lty = lty, lwd = lwd)
      if (drawRect) {
        lines(at[c(i, i)], c(lower[i], upper[i]), lwd = lwd,
              lty = lty)
        rect(at[i] - boxwidth/2, q1[i], at[i] + boxwidth/2,
             q3[i], col = rectCol)
        points(at[i], med[i], pch = pchMed, col = colMed)
      }
    }
  }
  else {
    if (!add) {
      plot.window(xlim = ylim, ylim = xlim)
      axis(1)
      axis(2, at = at, label = label)
    }
    box()
    for (i in 1:n) {
      polygon(c(base[[i]], rev(base[[i]])), c(at[i] -
                                                height[[i]], rev(at[i] + height[[i]])), col = col,
              border = border, lty = lty, lwd = lwd)
      if (drawRect) {
        lines(c(lower[i], upper[i]), at[c(i, i)], lwd = lwd,
              lty = lty)
        rect(q1[i], at[i] - boxwidth/2, q3[i], at[i] +
               boxwidth/2, col = rectCol)
        points(med[i], at[i], pch = pchMed, col = colMed)
      }
    }
  }
  invisible(list(upper = upper, lower = lower, median = med,
                 q1 = q1, q3 = q3))
}

#' @export
vioplot.formula <- function (formula, data = NULL, ..., subset, na.action = NULL)
{
  if (missing(formula) || (length(formula) != 3L))
    stop("'formula' missing or incorrect")
  m <- match.call(expand.dots = FALSE)
  if (is.matrix(eval(m$data, parent.frame())))
    m$data <- as.data.frame(data)
  m$... <- NULL
  m$na.action <- na.action
  m[[1L]] <- quote(stats::model.frame)
  mf <- eval(m, parent.frame())
  response <- attr(attr(mf, "terms"), "response")

  DATA <- setNames(split(mf[[response]], mf[-response]), c("x"))
  y <- do.call(vioplot.default, c(DATA, list(...)))

  #vioplot(split(mf[[response]], mf[-response]), ...)
}