R/hdrscatterplot.R

Defines functions hdrscatterplot

Documented in hdrscatterplot

# Scatterplots coloured by HDR regions


#' Scatterplot showing bivariate highest density regions
#'
#' Produces a scatterplot where the points are coloured according to the
#' bivariate HDRs in which they fall.
#'
#' The bivariate density is estimated using kernel density estimation. Either
#' \code{\link[ash]{ash2}} or \code{\link[ks]{kde}} is used to do the
#' calculations. Then Hyndman's (1996) density quantile algorithm is used to
#' compute the HDRs. The scatterplot of (x,y) is created where the points are
#' coloured according to which HDR they fall. A ggplot object is returned.
#'
#' @param x Numeric vector or matrix with 2 columns.
#' @param y Numeric vector of same length as \code{x}.
#' @param levels Percentage coverage for HDRs
#' @param kde.package Package to be used in calculating the kernel density
#' estimate when \code{den=NULL}.
#' @param noutliers Number of outliers to be labelled. By default, all points
#' outside the largest HDR are labelled.
#' @param label Label of outliers of same length as \code{x} and \code{y}. By default, all outliers are labelled as the row index of the point \code{(x, y)}.
#' @author Rob J Hyndman
#' @seealso \code{\link{hdr.boxplot.2d}}
#' @keywords smooth distribution hplot
#' @examples
#' x <- c(rnorm(200, 0, 1), rnorm(200, 4, 1))
#' y <- c(rnorm(200, 0, 1), rnorm(200, 4, 1))
#' hdrscatterplot(x, y)
#' hdrscatterplot(x, y, label = paste0("p", 1:length(x)))
#' @export hdrscatterplot
hdrscatterplot <- function(x, y, levels = c(1, 50, 99), kde.package = c("ash", "ks"), noutliers = NULL, label = NULL) {
  levels <- sort(levels)
  if (missing(y)) {
    data <- x
  } else {
    data <- data.frame(x = x, y = y)
    names(data) <- make.names(c(deparse(substitute(x)), deparse(substitute(y))))
  }

  vnames <- names(data)

  den <- hdr.2d(data[, 1], data[, 2], prob = levels, kde.package = kde.package)

  region <- numeric(NROW(data)) + 100
  for (i in seq_along(levels))
    region[den$fxy > den$falpha[i]] <- 100 - levels[i]
  if (is.null(noutliers)) {
    noutliers <- sum(region > max(levels))
  }

  noutliers <- min(noutliers, NROW(data))


  xlim <- diff(range(data[, 1]))
  ylim <- diff(range(data[, 2]))

  # Construct region factor
  levels <- sort(unique(region[region < 100]), decreasing = TRUE)
  levels <- c(levels, 100)
  data$Region <- factor(region,
    levels = levels,
    labels = c(paste(head(levels, -1)), ">99")
  )
  # Sort data so the larger regions go first (other than outliers)
  k <- region
  k[region == 100] <- 0
  ord <- order(k, decreasing = TRUE)
  data <- data[ord, ]

  if (noutliers > 0) {
    outliers <- order(den$fxy[ord])[seq(noutliers)]
  }

  p <- ggplot2::ggplot(data, ggplot2::aes_string(vnames[1], vnames[2])) +
    ggplot2::geom_point(ggplot2::aes_string(col = "Region"))
  p <- p + ggplot2::scale_colour_manual(
    name = "HDRs",
    breaks = c(paste(head(sort(levels), -1)), ">99"),
    values = c(RColorBrewer::brewer.pal(length(levels), "YlOrRd")[-1], "#000000")
  )

  # Show outliers
  if (is.null(label)) {
    label <- rownames(data)[outliers]
  } else {
    if (length(label) != nrow(data)) stop("The length of label is not the same as x and y!")
    label <- label[ord[outliers]]
  }
  if (noutliers > 0) {
    p <- p + ggplot2::annotate("text",
      x = data[outliers, 1] + xlim / 50, y = data[outliers, 2] + ylim / 50,
      label = label, col = "blue", cex = 2.5
    )
  }
  return(p)
}
robjhyndman/hdrcde documentation built on Jan. 19, 2021, 12:08 p.m.