peter.utilities: Peter's utility functions

#' legend_modified
#'
#' This is a modified version of the base function \code{\link{legend}}. In particular it adds xbox, ybox, title.cex and returns functionality to pt.cex which is broken in the base version.
#'
#' @param xbox Scales up the x-direction of boxes (generated when colours are provided to fill)Default 1.
#' @param ybox Scales up the y-direction of boxes (generated when colours are provided to fill). If this is 2 then the boxes will touch in vertical mode. Default 1.
#' @param pt.cex the sizing for the text
#' @param title.cex the sizing for the title if provided.
#'
#' @export legend_modified
legend_modified = function (x, y = NULL, legend, fill = NULL, col = par("col"),
                            border = "black", lty, lwd, pch, angle = 45, density = NULL,
                            bty = "o", bg = par("bg"), box.lwd = par("lwd"), box.lty = par("lty"),
                            box.col = par("fg"), pt.bg = NA, cex = 1, pt.cex = cex, pt.lwd = lwd,
                            xjust = 0, yjust = 1, x.intersp = 0.75, y.intersp = 0.75, adj = c(0, 0.5),
                            text.width = NULL, text.col = par("col"), text.font = NULL,
                            merge = do.lines && has.pch, trace = FALSE, plot = TRUE,
                            ncol = 1, horiz = FALSE, title = NULL, inset = 0, xpd, title.col = text.col,
                            title.adj = 0.5, seg.len = 2, xbox = 1, ybox = 1, title.cex = cex)
{



  if (missing(legend) && !missing(y) && (is.character(y) ||
                                         is.expression(y))) {
    legend <- y
    y <- NULL
  }
  mfill <- !missing(fill) || !missing(density)
  if (!missing(xpd)) {
    op <- par("xpd")
    on.exit(par(xpd = op))
    par(xpd = xpd)
  }
  title <- as.graphicsAnnot(title)
  if (length(title) > 1)
    stop("invalid 'title'")
  legend <- as.graphicsAnnot(legend)
  n.leg <- if (is.call(legend))
    1
  else length(legend)
  if (n.leg == 0)
    stop("'legend' is of length 0")
  auto <- if (is.character(x))
    match.arg(x, c("bottomright", "bottom", "bottomleft",
                   "left", "topleft", "top", "topright", "right", "center"))
  else NA
  if (is.na(auto)) {
    xy <- xy.coords(x, y)
    x <- xy$x
    y <- xy$y
    nx <- length(x)
    if (nx < 1 || nx > 2)
      stop("invalid coordinate lengths")
  }
  else nx <- 0
  xlog <- par("xlog")
  ylog <- par("ylog")

  rect2 <- function(left, top, dx, dy, density = NULL, angle,
                    ...) {
    r <- left + dx
    if (xlog) {
      left <- 10^left
      r <- 10^r
    }
    b <- top - dy
    if (ylog) {
      top <- 10^top
      b <- 10^b
    }
    rect(left, top, r, b, angle = angle, density = density,
         ...)
  }
  segments2 <- function(x1, y1, dx, dy, ...) {
    x2 <- x1 + dx
    if (xlog) {
      x1 <- 10^x1
      x2 <- 10^x2
    }
    y2 <- y1 + dy
    if (ylog) {
      y1 <- 10^y1
      y2 <- 10^y2
    }
    segments(x1, y1, x2, y2, ...)
  }
  points2 <- function(x, y, ...) {
    if (xlog)
      x <- 10^x
    if (ylog)
      y <- 10^y
    points(x, y, ...)
  }
  text2 <- function(x, y, ...) {
    if (xlog)
      x <- 10^x
    if (ylog)
      y <- 10^y
    text(x, y, ...)
  }
  if (trace)
    catn <- function(...) do.call("cat", c(lapply(list(...),
                                                  formatC), list("\n")))
  cin <- par("cin")
  Cex <- cex * par("cex")
  pt.cex = pt.cex * par("cex")
  title.cex = title.cex * par("cex")
  if (is.null(text.width))
    text.width <- max(abs(strwidth(legend, units = "user",
                                   cex = pt.cex, font = text.font)))
  else if (!is.numeric(text.width) || text.width < 0)
    stop("'text.width' must be numeric, >= 0")
  xc <- Cex * xinch(cin[1L], warn.log = FALSE)
  yc <- Cex * yinch(cin[2L], warn.log = FALSE)

  if (xc < 0)
    text.width <- -text.width
  xchar <- xc
  xextra <- 0
  yextra <- yc * (y.intersp - 1)
  ymax <- yc * max(1, strheight(legend, units = "user", cex = pt.cex)/yc)
  ychar <- yextra + ymax
  if (trace)
    catn("  xchar=", xchar, "; (yextra,ychar)=", c(yextra,
                                                   ychar))
  if (mfill) {
    xbox <- xc * xbox * 0.8
    ybox <- yc * ybox * 0.5
    dx.fill <- xbox
  }
  do.lines <- (!missing(lty) && (is.character(lty) || any(lty >
                                                            0))) || !missing(lwd)
  n.legpercol <- if (horiz) {
    if (ncol != 1)
      warning(gettextf("horizontal specification overrides: Number of columns := %d",
                       n.leg), domain = NA)
    ncol <- n.leg
    1
  }
  else ceiling(n.leg/ncol)
  has.pch <- !missing(pch) && length(pch) > 0
  if (do.lines) {
    x.off <- if (merge)
      -0.7
    else 0
  }
  else if (merge)
    warning("'merge = TRUE' has no effect when no line segments are drawn")
  if (has.pch) {
    if (is.character(pch) && !is.na(pch[1L]) && nchar(pch[1L],
                                                      type = "c") > 1) {
      if (length(pch) > 1)
        warning("not using pch[2..] since pch[1L] has multiple chars")
      np <- nchar(pch[1L], type = "c")
      pch <- substr(rep.int(pch[1L], np), 1L:np, 1L:np)
    }
    if (!is.character(pch))
      pch <- as.integer(pch)
  }
  if (is.na(auto)) {
    if (xlog)
      x <- log10(x)
    if (ylog)
      y <- log10(y)
  }
  if (nx == 2) {
    x <- sort(x)
    y <- sort(y)
    left <- x[1L]
    top <- y[2L]
    w <- diff(x)
    h <- diff(y)
    w0 <- w/ncol
    x <- mean(x)
    y <- mean(y)
    if (missing(xjust))
      xjust <- 0.5
    if (missing(yjust))
      yjust <- 0.5
  }
  else {
    h <- (n.legpercol + (!is.null(title))) * ychar + yc
    w0 <- text.width + (x.intersp + 1) * xchar
    if (mfill)
      w0 <- w0 + dx.fill
    if (do.lines)
      w0 <- w0 + (seg.len + x.off) * xchar
    w <- ncol * w0 + 0.5 * xchar
    if (!is.null(title) && (abs(tw <- strwidth(title, units = "user",
                                               cex = title.cex) + 0.5 * xchar)) > abs(w)) {
      xextra <- (tw - w)/2
      w <- tw
    }
    if (is.na(auto)) {
      left <- x - xjust * w
      top <- y + (1 - yjust) * h
    }
    else {
      usr <- par("usr")
      inset <- rep_len(inset, 2)
      insetx <- inset[1L] * (usr[2L] - usr[1L])
      left <- switch(auto, bottomright = , topright = ,
                     right = usr[2L] - w - insetx, bottomleft = ,
                     left = , topleft = usr[1L] + insetx, bottom = ,
                     top = , center = (usr[1L] + usr[2L] - w)/2)
      insety <- inset[2L] * (usr[4L] - usr[3L])
      top <- switch(auto, bottomright = , bottom = , bottomleft = usr[3L] +
                      h + insety, topleft = , top = , topright = usr[4L] -
                      insety, left = , right = , center = (usr[3L] +
                                                             usr[4L] + h)/2)
    }
  }
  if (plot && bty != "n") {
    if (trace)
      catn("  rect2(", left, ",", top, ", w=", w, ", h=",
           h, ", ...)", sep = "")
    rect2(left, top, dx = w, dy = h, col = bg, density = NULL,
          lwd = box.lwd, lty = box.lty, border = box.col)
  }
  xt <- left + xchar + xextra + (w0 * rep.int(0:(ncol - 1),
                                              rep.int(n.legpercol, ncol)))[1L:n.leg]
  yt <- top - 0.5 * yextra - ymax - (rep.int(1L:n.legpercol,
                                             ncol)[1L:n.leg] - 1 + (!is.null(title))) * ychar

  if (mfill) {
    if (plot) {
      if (!is.null(fill))
        fill <- rep_len(fill, n.leg)
      rect2(left = xt, top = yt + ybox/2, dx = xbox, dy = ybox,
            col = fill, density = density, angle = angle,
            border = border)
    }
    xt <- xt + dx.fill
  }
  if (plot && (has.pch || do.lines))
    col <- rep_len(col, n.leg)
  if (missing(lwd) || is.null(lwd))
    lwd <- par("lwd")
  if (do.lines) {
    if (missing(lty) || is.null(lty))
      lty <- 1
    lty <- rep_len(lty, n.leg)
    lwd <- rep_len(lwd, n.leg)
    ok.l <- !is.na(lty) & (is.character(lty) | lty > 0) &
      !is.na(lwd)
    if (trace)
      catn("  segments2(", xt[ok.l] + x.off * xchar, ",",
           yt[ok.l], ", dx=", seg.len * xchar, ", dy=0, ...)")
    if (plot)
      segments2(xt[ok.l] + x.off * xchar, yt[ok.l], dx = seg.len *
                  xchar, dy = 0, lty = lty[ok.l], lwd = lwd[ok.l],
                col = col[ok.l])
    xt <- xt + (seg.len + x.off) * xchar
  }
  if (has.pch) {
    pch <- rep_len(pch, n.leg)
    pt.bg <- rep_len(pt.bg, n.leg)
    pt.cex <- rep_len(pt.cex, n.leg)
    pt.lwd <- rep_len(pt.lwd, n.leg)
    ok <- !is.na(pch)
    if (!is.character(pch)) {
      ok <- ok & (pch >= 0 | pch <= -32)
    }
    else {
      ok <- ok & nzchar(pch)
    }
    x1 <- (if (merge && do.lines)
      xt - (seg.len/2) * xchar
      else xt)[ok]
    y1 <- yt[ok]
    if (trace)
      catn("  points2(", x1, ",", y1, ", pch=", pch[ok],
           ", ...)")
    if (plot)
      points2(x1, y1, pch = pch[ok], col = col[ok], cex = pt.cex[ok],
              bg = pt.bg[ok], lwd = pt.lwd[ok])
  }
  xt <- xt + x.intersp * xchar
  if (plot) {
    if (!is.null(title))
      text2(left + w * title.adj, top - ymax, labels = title,
            adj = c(title.adj, 0), cex = title.cex, col = title.col)
    text2(xt, yt, labels = legend, adj = adj, cex = pt.cex,
          col = text.col, font = text.font)
  }
  invisible(list(rect = list(w = w, h = h, left = left, top = top),
                 text = list(x = xt, y = yt)))
}