#' Annotation: tick marks
#'
#' This annotation adds tick marks to an axis
#'
#' @export
#' @inheritParams ggplot2::annotation_logticks
#' @param scale character, vector of type of scale attributed to each corresponding side, Default: 'identity'
#' @param ticks_per_base integer, number of minor ticks between each pair of major ticks, Default: NULL
#' @details
#' If scale is of length one it will be replicated to the number of sides given, but if the
#' length of scale is larger than one it must match the number of sides given.
#' If ticks_per_base is set to NULL the function infers the number of ticks per base to be
#' the base of the scale - 1, for example log scale is base exp(1) and
#' log10 and identity are base 10. If ticks_per_base is given it follows the same logic as scale.
#' @examples
#'
#' p <- ggplot(msleep, aes(bodywt, brainwt)) + geom_point()
#'
#' # Default behavior
#'
#' # add identity scale minor ticks on y axis
#' p + annotation_ticks(sides = 'l')
#'
#' # add identity scale minor ticks on x,y axis
#' p + annotation_ticks(sides = 'lb')
#'
#' # Control number of minor ticks of each side independently
#'
#' # add identity scale minor ticks on x,y axis
#' p + annotation_ticks(sides = 'lb', ticks_per_base = c(10,5))
#'
#' # log10 scale
#' p1 <- p + scale_x_log10()
#'
#' # add minor ticks on log10 scale
#' p1 + annotation_ticks(sides = 'b', scale = 'log10')
#'
#' # add minor ticks on both scales
#' p1 + annotation_ticks(sides = 'lb', scale = c('identity','log10'))
#'
#' # add minor ticks on both scales, but force x axis to be identity
#' p1 + annotation_ticks(sides = 'lb', scale = 'identity')
#'
#' # log scale
#' p2 <- p + scale_x_continuous(trans = 'log')
#'
#' # add minor ticks on log scale
#' p2 + annotation_ticks(sides = 'b', scale = 'log')
#'
#' # add minor ticks on both scales
#' p2 + annotation_ticks(sides = 'lb', scale = c('identity','log'))
#'
#' # add minor ticks on both scales, but force x axis to be identity
#' p2 + annotation_ticks(sides = 'lb', scale = 'identity')
#'
#' @import grid
#' @import ggplot2
#' @author Jonathan Sidi
#' @rdname annotation_ticks
annotation_ticks <- function(sides = "b",
                             scale = "identity",
                             scaled = TRUE,
                             short = unit(0.1, "cm"),
                             mid = unit(0.2, "cm"),
                             long = unit(0.3, "cm"),
                             colour = "black",
                             size = 0.5,
                             linetype = 1,
                             alpha = 1,
                             color = NULL,
                             ticks_per_base = NULL,
                             ...) {
  if (!is.null(color)) {
    colour <- color
  }

  # check for invalid side
  if (grepl("[^btlr]", sides)) {
    stop(gsub("[btlr]", "", sides), " is not a valid side: b,t,l,r are valid")
  }

  # split sides to character vector
  sides <- strsplit(sides, "")[[1]]

  if (length(sides) != length(scale)) {
    if (length(scale) == 1) {
      scale <- rep(scale, length(sides))
    } else {
      stop("Number of scales does not match the number of sides")
    }
  }

  base <- sapply(scale, function(x) switch(x, "identity" = 10, "log10" = 10, "log" = exp(1)), USE.NAMES = FALSE)

  if (missing(ticks_per_base)) {
    ticks_per_base <- base - 1
  } else {
    if ((length(sides) != length(ticks_per_base))) {
      if (length(ticks_per_base) == 1) {
        ticks_per_base <- rep(ticks_per_base, length(sides))
      } else {
        stop("Number of ticks_per_base does not match the number of sides")
      }
    }
  }

  delog <- scale %in% "identity"

  layer(
    data = data.frame(x = NA),
    mapping = NULL,
    stat = StatIdentity,
    geom = GeomTicks,
    position = PositionIdentity,
    show.legend = FALSE,
    inherit.aes = FALSE,
    params = list(
      base = base,
      sides = sides,
      scaled = scaled,
      short = short,
      mid = mid,
      long = long,
      colour = colour,
      size = size,
      linetype = linetype,
      alpha = alpha,
      ticks_per_base = ticks_per_base,
      delog = delog,
      ...
    )
  )
}

#' Base ggproto classes for ggplot2
#'
#' If you are creating a new geom, stat, position, or scale in another package,
#' you'll need to extend from ggplot2::Geom, ggplot2::Stat, ggplot2::Position, or ggplot2::Scale.
#'
#' @seealso \code{\link[ggplot2]{ggplot2-ggproto}}
#' @usage NULL
#' @format NULL
#' @rdname ggplot2-ggproto
#' @export
GeomTicks <- ggproto(
  "GeomTicks", Geom,
  extra_params = "",
  handle_na = function(data, params) {
    data
  },

  draw_panel = function(data,
                        panel_scales,
                        coord,
                        base = c(10, 10),
                        sides = c("b", "l"),
                        scaled = TRUE,
                        short = unit(0.1, "cm"),
                        mid = unit(0.2, "cm"),
                        long = unit(0.3, "cm"),
                        ticks_per_base = base - 1,
                        delog = c(x = TRUE, y = TRUE)) {
    ticks <- list()

    # Convert these units to numbers so that they can be put in data frames
    short <- convertUnit(short, "cm", valueOnly = TRUE)
    mid <- convertUnit(mid, "cm", valueOnly = TRUE)
    long <- convertUnit(long, "cm", valueOnly = TRUE)

    for (s in 1:length(sides)) {
      if (grepl("[b|t]", sides[s])) {

        # Get positions of x tick marks
        xticks <- calc_ticks(
          base = base[s],
          minpow = floor(panel_scales$x.range[1]),
          maxpow = ceiling(panel_scales$x.range[2]),
          majorTicks = panel_scales$x.major_source,
          start = 0,
          shortend = short,
          midend = mid,
          longend = long,
          ticks_per_base = ticks_per_base[s],
          delog = delog[s]
        )

        if (scaled) {
          if (!delog[s]) {
            xticks$value <- log(xticks$value, base[s])
          }
        }

        names(xticks)[names(xticks) == "value"] <- "x" # Rename to 'x' for coordinates$transform

        xticks <- coord$transform(xticks, panel_scales)

        # Make the grobs
        if (grepl("b", sides[s])) {
          ticks$x_b <- with(
            data,
            segmentsGrob(
              x0 = unit(xticks$x, "native"),
              x1 = unit(xticks$x, "native"),
              y0 = unit(xticks$start, "cm"),
              y1 = unit(xticks$end, "cm"),
              gp = gpar(
                col = alpha(colour, alpha),
                lty = linetype,
                lwd = size * .pt
              )
            )
          )
        }
        if (grepl("t", sides[s])) {
          ticks$x_t <- with(
            data,
            segmentsGrob(
              x0 = unit(xticks$x, "native"),
              x1 = unit(xticks$x, "native"),
              y0 = unit(1, "npc") - unit(xticks$start, "cm"),
              y1 = unit(1, "npc") - unit(xticks$end, "cm"),
              gp = gpar(
                col = alpha(colour, alpha),
                lty = linetype,
                lwd = size * .pt
              )
            )
          )
        }
      }


      if (grepl("[l|r]", sides[s])) {
        yticks <- calc_ticks(
          base = base[s],
          minpow = floor(panel_scales$y.range[1]),
          maxpow = ceiling(panel_scales$y.range[2]),
          majorTicks = panel_scales$y.major_source,
          start = 0,
          shortend = short,
          midend = mid,
          longend = long,
          ticks_per_base = ticks_per_base[s],
          delog = delog[s]
        )

        if (scaled) {
          if (!delog[s]) {
            yticks$value <- log(yticks$value, base[s])
          }
        }

        names(yticks)[names(yticks) == "value"] <- "y" # Rename to 'y' for coordinates$transform
        yticks <- coord$transform(yticks, panel_scales)

        # Make the grobs
        if (grepl("l", sides[s])) {
          ticks$y_l <- with(
            data,
            segmentsGrob(
              y0 = unit(yticks$y, "native"),
              y1 = unit(yticks$y, "native"),
              x0 = unit(yticks$start, "cm"),
              x1 = unit(yticks$end, "cm"),
              gp = gpar(
                col = alpha(colour, alpha),
                lty = linetype, lwd = size * .pt
              )
            )
          )
        }
        if (grepl("r", sides[s])) {
          ticks$y_r <- with(
            data,
            segmentsGrob(
              y0 = unit(yticks$y, "native"),
              y1 = unit(yticks$y, "native"),
              x0 = unit(1, "npc") - unit(yticks$start, "cm"),
              x1 = unit(1, "npc") - unit(yticks$end, "cm"),
              gp = gpar(
                col = alpha(colour, alpha),
                lty = linetype,
                lwd = size * .pt
              )
            )
          )
        }
      }
    }
    gTree(children = do.call("gList", ticks))
  },
  default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = 1)
)


# Calculate the position of log tick marks Returns data frame with: - value: the
# position of the log tick on the data axis, for example 1, 2, ..., 9, 10, 20, ...
# - start: on the other axis, start position of the line (usually 0) - end: on the
# other axis, end position of the line (for example, .1, .2, or .3)
calc_ticks <- function(base = 10,
                       ticks_per_base = base - 1,
                       minpow = 0,
                       maxpow = minpow + 1,
                       majorTicks = 0,
                       start = 0,
                       shortend = 0.1,
                       midend = 0.2,
                       longend = 0.3,
                       delog = FALSE) {

  # Number of blocks of tick marks
  reps <- maxpow - minpow

  # For base 10: 1, 2, 3, ..., 7, 8, 9, 1, 2, ...
  ticknums <- rep(seq(1, base - 1, length.out = ticks_per_base), reps)

  # For base 10: 1, 1, 1, ..., 1, 1, 1, 2, 2, ... (for example)
  powers <- rep(seq(minpow, maxpow - 1), each = ticks_per_base)

  ticks <- ticknums * base ^ powers

  ticks <- c(ticks, base ^ maxpow) # Add the last tick mark

  # Set all of the ticks short
  tickend <- rep(shortend, length(ticks))

  # Get the position within each cycle, 0, 1, 2, ..., 8, 0, 1, 2. ...
  cycleIdx <- ticknums - 1

  # Set the 'major' ticks long
  tickend[cycleIdx == 0] <- longend

  # Where to place the longer tick marks that are between each base For base 10, this
  # will be at each 5
  longtick_after_base <- floor(ticks_per_base / 2)
  tickend[cycleIdx == longtick_after_base] <- midend

  if (delog) {
    ticksCopy <- ticks

    regScale <- log(ticks, base)

    majorTicks <- sort(
      unique(
        c(
          minpow,
          regScale[which(regScale %in% majorTicks)],
          maxpow,
          majorTicks
        )
      )
    )

    expandScale <- c()

    if (length(majorTicks) > 1) {
      for (i in 1:(length(majorTicks) - 1)) {
        expandScale <- c(
          expandScale,
          seq(majorTicks[i], majorTicks[i + 1], length.out = (ticks_per_base + 1))
        )
      }

      ticks <- unique(expandScale)

      # Set all of the ticks short
      tickend <- rep(shortend, length(ticks))

      # Set the 'major' ticks long
      tickend[which(ticks %in% majorTicks)] <- longend
    }
  }

  tickdf <- data.frame(value = ticks, start = start, end = tickend)

  tickdf
}