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#' Annotation: log tick marks
#'
#' This annotation adds log tick marks with diminishing spacing.
#' These tick marks probably make sense only for base 10.
#'
#' @param base the base of the log (default 10)
#' @param sides a string that controls which sides of the plot the log ticks appear on.
#' It can be set to a string containing any of \code{"trbl"}, for top, right,
#' bottom, and left.
#' @param short a \code{unit} object specifying the length of the short tick marks
#' @param mid a \code{unit} object specifying the length of the middle tick marks.
#' In base 10, these are the "5" ticks.
#' @param long a \code{unit} object specifying the length of the long tick marks.
#' In base 10, these are the "1" (or "10") ticks.
#' @param scaled is the data already log-scaled? This should be \code{TRUE}
#' (default) when the data is already transformed with \code{log10()} or when
#' using \code{scale_y_log10}. It should be \code{FALSE} when using
#' \code{coord_trans(y = "log10")}.
#' @param colour Colour of the tick marks.
#' @param size Thickness of tick marks, in mm.
#' @param linetype Linetype of tick marks (\code{solid}, \code{dashed}, etc.)
#' @param alpha The transparency of the tick marks.
#' @param color An alias for \code{colour}.
#' @param ... Other parameters passed on to the layer
#'
#' @export
#' @seealso \code{\link{scale_y_continuous}}, \code{\link{scale_y_log10}} for log scale
#' transformations.
#' @seealso \code{\link{coord_trans}} for log coordinate transformations.
#'
#' @examples
#' # Make a log-log plot (without log ticks)
#' library(MASS)
#' library(scales)
#' a <- ggplot(Animals, aes(x = body, y = brain)) + geom_point() +
#' scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x),
#' labels = trans_format("log10", math_format(10^.x))) +
#' scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x),
#' labels = trans_format("log10", math_format(10^.x))) +
#' theme_bw()
#'
#' a + annotation_logticks() # Default: log ticks on bottom and left
#' a + annotation_logticks(sides = "lr") # Log ticks for y, on left and right
#' a + annotation_logticks(sides = "trbl") # All four sides
#'
#' # Hide the minor grid lines because they don't align with the ticks
#' a + annotation_logticks(sides = "trbl") + theme(panel.grid.minor = element_blank())
#'
#'
#' # Another way to get the same results as 'a' above: log-transform the data before
# plotting it. Also hide the minor grid lines.
#' b <- ggplot(Animals, aes(x = log10(body), y = log10(brain))) + geom_point() +
#' scale_x_continuous(name = "body", labels = math_format(10^.x)) +
#' scale_y_continuous(name = "brain", labels = math_format(10^.x)) +
#' theme_bw()+ theme(panel.grid.minor = element_blank())
#'
#' b + annotation_logticks()
#'
#'
#' # This shows log(x) on the axes
#' d <- ggplot(Animals, aes(x = log10(body), y = log10(brain))) + geom_point() +
#' theme_bw()
#'
#' d + annotation_logticks()
#'
#'
#' # Using a coordinate transform requires scaled = FALSE
#' t <- ggplot(Animals, aes(x = body, y = brain)) + geom_point() +
#' coord_trans(xtrans = "log10", ytrans = "log10") + theme_bw()
#'
#' t + annotation_logticks(scaled = FALSE)
#'
#'
#' # Change the length of the ticks
#' library(grid)
#' a + annotation_logticks(short = unit(.5,"mm"), mid = unit(3,"mm"), long = unit(4,"mm"))
#'
annotation_logticks <- function (base = 10, sides = "bl", 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, ...) {
if (!is.null(color))
colour <- color
layer(
geom = "logticks",
geom_params = list(base = base, sides = sides, raw = raw, scaled = scaled,
short = short, mid = mid, long = long, colour = colour,
size = size, linetype = linetype, alpha = alpha, ...),
stat = "identity",
data = data.frame(x = NA),
mapping = NULL,
inherit.aes = FALSE,
show_guide = FALSE
)
}
GeomLogticks <- proto(Geom, {
objname <- "logticks"
draw_groups <- function(., data, scales, coordinates, base = 10, sides = "bl",
scaled = TRUE, short = unit(0.1, "cm"), mid = unit(0.2, "cm"),
long = unit(0.3, "cm"), ...) {
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)
if (grepl("[b|t]", sides)) {
# Get positions of x tick marks
xticks <- calc_logticks(base = base,
minpow = floor(scales$x.range[1]), maxpow = ceiling(scales$x.range[2]),
start = 0, shortend = short, midend = mid, longend = long)
if (scaled)
xticks$value <- log(xticks$value, base)
names(xticks)[names(xticks)=="value"] <- "x" # Rename to 'x' for coord_transform
xticks <- coord_transform(coordinates, xticks, scales)
# Make the grobs
if(grepl("b", sides)) {
ticks$x_b <- with(data, segmentsGrob(
x0 = unit(xticks$x, "native"), x1 = unit(xticks$x, "native"),
y0 = unit(xticks$start, "cm"), y1 = unit(xticks$end, "cm"),
gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = size * .pt)
))
}
if(grepl("t", sides)) {
ticks$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)) {
yticks <- calc_logticks(base = base,
minpow = floor(scales$y.range[1]), maxpow = ceiling(scales$y.range[2]),
start = 0, shortend = short, midend = mid, longend = long)
if (scaled)
yticks$value <- log(yticks$value, base)
names(yticks)[names(yticks)=="value"] <- "y" # Rename to 'y' for coord_transform
yticks <- coord_transform(coordinates, yticks, scales)
# Make the grobs
if(grepl("l", sides)) {
ticks$y_l <- with(data, segmentsGrob(
y0 = unit(yticks$y, "native"), y1 = unit(yticks$y, "native"),
x0 = unit(yticks$start, "cm"), x1 = unit(yticks$end, "cm"),
gp = gpar(col = alpha(colour, alpha), lty = linetype, lwd = size * .pt)
))
}
if(grepl("r", sides)) {
ticks$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_stat <- function(.) StatIdentity
default_aes <- function(.) 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_logticks <- function(base = 10, ticks_per_base = base - 1,
minpow = 0, maxpow = minpow + 1, start = 0, shortend = .1, midend = .2, longend = .3) {
# 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
tickdf <- data.frame(value = ticks, start = start, end = tickend)
return(tickdf)
}
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