From 7267f02b3c3c848473b4bc5b3f8ed49b98599693 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Fri, 27 Oct 2023 16:19:13 +0200
Subject: [PATCH 01/18] fix recycle bug

---
 R/guide-.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/guide-.R b/R/guide-.R
index a3f449b9ed..4acbf855d2 100644
--- a/R/guide-.R
+++ b/R/guide-.R
@@ -381,7 +381,7 @@ Guide <- ggproto(
     pos <- unname(c(top = 1, bottom = 0, left = 0, right = 1)[position])
     dir <- -2 * pos + 1
     pos <- unit(rep(pos, 2 * n_breaks), "npc")
-    dir <- rep(vec_interleave(dir, 0), n_breaks) * tick_len
+    dir <- rep(vec_interleave(dir, 0), n_breaks) * rep(tick_len, each = 2)
     tick <- pos + dir
 
     # Build grob

From 77d83ba208bf6cb1dceb2582d48a3d887ab37a90 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Fri, 27 Oct 2023 16:19:59 +0200
Subject: [PATCH 02/18] set default minor.ticks in axis

---
 R/guide-axis.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/guide-axis.R b/R/guide-axis.R
index 6f15c1f23e..dd7ca85cdc 100644
--- a/R/guide-axis.R
+++ b/R/guide-axis.R
@@ -108,7 +108,7 @@ GuideAxis <- ggproto(
     minor_length = "axis.minor.ticks.length"
   ),
 
-  extract_key = function(scale, aesthetic, minor.ticks, ...) {
+  extract_key = function(scale, aesthetic, minor.ticks = FALSE, ...) {
     major <- Guide$extract_key(scale, aesthetic, ...)
     if (!minor.ticks) {
       return(major)

From 43964f7ffdb37e4e665fc2fdcc3f428e5ba1bbf0 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Fri, 27 Oct 2023 16:28:41 +0200
Subject: [PATCH 03/18] Draft guide

---
 R/guide-axis-logticks.R | 145 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 145 insertions(+)
 create mode 100644 R/guide-axis-logticks.R

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
new file mode 100644
index 0000000000..8d70fbcd12
--- /dev/null
+++ b/R/guide-axis-logticks.R
@@ -0,0 +1,145 @@
+
+guide_axis_logticks <- function(
+  long  = rel(2.25),
+  mid   = rel(1.5),
+  short = rel(0.75),
+  prescale_base = NULL,
+  negative_small = 0.1,
+  cap = "none",
+  ...
+) {
+  if (is.logical(cap)) {
+    check_bool(cap)
+    cap <- if (cap) "both" else "none"
+  }
+  cap <- arg_match0(cap, c("none", "both", "upper", "lower"))
+
+  check_fun <- function(x) (is.rel(x) || is.unit(x)) && length(x) == 1
+  what <- "a {.cls rel} or {.cls unit} object of length 1"
+  check_object(long,  check_fun, what)
+  check_object(mid,   check_fun, what)
+  check_object(short, check_fun, what)
+
+  new_guide(
+    available_aes  = c("x", "y"),
+    prescale_base  = prescale_base,
+    negative_small = negative_small,
+    long  = long,
+    mid   = mid,
+    short = short,
+    minor.ticks = TRUE,
+    ...,
+    super = GuideAxisLogticks
+  )
+}
+
+
+GuideAxisLogticks <- ggproto(
+  "GuideAxisLogticks", GuideAxis,
+
+  params = defaults(
+    list(
+      prescale_base  = NULL,
+      negative_small = 0.1,
+      minor.ticks    = TRUE, # for spacing calculation
+      long  = rel(2.25),
+      mid   = rel(1.5),
+      short = rel(0.75)
+    ),
+    GuideAxis$params
+  ),
+
+  # Here we calculate a 'shadow key' that only applies to the tickmarks.
+  extract_params = function(scale, params, ...) {
+
+    if (scale$is_discrete()) {
+      cli::cli_abort("Cannot calculate logarithmic ticks for discrete scales.")
+    }
+
+    aesthetic   <- params$aesthetic
+    params$name <- paste0(params$name, "_", aesthetic)
+    params
+
+    # Reconstruct a transformation if user has prescaled data
+    if (!is.null(params$prescale_base)) {
+      trans <- log_trans(base = params$prescale_base)
+    } else {
+      trans <- scale$scale$trans
+    }
+
+    # Reconstruct original range
+    limits <- trans$inverse(scale$get_limits())
+    has_negatives <- any(limits < 0)
+
+    if (!has_negatives) {
+      start <- floor(log10(min(limits))) - 1L
+      end   <- ceiling(log10(max(limits))) + 1L
+    } else {
+      start <- log10(abs(params$negative_small))
+      end   <- ceiling(log10(max(abs(limits)))) + 1L
+    }
+
+    # Calculate tick marks
+    tens  <- 10^seq(start, end, by = 1)
+    fives <- tens * 5
+    ones  <- as.vector(outer(tens, setdiff(2:9, 5)))
+
+    # Set ticks back into transformed space
+    ticks  <- trans$transform(c(tens, fives, ones))
+    nticks <- c(length(tens), length(fives), length(ones))
+    type   <- 1:3
+
+    if (has_negatives) {
+      # Mirror ticks around 0
+      ticks  <- c(ticks, -ticks,  0)
+      nticks <- c(nticks, nticks, 1)
+      type   <- c(type,   type,   1)
+    }
+
+    logkey <- data_frame0(
+      !!aesthetic := ticks,
+      .type = rep(type, times = nticks)
+    )
+
+    # Discard out-of-bounds ticks
+    range  <- scale$continuous_range
+    logkey <- vec_slice(logkey, ticks > range[1] & ticks < range[2])
+
+    params$logkey <- logkey
+    params
+  },
+
+  transform = function(self, params, coord, panel_params) {
+    params <- GuideAxis$transform(params, coord, panel_params)
+    # Also transform the logkey
+    params$logkey <- coord$transform(params$logkey, panel_params)
+    params
+  },
+
+  override_elements = function(params, elements, theme) {
+    elements <- GuideAxis$override_elements(params, elements, theme)
+    length <- elements$major_length
+
+    # Multiply rel units with theme's tick length
+    tick_length <- lapply(params[c("long", "mid", "short")], function(x) {
+      if (is.rel(x)) unclass(x) * length else x
+    })
+    tick_length <- inject(unit.c(!!!tick_length))
+    elements$tick_length  <- tick_length
+
+    # We replace the lengths so that spacing calculation works out as intended
+    elements$major_length <- max(tick_length)
+    elements$minor_length <- min(tick_length)
+    elements
+  },
+
+  build_ticks = function(key, elements, params, position = params$opposite) {
+    # Instead of passing regular key, we pass the logkey
+    # In addition, we pass tick lengths directly
+    Guide$build_ticks(
+      params$logkey,
+      elements$ticks, params, position,
+      elements$tick_length[params$logkey$.type]
+    )
+  }
+)

From 59cca1060f722476ba7cf54a70ebecf5e09e26d3 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Fri, 27 Oct 2023 17:11:15 +0200
Subject: [PATCH 04/18] Better censoring in symmetric scales

---
 R/guide-axis-logticks.R | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 8d70fbcd12..f7dd33fb8e 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -69,13 +69,13 @@ GuideAxisLogticks <- ggproto(
 
     # Reconstruct original range
     limits <- trans$inverse(scale$get_limits())
-    has_negatives <- any(limits < 0)
+    has_negatives <- any(limits <= 0)
 
     if (!has_negatives) {
       start <- floor(log10(min(limits))) - 1L
       end   <- ceiling(log10(max(limits))) + 1L
     } else {
-      start <- log10(abs(params$negative_small))
+      start <- floor(log10(abs(params$negative_small)))
       end   <- ceiling(log10(max(abs(limits)))) + 1L
     }
 
@@ -87,19 +87,22 @@ GuideAxisLogticks <- ggproto(
     # Set ticks back into transformed space
     ticks  <- trans$transform(c(tens, fives, ones))
     nticks <- c(length(tens), length(fives), length(ones))
-    type   <- 1:3
+
+    logkey <- data_frame0(
+      !!aesthetic := ticks,
+      .type = rep(1:3, times = nticks)
+    )
 
     if (has_negatives) {
       # Mirror ticks around 0
-      ticks  <- c(ticks, -ticks,  0)
-      nticks <- c(nticks, nticks, 1)
-      type   <- c(type,   type,   1)
+      logkey <- vec_slice(logkey, logkey[[aesthetic]] >= params$negative_small)
+      mirror <- logkey
+      mirror[[aesthetic]] <- 1 * mirror[[aesthetic]]
+      zero <- data_frame0(!!aesthetic := 0, .type = 1L)
+      logkey <- vec_rbind(logkey, mirror, zero)
     }
 
-    logkey <- data_frame0(
-      !!aesthetic := ticks,
-      .type = rep(type, times = nticks)
-    )
+
 
     # Discard out-of-bounds ticks
     range  <- scale$continuous_range

From 788138b55bad100ce1b62f2e19605a21139bdd78 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Fri, 27 Oct 2023 17:11:37 +0200
Subject: [PATCH 05/18] internally cast args to `rel()`

---
 R/guide-axis-logticks.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index f7dd33fb8e..db727417a6 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -1,8 +1,8 @@
 
 guide_axis_logticks <- function(
-  long  = rel(2.25),
-  mid   = rel(1.5),
-  short = rel(0.75),
+  long  = 2.25,
+  mid   = 1.5,
+  short = 0.75,
   prescale_base = NULL,
   negative_small = 0.1,
   cap = "none",
@@ -14,6 +14,10 @@ guide_axis_logticks <- function(
   }
   cap <- arg_match0(cap, c("none", "both", "upper", "lower"))
 
+  if (is_bare_numeric(long))   long <- rel(long)
+  if (is_bare_numeric(mid))    mid  <- rel(mid)
+  if (is_bare_numeric(short)) short <- rel(short)
+
   check_fun <- function(x) (is.rel(x) || is.unit(x)) && length(x) == 1
   what <- "a {.cls rel} or {.cls unit} object of length 1"
   check_object(long,  check_fun, what)

From 47440a190965ca12cd22191b39a84101d8bbbe04 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Fri, 27 Oct 2023 17:23:39 +0200
Subject: [PATCH 06/18] change mirror strategy

---
 R/guide-axis-logticks.R | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index db727417a6..117df72c69 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -79,6 +79,7 @@ GuideAxisLogticks <- ggproto(
       start <- floor(log10(min(limits))) - 1L
       end   <- ceiling(log10(max(limits))) + 1L
     } else {
+      params$negative_small <- params$negative_small %||% 0.1
       start <- floor(log10(abs(params$negative_small)))
       end   <- ceiling(log10(max(abs(limits)))) + 1L
     }
@@ -88,6 +89,16 @@ GuideAxisLogticks <- ggproto(
     fives <- tens * 5
     ones  <- as.vector(outer(tens, setdiff(2:9, 5)))
 
+    if (has_negatives) {
+      # Filter and mirror ticks around 0
+      tens  <- tens[tens >= params$negative_small]
+      tens  <- c(tens, -tens, 0)
+      fives <- fives[fives >= params$negative_small]
+      fives <- c(fives, -fives)
+      ones  <- ones[ones >= params$negative_small]
+      ones  <- c(ones, -ones)
+    }
+
     # Set ticks back into transformed space
     ticks  <- trans$transform(c(tens, fives, ones))
     nticks <- c(length(tens), length(fives), length(ones))
@@ -97,17 +108,6 @@ GuideAxisLogticks <- ggproto(
       .type = rep(1:3, times = nticks)
     )
 
-    if (has_negatives) {
-      # Mirror ticks around 0
-      logkey <- vec_slice(logkey, logkey[[aesthetic]] >= params$negative_small)
-      mirror <- logkey
-      mirror[[aesthetic]] <- 1 * mirror[[aesthetic]]
-      zero <- data_frame0(!!aesthetic := 0, .type = 1L)
-      logkey <- vec_rbind(logkey, mirror, zero)
-    }
-
-
-
     # Discard out-of-bounds ticks
     range  <- scale$continuous_range
     logkey <- vec_slice(logkey, ticks > range[1] & ticks < range[2])

From 5777f6ebd3380e9d43f8c3b107a4b33c9b6aec80 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 09:36:16 +0200
Subject: [PATCH 07/18] interpret numeric as `rel()`

---
 R/guide-axis-logticks.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 117df72c69..4993381b81 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -46,9 +46,9 @@ GuideAxisLogticks <- ggproto(
       prescale_base  = NULL,
       negative_small = 0.1,
       minor.ticks    = TRUE, # for spacing calculation
-      long  = rel(2.25),
-      mid   = rel(1.5),
-      short = rel(0.75)
+      long  = 2.25,
+      mid   = 1.5,
+      short = 0.75
     ),
     GuideAxis$params
   ),
@@ -129,7 +129,7 @@ GuideAxisLogticks <- ggproto(
 
     # Multiply rel units with theme's tick length
     tick_length <- lapply(params[c("long", "mid", "short")], function(x) {
-      if (is.rel(x)) unclass(x) * length else x
+      if (is.unit(x)) x else unclass(x) * length
     })
     tick_length <- inject(unit.c(!!!tick_length))
     elements$tick_length  <- tick_length

From e39ea607e3bd097242ae3fbf70c3163e72440146 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 10:37:08 +0200
Subject: [PATCH 08/18] warn when prescale_base and scale transform are set

---
 R/guide-axis-logticks.R | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 4993381b81..084c9a9f1e 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -66,6 +66,13 @@ GuideAxisLogticks <- ggproto(
 
     # Reconstruct a transformation if user has prescaled data
     if (!is.null(params$prescale_base)) {
+      trans_name <- scale$scale$trans$name
+      if (trans_name != "identity") {
+        cli::cli_warn(paste0(
+          "The {.arg prescale_base} argument will override the scale's ",
+          "{.field {trans_name}} transformation in log-tick positioning."
+        ))
+      }
       trans <- log_trans(base = params$prescale_base)
     } else {
       trans <- scale$scale$trans
@@ -87,7 +94,7 @@ GuideAxisLogticks <- ggproto(
     # Calculate tick marks
     tens  <- 10^seq(start, end, by = 1)
     fives <- tens * 5
-    ones  <- as.vector(outer(tens, setdiff(2:9, 5)))
+    ones  <- as.vector(outer(setdiff(2:9, 5), tens))
 
     if (has_negatives) {
       # Filter and mirror ticks around 0
@@ -110,7 +117,7 @@ GuideAxisLogticks <- ggproto(
 
     # Discard out-of-bounds ticks
     range  <- scale$continuous_range
-    logkey <- vec_slice(logkey, ticks > range[1] & ticks < range[2])
+    logkey <- vec_slice(logkey, ticks >= range[1] & ticks <= range[2])
 
     params$logkey <- logkey
     params

From 02913a1d7bf2f71ee962cab469676585de345e93 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 10:49:09 +0200
Subject: [PATCH 09/18] add control over whether to use expanded range

---
 R/guide-axis-logticks.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 084c9a9f1e..06145748e7 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -5,6 +5,7 @@ guide_axis_logticks <- function(
   short = 0.75,
   prescale_base = NULL,
   negative_small = 0.1,
+  expanded = TRUE,
   cap = "none",
   ...
 ) {
@@ -23,11 +24,13 @@ guide_axis_logticks <- function(
   check_object(long,  check_fun, what)
   check_object(mid,   check_fun, what)
   check_object(short, check_fun, what)
+  check_bool(expanded)
 
   new_guide(
     available_aes  = c("x", "y"),
     prescale_base  = prescale_base,
     negative_small = negative_small,
+    expanded       = expanded,
     long  = long,
     mid   = mid,
     short = short,
@@ -48,7 +51,8 @@ GuideAxisLogticks <- ggproto(
       minor.ticks    = TRUE, # for spacing calculation
       long  = 2.25,
       mid   = 1.5,
-      short = 0.75
+      short = 0.75,
+      expanded = TRUE
     ),
     GuideAxis$params
   ),
@@ -116,7 +120,7 @@ GuideAxisLogticks <- ggproto(
     )
 
     # Discard out-of-bounds ticks
-    range  <- scale$continuous_range
+    range <- if (params$expanded) scale$continuous_range else scale$get_limits()
     logkey <- vec_slice(logkey, ticks >= range[1] & ticks <= range[2])
 
     params$logkey <- logkey

From 732478a005a9bc06d4adc3c9663a0b37eb282424 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 10:49:41 +0200
Subject: [PATCH 10/18] negative_small cannot be 0 or negative

---
 R/guide-axis-logticks.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 06145748e7..76ac071af2 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -24,6 +24,11 @@ guide_axis_logticks <- function(
   check_object(long,  check_fun, what)
   check_object(mid,   check_fun, what)
   check_object(short, check_fun, what)
+  check_number_decimal(
+    negative_small, min = 1e-100, # minimal domain of scales::log_trans
+    allow_infinite = FALSE,
+    allow_null = TRUE
+  )
   check_bool(expanded)
 
   new_guide(

From 94bcae9d1e4940fabfa03b44ef4a56c19dcff7a7 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 11:04:08 +0200
Subject: [PATCH 11/18] capping works with new ticks

---
 R/guide-axis-logticks.R | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 76ac071af2..b0dd0acc16 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -39,6 +39,7 @@ guide_axis_logticks <- function(
     long  = long,
     mid   = mid,
     short = short,
+    cap   = cap,
     minor.ticks = TRUE,
     ...,
     super = GuideAxisLogticks
@@ -128,6 +129,14 @@ GuideAxisLogticks <- ggproto(
     range <- if (params$expanded) scale$continuous_range else scale$get_limits()
     logkey <- vec_slice(logkey, ticks >= range[1] & ticks <= range[2])
 
+    # Adjust capping based on these ticks instead of regular ticks
+    if (params$cap %in% c("both", "upper")) {
+      params$decor[[aesthetic]][2] <- max(logkey[[aesthetic]])
+    }
+    if (params$cap %in% c("both", "lower")) {
+      params$decor[[aesthetic]][1] <- min(logkey[[aesthetic]])
+    }
+
     params$logkey <- logkey
     params
   },

From adb00d03869113ceee12fdb9dbe038b69b962f0c Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 11:47:42 +0200
Subject: [PATCH 12/18] Add tests

---
 tests/testthat/_snaps/guides.md               |   4 +
 .../logtick-axes-with-customisation.svg       | 206 ++++++++++++++++++
 tests/testthat/test-guides.R                  | 101 +++++++++
 3 files changed, 311 insertions(+)
 create mode 100644 tests/testthat/_snaps/guides/logtick-axes-with-customisation.svg

diff --git a/tests/testthat/_snaps/guides.md b/tests/testthat/_snaps/guides.md
index 6fb109ecbd..f9c0dddd45 100644
--- a/tests/testthat/_snaps/guides.md
+++ b/tests/testthat/_snaps/guides.md
@@ -65,6 +65,10 @@
     Breaks are not formatted correctly for a bin legend.
     i Use `(<lower>, <upper>]` format to indicate bins.
 
+# guide_axis_logticks calculates appropriate ticks
+
+    The `prescale_base` argument will override the scale's log-10 transformation in log-tick positioning.
+
 # binning scales understand the different combinations of limits, breaks, labels, and show.limits
 
     `show.limits` is ignored when `labels` are given as a character vector.
diff --git a/tests/testthat/_snaps/guides/logtick-axes-with-customisation.svg b/tests/testthat/_snaps/guides/logtick-axes-with-customisation.svg
new file mode 100644
index 0000000000..8ad941b27d
--- /dev/null
+++ b/tests/testthat/_snaps/guides/logtick-axes-with-customisation.svg
@@ -0,0 +1,206 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' class='svglite' data-engine-version='2.0' width='720.00pt' height='576.00pt' viewBox='0 0 720.00 576.00'>
+<defs>
+  <style type='text/css'><![CDATA[
+    .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle {
+      fill: none;
+      stroke: #000000;
+      stroke-linecap: round;
+      stroke-linejoin: round;
+      stroke-miterlimit: 10.00;
+    }
+  ]]></style>
+</defs>
+<rect width='100%' height='100%' style='stroke: none; fill: #FFFFFF;'/>
+<defs>
+  <clipPath id='cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA='>
+    <rect x='0.00' y='0.00' width='720.00' height='576.00' />
+  </clipPath>
+</defs>
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+<text x='360.00' y='32.64' text-anchor='middle' style='font-size: 11.00px; font-family: sans;' textLength='274.57px' lengthAdjust='spacingAndGlyphs'>Negative length pseudo-logticks with 0.1 as smallest tick</text>
+<text x='360.00' y='568.24' text-anchor='middle' style='font-size: 11.00px; font-family: sans;' textLength='187.11px' lengthAdjust='spacingAndGlyphs'>Pseudo-logticks with 1 as smallest tick</text>
+<text transform='translate(13.05,293.57) rotate(-90)' text-anchor='middle' style='font-size: 11.00px; font-family: sans;' textLength='207.31px' lengthAdjust='spacingAndGlyphs'>Inverted logticks with swapped tick lengths</text>
+<text transform='translate(704.67,293.57) rotate(90)' text-anchor='middle' style='font-size: 11.00px; font-family: sans;' textLength='212.23px' lengthAdjust='spacingAndGlyphs'>Capped and not-expanded inverted logticks</text>
+<text x='46.01' y='14.56' style='font-size: 13.20px; font-family: sans;' textLength='180.51px' lengthAdjust='spacingAndGlyphs'>logtick axes with customisation</text>
+</g>
+</svg>
diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R
index 6f7e241c92..a2f0e59529 100644
--- a/tests/testthat/test-guides.R
+++ b/tests/testthat/test-guides.R
@@ -344,6 +344,71 @@ test_that("guide_colourbar warns about discrete scales", {
 
 })
 
+test_that("guide_axis_logticks calculates appropriate ticks", {
+
+  test_scale <- function(trans = "identity", limits = c(NA, NA)) {
+    scale <- scale_x_continuous(trans = trans)
+    scale$train(scale$transform(limits))
+    view_scale_primary(scale)
+  }
+
+  train_guide <- function(guide, scale) {
+    params <- guide$params
+    params$position <- "bottom"
+    guide$train(params, scale, "x")
+  }
+
+  guide <- guide_axis_logticks(negative_small = 10)
+  outcome <- c((1:10)*10, (2:10)*100)
+
+  # Test the classic log10 transformation
+  scale <- test_scale("log10", c(10, 1000))
+  key <- train_guide(guide, scale)$logkey
+
+  expect_equal(sort(key$x), log10(outcome))
+  expect_equal(key$.type, rep(c(1,2,3), c(3, 2, 14)))
+
+  # Test compound transformation
+  scale <- test_scale(c("log10", "reverse"), c(10, 1000))
+  key   <- train_guide(guide, scale)$logkey
+
+  expect_equal(sort(key$x), -log10(rev(outcome)))
+
+  # Test transformation with negatives
+  scale <- test_scale("pseudo_log", c(-1000, 1000))
+  key   <- train_guide(guide, scale)$logkey
+
+  unlog <- sort(pseudo_log_trans()$inverse(key$x))
+  expect_equal(unlog, c(-rev(outcome), 0, outcome))
+  expect_equal(key$.type, rep(c(1,2,3), c(7, 4, 28)))
+
+  # Test expanded argument
+  scale <- test_scale("log10", c(20, 900))
+  scale$continuous_range <- c(1, 3)
+
+  guide <- guide_axis_logticks(expanded = TRUE)
+  key   <- train_guide(guide, scale)$logkey
+
+  expect_equal(sort(key$x), log10(outcome))
+
+  guide <- guide_axis_logticks(expanded = FALSE)
+  key   <- train_guide(guide, scale)$logkey
+
+  expect_equal(sort(key$x), log10(outcome[-c(1, length(outcome))]))
+
+  # Test with prescaled input
+  guide <- guide_axis_logticks(prescale_base = 2)
+  scale <- test_scale(limits = log2(c(10, 1000)))
+
+  key <- train_guide(guide, scale)$logkey
+  expect_equal(sort(key$x), log2(outcome))
+
+  # Should warn when scale also has transformation
+  scale <- test_scale("log10", limits = c(10, 1000))
+  expect_snapshot_warning(train_guide(guide, scale)$logkey)
+
+})
+
 # Visual tests ------------------------------------------------------------
 
 test_that("axis guides are drawn correctly", {
@@ -549,6 +614,42 @@ test_that("axis guides can be capped", {
   expect_doppelganger("axis guides with capped ends", p)
 })
 
+test_that("logticks look as they should", {
+
+  p <- ggplot(data.frame(x = c(-100, 100), y = c(10, 1000)), aes(x, y)) +
+    geom_point() +
+    scale_y_continuous(trans = c("log10", "reverse"),
+                       expand = expansion(add = 0.5)) +
+    scale_x_continuous(
+      breaks = c(-100, -10, -1, 0, 1, 10, 100)
+    ) +
+    coord_trans(x = "pseudo_log") +
+    theme_test() +
+    theme(axis.line = element_line(colour = "black"),
+          panel.border = element_blank(),
+          axis.ticks.length.x.top = unit(-2.75, "pt")) +
+    guides(
+      x = guide_axis_logticks(
+        title = "Pseudo-logticks with 1 as smallest tick",
+        negative_small = 1
+      ),
+      y = guide_axis_logticks(
+        title = "Inverted logticks with swapped tick lengths",
+        long = 0.75, short = 2.25
+      ),
+      x.sec = guide_axis_logticks(
+        negative_small = 0.1,
+        title = "Negative length pseudo-logticks with 0.1 as smallest tick"
+      ),
+      y.sec = guide_axis_logticks(
+        expanded = FALSE, cap = "both",
+        title = "Capped and not-expanded inverted logticks"
+      )
+    )
+  expect_doppelganger("logtick axes with customisation", p)
+
+})
+
 test_that("guides are positioned correctly", {
   df <- data_frame(x = 1, y = 1, z = factor("a"))
 

From 5b3271f03eb89d25b382f7c6a3e5c428dcd3952f Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 11:49:27 +0200
Subject: [PATCH 13/18] Document

---
 DESCRIPTION                |   1 +
 NAMESPACE                  |   2 +
 R/guide-axis-logticks.R    |  68 +++++++++++++++++++++++-
 man/ggplot2-ggproto.Rd     |  44 ++++++++--------
 man/guide_axis_logticks.Rd | 105 +++++++++++++++++++++++++++++++++++++
 5 files changed, 197 insertions(+), 23 deletions(-)
 create mode 100644 man/guide_axis_logticks.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 0f931609d9..281656cb67 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -174,6 +174,7 @@ Collate:
     'grouping.R'
     'guide-.R'
     'guide-axis.R'
+    'guide-axis-logticks.R'
     'guide-legend.R'
     'guide-bins.R'
     'guide-colorbar.R'
diff --git a/NAMESPACE b/NAMESPACE
index 717abb2e18..b0a5f61c82 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -211,6 +211,7 @@ export(GeomViolin)
 export(GeomVline)
 export(Guide)
 export(GuideAxis)
+export(GuideAxisLogticks)
 export(GuideBins)
 export(GuideColourbar)
 export(GuideColoursteps)
@@ -418,6 +419,7 @@ export(ggproto_parent)
 export(ggsave)
 export(ggtitle)
 export(guide_axis)
+export(guide_axis_logticks)
 export(guide_bins)
 export(guide_colorbar)
 export(guide_colorsteps)
diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index b0dd0acc16..2fe9ca5b35 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -1,4 +1,65 @@
-
+#' @include guide-axis.R
+NULL
+
+#' Axis with logarithmic tick marks
+#'
+#' This axis guide replaces the placement of ticks marks at intervals in
+#' log10 space.
+#'
+#' @param long,mid,short A [grid::unit()] object or [rel()] object setting
+#'   the (relative) length of the long, middle and short ticks. Numeric values
+#'   are interpreted as [rel()] objects. The [rel()] values are used to multiply
+#'   values of the `axis.ticks.length` theme setting.
+#' @param prescale_base Base of logarithm used to transform data manually. The
+#'   default, `NULL`, will use the scale transformation to calculate positions.
+#'   Only set `prescale_base` if the data has already been log-transformed.
+#'   When using a log-transform in the position scale or in `coord_trans()`,
+#'   keep the default `NULL` argument.
+#' @param negative_small When the scale limits include 0 or negative numbers,
+#'   what should be the smallest absolute value that is marked with a tick?
+#' @param expanded Whether the ticks should cover the range after scale
+#'   expansion (`TRUE`, default), or be restricted to the scale limits
+#'   (`FALSE`).
+#' @inheritParams guide_axis
+#' @inheritDotParams guide_axis -minor.ticks
+#'
+#' @export
+#'
+#' @examples
+#' # A standard plot
+#' p <- ggplot(msleep, aes(bodywt, brainwt)) +
+#'   geom_point(na.rm = TRUE)
+#'
+#' # The logticks axis works well with log scales
+#' p + scale_x_log10(guide = "axis_logticks") +
+#'   scale_y_log10(guide = "axis_logticks")
+#'
+#' # Or with log-transformed coordinates
+#' p + coord_trans(x = "log10", y = "log10") +
+#'   guides(x = "axis_logticks", y = "axis_logticks")
+#'
+#' # When data is transformed manually, one should provide `prescale_base`
+#' # Keep in mind that this axis uses log10 space for placement, not log2
+#' p + aes(x = log2(bodywt), y = log10(brainwt)) +
+#'   guides(
+#'     x = guide_axis_logticks(prescale_base = 2),
+#'     y = guide_axis_logticks(prescale_base = 10)
+#'   )
+#'
+#' # A plot with both positive and negative extremes, pseudo-log transformed
+#' set.seed(42)
+#' p2 <- ggplot(data.frame(x = rcauchy(1000)), aes(x = x)) +
+#'   geom_density() +
+#'   scale_x_continuous(
+#'     breaks = c(-10^(4:0), 0, 10^(0:4)),
+#'     trans = "pseudo_log"
+#'   )
+#'
+#' # The log ticks are mirrored when 0 is included
+#' p2 + guides(x = "axis_logticks")
+#'
+#' # To control the tick density around 0, one can set `negative_small`
+#' p2 + guides(x = guide_axis_logticks(negative_small = 1))
 guide_axis_logticks <- function(
   long  = 2.25,
   mid   = 1.5,
@@ -46,7 +107,10 @@ guide_axis_logticks <- function(
   )
 }
 
-
+#' @rdname ggplot2-ggproto
+#' @format NULL
+#' @usage NULL
+#' @export
 GuideAxisLogticks <- ggproto(
   "GuideAxisLogticks", GuideAxis,
 
diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd
index 37a042dd68..3bd6d924c6 100644
--- a/man/ggplot2-ggproto.Rd
+++ b/man/ggplot2-ggproto.Rd
@@ -4,27 +4,28 @@
 %   R/geom-raster.R, R/annotation-raster.R, R/axis-secondary.R, R/coord-.R,
 %   R/coord-cartesian-.R, R/coord-fixed.R, R/coord-flip.R, R/coord-map.R,
 %   R/coord-polar.R, R/coord-quickmap.R, R/coord-transform.R, R/facet-.R,
-%   R/facet-grid-.R, R/facet-null.R, R/facet-wrap.R, R/stat-.R, R/geom-abline.R,
-%   R/geom-rect.R, R/geom-bar.R, R/geom-blank.R, R/geom-boxplot.R, R/geom-col.R,
-%   R/geom-path.R, R/geom-contour.R, R/geom-crossbar.R, R/geom-segment.R,
-%   R/geom-curve.R, R/geom-ribbon.R, R/geom-density.R, R/geom-density2d.R,
-%   R/geom-dotplot.R, R/geom-errorbar.R, R/geom-errorbarh.R, R/geom-function.R,
-%   R/geom-hex.R, R/geom-hline.R, R/geom-label.R, R/geom-linerange.R,
-%   R/geom-point.R, R/geom-pointrange.R, R/geom-quantile.R, R/geom-rug.R,
-%   R/geom-smooth.R, R/geom-spoke.R, R/geom-text.R, R/geom-tile.R,
-%   R/geom-violin.R, R/geom-vline.R, R/guide-.R, R/guide-axis.R,
-%   R/guide-legend.R, R/guide-bins.R, R/guide-colorbar.R, R/guide-colorsteps.R,
-%   R/guide-none.R, R/guide-old.R, R/layout.R, R/position-.R,
-%   R/position-dodge.R, R/position-dodge2.R, R/position-identity.R,
-%   R/position-jitter.R, R/position-jitterdodge.R, R/position-nudge.R,
-%   R/position-stack.R, R/scale-.R, R/scale-binned.R, R/scale-continuous.R,
-%   R/scale-date.R, R/scale-discrete-.R, R/scale-identity.R, R/stat-align.R,
-%   R/stat-bin.R, R/stat-bin2d.R, R/stat-bindot.R, R/stat-binhex.R,
-%   R/stat-boxplot.R, R/stat-contour.R, R/stat-count.R, R/stat-density-2d.R,
-%   R/stat-density.R, R/stat-ecdf.R, R/stat-ellipse.R, R/stat-function.R,
-%   R/stat-identity.R, R/stat-qq-line.R, R/stat-qq.R, R/stat-quantilemethods.R,
-%   R/stat-smooth.R, R/stat-sum.R, R/stat-summary-2d.R, R/stat-summary-bin.R,
-%   R/stat-summary-hex.R, R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R
+%   R/facet-grid-.R, R/facet-null.R, R/facet-wrap.R, R/stat-.R,
+%   R/geom-abline.R, R/geom-rect.R, R/geom-bar.R, R/geom-blank.R,
+%   R/geom-boxplot.R, R/geom-col.R, R/geom-path.R, R/geom-contour.R,
+%   R/geom-crossbar.R, R/geom-segment.R, R/geom-curve.R, R/geom-ribbon.R,
+%   R/geom-density.R, R/geom-density2d.R, R/geom-dotplot.R, R/geom-errorbar.R,
+%   R/geom-errorbarh.R, R/geom-function.R, R/geom-hex.R, R/geom-hline.R,
+%   R/geom-label.R, R/geom-linerange.R, R/geom-point.R, R/geom-pointrange.R,
+%   R/geom-quantile.R, R/geom-rug.R, R/geom-smooth.R, R/geom-spoke.R,
+%   R/geom-text.R, R/geom-tile.R, R/geom-violin.R, R/geom-vline.R, R/guide-.R,
+%   R/guide-axis.R, R/guide-axis-logticks.R, R/guide-legend.R, R/guide-bins.R,
+%   R/guide-colorbar.R, R/guide-colorsteps.R, R/guide-none.R, R/guide-old.R,
+%   R/layout.R, R/position-.R, R/position-dodge.R, R/position-dodge2.R,
+%   R/position-identity.R, R/position-jitter.R, R/position-jitterdodge.R,
+%   R/position-nudge.R, R/position-stack.R, R/scale-.R, R/scale-binned.R,
+%   R/scale-continuous.R, R/scale-date.R, R/scale-discrete-.R,
+%   R/scale-identity.R, R/stat-align.R, R/stat-bin.R, R/stat-bin2d.R,
+%   R/stat-bindot.R, R/stat-binhex.R, R/stat-boxplot.R, R/stat-contour.R,
+%   R/stat-count.R, R/stat-density-2d.R, R/stat-density.R, R/stat-ecdf.R,
+%   R/stat-ellipse.R, R/stat-function.R, R/stat-identity.R, R/stat-qq-line.R,
+%   R/stat-qq.R, R/stat-quantilemethods.R, R/stat-smooth.R, R/stat-sum.R,
+%   R/stat-summary-2d.R, R/stat-summary-bin.R, R/stat-summary-hex.R,
+%   R/stat-summary.R, R/stat-unique.R, R/stat-ydensity.R
 \docType{data}
 \name{ggplot2-ggproto}
 \alias{ggplot2-ggproto}
@@ -89,6 +90,7 @@
 \alias{GeomVline}
 \alias{Guide}
 \alias{GuideAxis}
+\alias{GuideAxisLogticks}
 \alias{GuideLegend}
 \alias{GuideBins}
 \alias{GuideColourbar}
diff --git a/man/guide_axis_logticks.Rd b/man/guide_axis_logticks.Rd
new file mode 100644
index 0000000000..23a5865f91
--- /dev/null
+++ b/man/guide_axis_logticks.Rd
@@ -0,0 +1,105 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/guide-axis-logticks.R
+\name{guide_axis_logticks}
+\alias{guide_axis_logticks}
+\title{Axis with logarithmic tick marks}
+\usage{
+guide_axis_logticks(
+  long = 2.25,
+  mid = 1.5,
+  short = 0.75,
+  prescale_base = NULL,
+  negative_small = 0.1,
+  expanded = TRUE,
+  cap = "none",
+  ...
+)
+}
+\arguments{
+\item{long, mid, short}{A \code{\link[grid:unit]{grid::unit()}} object or \code{\link[=rel]{rel()}} object setting
+the (relative) length of the long, middle and short ticks. Numeric values
+are interpreted as \code{\link[=rel]{rel()}} objects. The \code{\link[=rel]{rel()}} values are used to multiply
+values of the \code{axis.ticks.length} theme setting.}
+
+\item{prescale_base}{Base of logarithm used to transform data manually. The
+default, \code{NULL}, will use the scale transformation to calculate positions.
+Only set \code{prescale_base} if the data has already been log-transformed.
+When using a log-transform in the position scale or in \code{coord_trans()},
+keep the default \code{NULL} argument.}
+
+\item{negative_small}{When the scale limits include 0 or negative numbers,
+what should be the smallest absolute value that is marked with a tick?}
+
+\item{expanded}{Whether the ticks should cover the range after scale
+expansion (\code{TRUE}, default), or be restricted to the scale limits
+(\code{FALSE}).}
+
+\item{cap}{A \code{character} to cut the axis line back to the last breaks. Can
+be \code{"none"} (default) to draw the axis line along the whole panel, or
+\code{"upper"} and \code{"lower"} to draw the axis to the upper or lower break, or
+\code{"both"} to only draw the line in between the most extreme breaks. \code{TRUE}
+and \code{FALSE} are shorthand for \code{"both"} and \code{"none"} respectively.}
+
+\item{...}{
+  Arguments passed on to \code{\link[=guide_axis]{guide_axis}}
+  \describe{
+    \item{\code{check.overlap}}{silently remove overlapping labels,
+(recursively) prioritizing the first, last, and middle labels.}
+    \item{\code{angle}}{Compared to setting the angle in \code{\link[=theme]{theme()}} / \code{\link[=element_text]{element_text()}},
+this also uses some heuristics to automatically pick the \code{hjust} and \code{vjust} that
+you probably want.}
+    \item{\code{n.dodge}}{The number of rows (for vertical axes) or columns (for
+horizontal axes) that should be used to render the labels. This is
+useful for displaying labels that would otherwise overlap.}
+    \item{\code{order}}{A positive \code{integer} of length 1 that specifies the order of
+this guide among multiple guides. This controls in which order guides are
+merged if there are multiple guides for the same position. If 0 (default),
+the order is determined by a secret algorithm.}
+    \item{\code{position}}{Where this guide should be drawn: one of top, bottom,
+left, or right.}
+    \item{\code{title}}{A character string or expression indicating a title of guide.
+If \code{NULL}, the title is not shown. By default
+(\code{\link[=waiver]{waiver()}}), the name of the scale object or the name
+specified in \code{\link[=labs]{labs()}} is used for the title.}
+  }}
+}
+\description{
+This axis guide replaces the placement of ticks marks at intervals in
+log10 space.
+}
+\examples{
+# A standard plot
+p <- ggplot(msleep, aes(bodywt, brainwt)) +
+  geom_point(na.rm = TRUE)
+
+# The logticks axis works well with log scales
+p + scale_x_log10(guide = "axis_logticks") +
+  scale_y_log10(guide = "axis_logticks")
+
+# Or with log-transformed coordinates
+p + coord_trans(x = "log10", y = "log10") +
+  guides(x = "axis_logticks", y = "axis_logticks")
+
+# When data is transformed manually, one should provide `prescale_base`
+# Keep in mind that this axis uses log10 space for placement, not log2
+p + aes(x = log2(bodywt), y = log10(brainwt)) +
+  guides(
+    x = guide_axis_logticks(prescale_base = 2),
+    y = guide_axis_logticks(prescale_base = 10)
+  )
+
+# A plot with both positive and negative extremes, pseudo-log transformed
+set.seed(42)
+p2 <- ggplot(data.frame(x = rcauchy(1000)), aes(x = x)) +
+  geom_density() +
+  scale_x_continuous(
+    breaks = c(-10^(4:0), 0, 10^(0:4)),
+    trans = "pseudo_log"
+  )
+
+# The log ticks are mirrored when 0 is included
+p2 + guides(x = "axis_logticks")
+
+# To control the tick density around 0, one can set `negative_small`
+p2 + guides(x = guide_axis_logticks(negative_small = 1))
+}

From 665e718446342bea5fb30b733955fb417e646d19 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Sat, 28 Oct 2023 13:42:47 +0200
Subject: [PATCH 14/18] declare trans as function rather than strings

---
 tests/testthat/test-guides.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R
index a2f0e59529..6e22ebc7a1 100644
--- a/tests/testthat/test-guides.R
+++ b/tests/testthat/test-guides.R
@@ -346,7 +346,7 @@ test_that("guide_colourbar warns about discrete scales", {
 
 test_that("guide_axis_logticks calculates appropriate ticks", {
 
-  test_scale <- function(trans = "identity", limits = c(NA, NA)) {
+  test_scale <- function(trans = identity_trans(), limits = c(NA, NA)) {
     scale <- scale_x_continuous(trans = trans)
     scale$train(scale$transform(limits))
     view_scale_primary(scale)
@@ -362,20 +362,20 @@ test_that("guide_axis_logticks calculates appropriate ticks", {
   outcome <- c((1:10)*10, (2:10)*100)
 
   # Test the classic log10 transformation
-  scale <- test_scale("log10", c(10, 1000))
+  scale <- test_scale(log10_trans(), c(10, 1000))
   key <- train_guide(guide, scale)$logkey
 
   expect_equal(sort(key$x), log10(outcome))
   expect_equal(key$.type, rep(c(1,2,3), c(3, 2, 14)))
 
   # Test compound transformation
-  scale <- test_scale(c("log10", "reverse"), c(10, 1000))
+  scale <- test_scale(compose_trans(log10_trans(), reverse_trans()), c(10, 1000))
   key   <- train_guide(guide, scale)$logkey
 
   expect_equal(sort(key$x), -log10(rev(outcome)))
 
   # Test transformation with negatives
-  scale <- test_scale("pseudo_log", c(-1000, 1000))
+  scale <- test_scale(pseudo_log_trans(), c(-1000, 1000))
   key   <- train_guide(guide, scale)$logkey
 
   unlog <- sort(pseudo_log_trans()$inverse(key$x))
@@ -383,7 +383,7 @@ test_that("guide_axis_logticks calculates appropriate ticks", {
   expect_equal(key$.type, rep(c(1,2,3), c(7, 4, 28)))
 
   # Test expanded argument
-  scale <- test_scale("log10", c(20, 900))
+  scale <- test_scale(log10_trans(), c(20, 900))
   scale$continuous_range <- c(1, 3)
 
   guide <- guide_axis_logticks(expanded = TRUE)
@@ -404,7 +404,7 @@ test_that("guide_axis_logticks calculates appropriate ticks", {
   expect_equal(sort(key$x), log2(outcome))
 
   # Should warn when scale also has transformation
-  scale <- test_scale("log10", limits = c(10, 1000))
+  scale <- test_scale(log10_trans(), limits = c(10, 1000))
   expect_snapshot_warning(train_guide(guide, scale)$logkey)
 
 })
@@ -618,12 +618,12 @@ test_that("logticks look as they should", {
 
   p <- ggplot(data.frame(x = c(-100, 100), y = c(10, 1000)), aes(x, y)) +
     geom_point() +
-    scale_y_continuous(trans = c("log10", "reverse"),
+    scale_y_continuous(trans = compose_trans(log10_trans(), reverse_trans()),
                        expand = expansion(add = 0.5)) +
     scale_x_continuous(
       breaks = c(-100, -10, -1, 0, 1, 10, 100)
     ) +
-    coord_trans(x = "pseudo_log") +
+    coord_trans(x = pseudo_log_trans()) +
     theme_test() +
     theme(axis.line = element_line(colour = "black"),
           panel.border = element_blank(),

From c0c1176def57a4f910fa78c7f8ee5ed1b9110fc9 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Tue, 31 Oct 2023 12:20:13 +0100
Subject: [PATCH 15/18] Add pkgdown item

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 7dbedc3062..44b6704dc7 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -126,6 +126,7 @@ reference:
   - guide_colourbar
   - guide_legend
   - guide_axis
+  - guide_axis_logticks
   - guide_bins
   - guide_coloursteps
   - guide_none

From d205944bf2c5fd16f135b3ba3be35ad821eb0590 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Wed, 22 Nov 2023 14:25:59 +0100
Subject: [PATCH 16/18] Enable theming for short ticks

---
 R/guide-axis-logticks.R    | 33 ++++++++++++++++++++++++++++-----
 man/guide_axis_logticks.Rd |  5 +++++
 2 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index 2fe9ca5b35..5e97d3f193 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -17,6 +17,9 @@ NULL
 #'   keep the default `NULL` argument.
 #' @param negative_small When the scale limits include 0 or negative numbers,
 #'   what should be the smallest absolute value that is marked with a tick?
+#' @param short_theme A theme [element][element_line()] for customising the
+#'   display of the shortest ticks. Must be a line or blank element, and
+#'   it inherits from the `axis.minor.ticks` setting for the relevant position.
 #' @param expanded Whether the ticks should cover the range after scale
 #'   expansion (`TRUE`, default), or be restricted to the scale limits
 #'   (`FALSE`).
@@ -66,6 +69,7 @@ guide_axis_logticks <- function(
   short = 0.75,
   prescale_base = NULL,
   negative_small = 0.1,
+  short_theme = element_line(),
   expanded = TRUE,
   cap = "none",
   ...
@@ -91,6 +95,7 @@ guide_axis_logticks <- function(
     allow_null = TRUE
   )
   check_bool(expanded)
+  check_inherits(short_theme, c("element_blank", "element_line"))
 
   new_guide(
     available_aes  = c("x", "y"),
@@ -102,6 +107,7 @@ guide_axis_logticks <- function(
     short = short,
     cap   = cap,
     minor.ticks = TRUE,
+    short_theme = short_theme,
     ...,
     super = GuideAxisLogticks
   )
@@ -122,7 +128,8 @@ GuideAxisLogticks <- ggproto(
       long  = 2.25,
       mid   = 1.5,
       short = 0.75,
-      expanded = TRUE
+      expanded = TRUE,
+      short_theme = NULL
     ),
     GuideAxis$params
   ),
@@ -216,6 +223,9 @@ GuideAxisLogticks <- ggproto(
     elements <- GuideAxis$override_elements(params, elements, theme)
     length <- elements$major_length
 
+    # Inherit short ticks from minor ticks
+    elements$short <- combine_elements(params$short_theme, elements$minor)
+
     # Multiply rel units with theme's tick length
     tick_length <- lapply(params[c("long", "mid", "short")], function(x) {
       if (is.unit(x)) x else unclass(x) * length
@@ -231,11 +241,24 @@ GuideAxisLogticks <- ggproto(
 
   build_ticks = function(key, elements, params, position = params$opposite) {
     # Instead of passing regular key, we pass the logkey
-    # In addition, we pass tick lengths directly
-    Guide$build_ticks(
-      params$logkey,
+    key <- params$logkey
+    long <- Guide$build_ticks(
+      vec_slice(key, key$.type == 1L),
       elements$ticks, params, position,
-      elements$tick_length[params$logkey$.type]
+      elements$tick_length[1L]
+    )
+
+    mid <- Guide$build_ticks(
+      vec_slice(key, key$.type == 2L),
+      elements$minor, params, position,
+      elements$tick_length[2L]
+    )
+
+    short <- Guide$build_ticks(
+      vec_slice(key, key$.type == 3L),
+      elements$short, params, position,
+      elements$tick_length[3L]
     )
+    grobTree(long, mid, short, name = "ticks")
   }
 )
diff --git a/man/guide_axis_logticks.Rd b/man/guide_axis_logticks.Rd
index 23a5865f91..c2e4a0c904 100644
--- a/man/guide_axis_logticks.Rd
+++ b/man/guide_axis_logticks.Rd
@@ -10,6 +10,7 @@ guide_axis_logticks(
   short = 0.75,
   prescale_base = NULL,
   negative_small = 0.1,
+  short_theme = element_line(),
   expanded = TRUE,
   cap = "none",
   ...
@@ -30,6 +31,10 @@ keep the default \code{NULL} argument.}
 \item{negative_small}{When the scale limits include 0 or negative numbers,
 what should be the smallest absolute value that is marked with a tick?}
 
+\item{short_theme}{A theme \link[=element_line]{element} for customising the
+display of the shortest ticks. Must be a line or blank element, and
+it inherits from the \code{axis.minor.ticks} setting for the relevant position.}
+
 \item{expanded}{Whether the ticks should cover the range after scale
 expansion (\code{TRUE}, default), or be restricted to the scale limits
 (\code{FALSE}).}

From 93377d4e8825aa2f12dcec7fff3bd8b99d8778e8 Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Wed, 22 Nov 2023 14:39:35 +0100
Subject: [PATCH 17/18] Mark `annotation_logticks()` as superseded

---
 R/annotation-logticks.R    | 5 +++++
 man/annotation_logticks.Rd | 4 ++++
 2 files changed, 9 insertions(+)

diff --git a/R/annotation-logticks.R b/R/annotation-logticks.R
index 1e7f60be65..8f3e8a63c2 100644
--- a/R/annotation-logticks.R
+++ b/R/annotation-logticks.R
@@ -1,5 +1,10 @@
 #' Annotation: log tick marks
 #'
+#' @description
+#' `r lifecycle::badge("superseded")`
+#'
+#' This function is superseded by using [`guide_axis_logticks()`].
+#'
 #' This annotation adds log tick marks with diminishing spacing.
 #' These tick marks probably make sense only for base 10.
 #'
diff --git a/man/annotation_logticks.Rd b/man/annotation_logticks.Rd
index 92a587e708..490a7d3b17 100644
--- a/man/annotation_logticks.Rd
+++ b/man/annotation_logticks.Rd
@@ -61,6 +61,10 @@ long tick marks. In base 10, these are the "1" (or "10") ticks.}
 \item{size}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}}
 }
 \description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}
+
+This function is superseded by using \code{\link[=guide_axis_logticks]{guide_axis_logticks()}}.
+
 This annotation adds log tick marks with diminishing spacing.
 These tick marks probably make sense only for base 10.
 }

From c5bf54ec9d21c6ebe7ab4c82dcd6997f0766422b Mon Sep 17 00:00:00 2001
From: Teun van den Brand <49372158+teunbrand@users.noreply.github.com>
Date: Wed, 22 Nov 2023 14:45:14 +0100
Subject: [PATCH 18/18] add news bullet

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index a7bd1b024e..bea2948661 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # ggplot2 (development version)
 
+* New `guide_axis_logticks()` can be used to draw logarithmic tick marks as
+  an axis. It supersedes the `annotation_logticks()` function 
+  (@teunbrand, #5325).
+
 * Glyphs drawing functions of the `draw_key_*()` family can now set `"width"`
   and `"height"` attributes (in centimetres) to the produced keys to control
   their displayed size in the legend.