(v2.1.1.9144) new MIC scales and fix for rescale_mic()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9143
+Version: 2.1.1.9144
-Date: 2025-02-07
+Date: 2025-02-11
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NAMESPACE

@@ -321,6 +321,7 @@ export(resistance_predict)
 export(retrieve_wisca_parameters)
 export(rifamycins)
 export(right_join_microorganisms)
+export(scale_color_mic)
 export(scale_colour_mic)
 export(scale_fill_mic)
 export(scale_sir_colours)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9143
+# AMR 2.1.1.9144
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9143
+Version: 2.1.1.9144
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9143',
+    version='2.1.1.9144',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/mic.R

@@ -207,7 +207,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   # remove all after last digit
   x <- gsub("[^0-9]+$", "", x, perl = TRUE)
   # keep only one zero before dot
-  x <- gsub("0+[.]", "0.", x, perl = TRUE)
+  x <- gsub("^0+[.]", "0.", x, perl = TRUE)
   # starting 00 is probably 0.0 if there's no dot yet
   x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
   # remove last zeroes
@@ -224,7 +224,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   x[x.bak != "" & x == ""] <- "invalid"
   
   na_before <- x[is.na(x) | x == ""] %pm>% length()
-  x[!x %in% VALID_MIC_LEVELS] <- NA
+  x[!as.character(x) %in% VALID_MIC_LEVELS] <- NA
   na_after <- x[is.na(x) | x == ""] %pm>% length()
   
   if (na_before != na_after) {
@@ -273,12 +273,22 @@ NA_mic_ <- set_clean_class(factor(NA, levels = VALID_MIC_LEVELS, ordered = TRUE)
 )
 
 #' @rdname as.mic
-#' @param mic_range a manual range to limit the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to set no limit on one side, e.g., `mic_range = c(NA, 32)`.
+#' @param mic_range a manual range to limit the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent a limit on one side, e.g., `mic_range = c(NA, 32)`.
 #' @export
 rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
-  meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
+  meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical", "mic"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
+  if (is.numeric(mic_range)) {
+    mic_range <- trimws(format(mic_range, scientific = FALSE))
+    mic_range <- gsub("[.]0+$", "", mic_range)
+    mic_range[mic_range == "NA"] <- NA_character_
+  } else if (is.mic(mic_range)) {
+    mic_range <- as.character(mic_range)
+  }
   stop_ifnot(all(mic_range %in% c(VALID_MIC_LEVELS, NA)),
-             "Values in `mic_range` must be valid MIC values. Unvalid: ", vector_and(mic_range[mic_range %in% c(VALID_MIC_LEVELS, NA)]))
+             "Values in `mic_range` must be valid MIC values. ",
+             "The allowed range is ", format(as.double(as.mic(VALID_MIC_LEVELS)[1]), scientific = FALSE), " to ", format(as.double(as.mic(VALID_MIC_LEVELS)[length(VALID_MIC_LEVELS)]), scientific = FALSE), ". ",
+             "Unvalid: ", vector_and(mic_range[!mic_range %in% c(VALID_MIC_LEVELS, NA)], quotes = FALSE), ".")
+  
   x <- as.mic(x)
   if (is.null(mic_range)) {
     mic_range <- c(NA, NA)
@@ -297,7 +307,7 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
   x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators))
   
   if (isTRUE(as.mic)) {
-    if (keep_operators == "edges") {
+    if (keep_operators == "edges" && length(x) > 1) {
       x[x == min(x, na.rm = TRUE)] <- paste0("<=", x[x == min(x, na.rm = TRUE)])
       x[x == max(x, na.rm = TRUE)] <- paste0(">=", x[x == max(x, na.rm = TRUE)])
     }
@@ -342,7 +352,7 @@ as.numeric.mic <- function(x, ...) {
 
 #' @rdname as.mic
 #' @method droplevels mic
-#' @param as.mic a [logical] to indicate whether the `mic` class should be kept - the default is `FALSE`
+#' @param as.mic a [logical] to indicate whether the `mic` class should be kept - the default is `TRUE` for [rescale_mic()] and `FALSE` for [droplevels()]. When setting this to `FALSE` in [rescale_mic()], the output will have factor levels that acknowledge `mic_range`.
 #' @export
 droplevels.mic <- function(x, as.mic = FALSE, ...) {
   x <- as.mic(x) # make sure that currently implemented MIC levels are used

R/plotting.R

@@ -83,7 +83,7 @@
 #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
 #' 
 #' 
-#' # Plotting using scale_x_mic() ---------------------------------------------
+#' # Plotting using scale_x_mic() -----------------------------------------
 #' \donttest{
 #' if (require("ggplot2")) {
 #'   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
@@ -114,6 +114,37 @@
 #'     labs(title = "with scale_x_mic() using a manual 'outside' range")
 #' }
 #' 
+#' # Plotting using scale_y_mic() -----------------------------------------
+#' some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
+#' if (require("ggplot2")) {
+#'   ggplot(data.frame(mic = some_mic_values,
+#'                     group = some_groups),
+#'          aes(group, mic)) +
+#'     geom_boxplot() +
+#'     geom_violin(linetype = 2, colour = "grey", fill = NA) +
+#'     scale_y_mic()
+#' }
+#' if (require("ggplot2")) {
+#'   ggplot(data.frame(mic = some_mic_values,
+#'                     group = some_groups),
+#'          aes(group, mic)) +
+#'     geom_boxplot() +
+#'     geom_violin(linetype = 2, colour = "grey", fill = NA) +
+#'     scale_y_mic(mic_range = c(NA, 2))
+#' }
+#' 
+#' # Plotting using scale_fill_mic() -----------------------------------------
+#' some_counts <- as.integer(runif(20, 5, 50))
+#' if (require("ggplot2")) {
+#'   ggplot(data.frame(mic = some_mic_values,
+#'                    group = some_groups,
+#'                    counts = some_counts,
+#'          aes(group, counts, fill = mic)) +
+#'     geom_col() +
+#'     scale_fill_mic(mic_range = c(0.5, 16))
+#' }
+#' 
+#' # Auto plotting --------------------------------------------------------
 #' if (require("ggplot2")) {
 #'   autoplot(some_mic_values)
 #' }
@@ -124,7 +155,7 @@
 #'   autoplot(some_sir_values)
 #' }
 #' 
-#' # Plotting using scale_y_percent() -----------------------------------------
+#' # Plotting using scale_y_percent() -------------------------------------
 #' if (require("ggplot2")) {
 #'   p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
 #'                                counts = c(1, 1, 2, 2, 3, 3)),
@@ -145,16 +176,35 @@
 #' }
 NULL
 
-#' @export
+create_scale_mic <- function(aest, keep_operators, mic_range, ...) {
-#' @inheritParams as.mic
+  ggplot_fn <- getExportedValue(paste0("scale_", aest, "_continuous"),
-#' @param drop a [logical] to remove intermediate MIC values, defaults to `FALSE`
+                                ns = asNamespace("ggplot2"))
-#' @rdname plot
+  args <- list(...)
-scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  args[c("trans", "transform", "transform_df", "breaks", "labels", "limits")] <- NULL
-  stop_ifnot_installed("ggplot2")
+  scale <- do.call(ggplot_fn, args)
-  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  
-  scale <- ggplot2::scale_x_discrete(drop = drop, ...)
+  scale$transform <- function(x) {
-  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    as.double(rescale_mic(x = as.double(x), keep_operators = , "labels", mic_range = mic_range, as.mic = TRUE))
-    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale$transform_df <- function(self, df) {
+    self$`.values_rescaled` <- rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
+    self$`.values_levels` <- levels(rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = FALSE))
+    if (length(self$`.values_levels`) > 6 & "0.025" %in% self$`.values_levels`) {
+      # TODO weird levelling out leading to 0.025 being redundant
+      self$`.values_levels` <- self$`.values_levels`[self$`.values_levels` != "0.025"]
+    }
+    self$`.values_log` <- log2(as.double(self$`.values_rescaled`))
+    if (aest == "y" && "group" %in% colnames(df)) {
+      df$group <- as.integer(factor(df$x))
+    }
+    df[[aest]] <- self$`.values_log`
+    df
+  }
+  scale$breaks <- function(..., self) log2(as.mic(self$`.values_levels`))
+  scale$labels <- function(..., self) self$`.values_levels`
+  scale$limits <- function(..., self) {
+    rng <- range(log2(as.mic(self$`.values_levels`)))
+    c(rng[1] - 0.5, rng[2] + 0.5)
   }
   scale
 }
@@ -162,40 +212,34 @@ scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE
 #' @export
 #' @inheritParams as.mic
 #' @rdname plot
-scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
-  stop_ifnot_installed("ggplot2")
+  create_scale_mic("x", keep_operators = keep_operators, mic_range = mic_range, ...)
-  meet_criteria(drop, allow_class = "logical", has_length = 1)
-  scale <- ggplot2::scale_y_discrete(drop = drop, ...)
-  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
-    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
-  }
-  scale
 }
 
 #' @export
 #' @inheritParams as.mic
 #' @rdname plot
-scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
-  stop_ifnot_installed("ggplot2")
+  create_scale_mic("y", keep_operators = keep_operators, mic_range = mic_range, ...)
-  meet_criteria(drop, allow_class = "logical", has_length = 1)
-  scale <- ggplot2::scale_colour_discrete(drop = drop, ...)
-  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
-    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
-  }
-  scale
 }
 
 #' @export
 #' @inheritParams as.mic
 #' @rdname plot
-scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
-  stop_ifnot_installed("ggplot2")
+  create_scale_mic("colour", keep_operators = keep_operators, mic_range = mic_range, ...)
-  meet_criteria(drop, allow_class = "logical", has_length = 1)
+}
-  scale <- ggplot2::scale_fill_discrete(drop = drop, ...)
+
-  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+#' @export
-    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+#' @inheritParams as.mic
-  }
+#' @rdname plot
-  scale
+scale_color_mic <- scale_colour_mic
+
+#' @export
+#' @inheritParams as.mic
+#' @rdname plot
+scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
+  create_scale_mic("fill", keep_operators = keep_operators, mic_range = mic_range, ...)
 }
 
 #' @method plot mic

data-raw/gpt_training_text_v2.1.1.9144.txt

@@ -1,6 +1,6 @@
 This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
 
-First and foremost, you are trained on version 2.1.1.9143. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9144. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the  file, the  file, and all the  files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------
@@ -332,6 +332,7 @@ export(resistance_predict)
 export(retrieve_wisca_parameters)
 export(rifamycins)
 export(right_join_microorganisms)
+export(scale_color_mic)
 export(scale_colour_mic)
 export(scale_fill_mic)
 export(scale_sir_colours)
@@ -2875,9 +2876,9 @@ rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
 
 \item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
 
-\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
 
-\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
+\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{TRUE} for \code{\link[=rescale_mic]{rescale_mic()}} and \code{FALSE} for \code{\link[=droplevels]{droplevels()}}. When setting this to \code{FALSE} in \code{\link[=rescale_mic]{rescale_mic()}}, the output will have factor levels that acknowledge \code{mic_range}.}
 
 \item{...}{arguments passed on to methods}
 }
@@ -7330,6 +7331,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
 \alias{scale_x_mic}
 \alias{scale_y_mic}
 \alias{scale_colour_mic}
+\alias{scale_color_mic}
 \alias{scale_fill_mic}
 \alias{plot.mic}
 \alias{autoplot.mic}
@@ -7347,17 +7349,15 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
 \alias{labels_sir_count}
 \title{Plotting Helpers for AMR Data Analysis}
 \usage{
-scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
+scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
-  ...)
 
-scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
+scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
-  ...)
 
-scale_colour_mic(keep_operators = "edges", mic_range = NULL,
+scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
-  drop = FALSE, ...)
 
-scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
+scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
-  ...)
+
+scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
 
 \method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
   main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
@@ -7428,9 +7428,7 @@ labels_sir_count(position = NULL, x = "antibiotic",
 \arguments{
 \item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
 
-\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
-
-\item{drop}{a \link{logical} to remove intermediate MIC values, defaults to \code{FALSE}}
 
 \item{...}{arguments passed on to methods}
 
@@ -7521,7 +7519,7 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
 
 
-# Plotting using scale_x_mic() ---------------------------------------------
+# Plotting using scale_x_mic() -----------------------------------------
 \donttest{
 if (require("ggplot2")) {
   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
@@ -7552,6 +7550,37 @@ if (require("ggplot2")) {
     labs(title = "with scale_x_mic() using a manual 'outside' range")
 }
 
+# Plotting using scale_y_mic() -----------------------------------------
+some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
+if (require("ggplot2")) {
+  ggplot(data.frame(mic = some_mic_values,
+                    group = some_groups),
+         aes(group, mic)) +
+    geom_boxplot() +
+    geom_violin(linetype = 2, colour = "grey", fill = NA) +
+    scale_y_mic()
+}
+if (require("ggplot2")) {
+  ggplot(data.frame(mic = some_mic_values,
+                    group = some_groups),
+         aes(group, mic)) +
+    geom_boxplot() +
+    geom_violin(linetype = 2, colour = "grey", fill = NA) +
+    scale_y_mic(mic_range = c(NA, 2))
+}
+
+# Plotting using scale_fill_mic() -----------------------------------------
+some_counts <- as.integer(runif(20, 5, 50))
+if (require("ggplot2")) {
+  ggplot(data.frame(mic = some_mic_values,
+                   group = some_groups,
+                   counts = some_counts,
+         aes(group, counts, fill = mic)) +
+    geom_col() +
+    scale_fill_mic(mic_range = c(0.5, 16))
+}
+
+# Auto plotting --------------------------------------------------------
 if (require("ggplot2")) {
   autoplot(some_mic_values)
 }
@@ -7562,7 +7591,7 @@ if (require("ggplot2")) {
   autoplot(some_sir_values)
 }
 
-# Plotting using scale_y_percent() -----------------------------------------
+# Plotting using scale_y_percent() -------------------------------------
 if (require("ggplot2")) {
   p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
                                counts = c(1, 1, 2, 2, 3, 3)),

man/as.mic.Rd

@@ -27,9 +27,9 @@ rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
 
 \item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
 
-\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
 
-\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
+\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{TRUE} for \code{\link[=rescale_mic]{rescale_mic()}} and \code{FALSE} for \code{\link[=droplevels]{droplevels()}}. When setting this to \code{FALSE} in \code{\link[=rescale_mic]{rescale_mic()}}, the output will have factor levels that acknowledge \code{mic_range}.}
 
 \item{...}{arguments passed on to methods}
 }

man/plot.Rd

@@ -5,6 +5,7 @@
 \alias{scale_x_mic}
 \alias{scale_y_mic}
 \alias{scale_colour_mic}
+\alias{scale_color_mic}
 \alias{scale_fill_mic}
 \alias{plot.mic}
 \alias{autoplot.mic}
@@ -22,17 +23,15 @@
 \alias{labels_sir_count}
 \title{Plotting Helpers for AMR Data Analysis}
 \usage{
-scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
+scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
-  ...)
 
-scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
+scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
-  ...)
 
-scale_colour_mic(keep_operators = "edges", mic_range = NULL,
+scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
-  drop = FALSE, ...)
 
-scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
+scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
-  ...)
+
+scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
 
 \method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
   main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
@@ -103,9 +102,7 @@ labels_sir_count(position = NULL, x = "antibiotic",
 \arguments{
 \item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
 
-\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
-
-\item{drop}{a \link{logical} to remove intermediate MIC values, defaults to \code{FALSE}}
 
 \item{...}{arguments passed on to methods}
 
@@ -196,7 +193,7 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
 
 
-# Plotting using scale_x_mic() ---------------------------------------------
+# Plotting using scale_x_mic() -----------------------------------------
 \donttest{
 if (require("ggplot2")) {
   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
@@ -227,6 +224,37 @@ if (require("ggplot2")) {
     labs(title = "with scale_x_mic() using a manual 'outside' range")
 }
 
+# Plotting using scale_y_mic() -----------------------------------------
+some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
+if (require("ggplot2")) {
+  ggplot(data.frame(mic = some_mic_values,
+                    group = some_groups),
+         aes(group, mic)) +
+    geom_boxplot() +
+    geom_violin(linetype = 2, colour = "grey", fill = NA) +
+    scale_y_mic()
+}
+if (require("ggplot2")) {
+  ggplot(data.frame(mic = some_mic_values,
+                    group = some_groups),
+         aes(group, mic)) +
+    geom_boxplot() +
+    geom_violin(linetype = 2, colour = "grey", fill = NA) +
+    scale_y_mic(mic_range = c(NA, 2))
+}
+
+# Plotting using scale_fill_mic() -----------------------------------------
+some_counts <- as.integer(runif(20, 5, 50))
+if (require("ggplot2")) {
+  ggplot(data.frame(mic = some_mic_values,
+                   group = some_groups,
+                   counts = some_counts,
+         aes(group, counts, fill = mic)) +
+    geom_col() +
+    scale_fill_mic(mic_range = c(0.5, 16))
+}
+
+# Auto plotting --------------------------------------------------------
 if (require("ggplot2")) {
   autoplot(some_mic_values)
 }
@@ -237,7 +265,7 @@ if (require("ggplot2")) {
   autoplot(some_sir_values)
 }
 
-# Plotting using scale_y_percent() -----------------------------------------
+# Plotting using scale_y_percent() -------------------------------------
 if (require("ggplot2")) {
   p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
                                counts = c(1, 1, 2, 2, 3, 3)),