(v2.1.1.9153) mic plot fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9152
+Version: 2.1.1.9153
-Date: 2025-02-18
+Date: 2025-02-22
 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

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9152
+# AMR 2.1.1.9153
 
 *(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: 2.1.1.9152
+Version: 2.1.1.9153
 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='2.1.1.9152',
+    version='2.1.1.9153',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/mic.R

@@ -283,7 +283,7 @@ 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 prevent a limit on one side, e.g., `mic_range = c(NA, 32)`.
+#' @param mic_range a manual range to rescale the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent rescaling 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", "mic"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)

R/plotting.R

@@ -45,6 +45,8 @@
 #' @param aesthetics aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"
 #' @param eucast_I a [logical] to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be `TRUE` if the default [AMR interpretation guideline][as.sir()] is set to EUCAST (which is the default). With `FALSE`, it will be interpreted as "Intermediate".
 #' @inheritParams as.sir
+#' @param mic_range A manual range to rescale the MIC values (using [rescale_mic()]), e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent rescaling on one side, e.g., `mic_range = c(NA, 32)`. **Note:** This rescales values but does not filter them - use the ggplot2 `limits` argument separately to exclude values from the plot.
+#' @inheritParams as.mic
 #' @inheritParams ggplot_sir
 #' @inheritParams proportion
 #' @details
@@ -232,71 +234,82 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
                                 ns = asNamespace("ggplot2"))
   args <- list(...)
   breaks_set <- args$breaks
-  if (!is.null(args$limits)) {
+  limits_set <- args$limits
-    stop_ifnot(is.null(mic_range),
+  
-               "In `scale_", aest, "_mic()`, `limits` cannot be combined with `mic_range`, as they working identically. Use `mic_range` OR `limits`.", call = FALSE)
-    mic_range <- args$limits
-  }
   # do not take these arguments into account, as they will be overwritten and seem to allow weird behaviour if set anyway
   args[c("aesthetics", "trans", "transform", "transform_df", "breaks", "labels", "limits")] <- NULL
   scale <- do.call(ggplot_fn, args)
+  scale$mic_breaks_set <- breaks_set
+  scale$mic_limits_set <- limits_set
   
   scale$transform <- function(x) {
     as.double(rescale_mic(x = as.double(x), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
   }
   scale$transform_df <- function(self, df) {
-    self$`.values_rescaled` <- rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
+    stop_if(all(is.na(df[[aest]])),
-    
+            "`scale_", aest, "_mic()`: All MIC values are `NA`. Check your input data.", call = FALSE)
+    self$mic_values_rescaled <- rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
     # create new breaks and labels here
-    lims <- range(self$`.values_rescaled`)
+    lims <- range(self$mic_values_rescaled, na.rm = TRUE)
-    if (!is.na(mic_range[1]) && mic_range[1] < lims[1]) {
+    # support inner and outer mic_range settings (e.g., data ranges 0.5-8 and mic_range is set to 0.025-64)
+    if (!is.null(mic_range) && !is.na(mic_range[1]) && !is.na(lims[1]) && mic_range[1] < lims[1]) {
       lims[1] <- mic_range[1]
     }
-    if (!is.na(mic_range[2]) && mic_range[2] > lims[2]) {
+    if (!is.null(mic_range) && !is.na(mic_range[2]) && !is.na(lims[2]) && mic_range[2] > lims[2]) {
       lims[2] <- mic_range[2]
     }
     ind_min <- which(COMMON_MIC_VALUES <= lims[1])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES <= lims[1]] - lims[1]))]  # Closest index where COMMON_MIC_VALUES <= lims[1]
     ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))]  # Closest index where COMMON_MIC_VALUES >= lims[2]
-    self$`.values_levels` <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
     
-    if (keep_operators %in% c("edges", "all") && length(self$`.values_levels`) > 1) {
+    self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
-      self$`.values_levels`[1] <- paste0("<=", self$`.values_levels`[1])
+    
-      self$`.values_levels`[length(self$`.values_levels`)] <- paste0(">=", self$`.values_levels`[length(self$`.values_levels`)])
+    if (keep_operators %in% c("edges", "all") && length(self$mic_values_levels) > 1) {
+      self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
+      self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
     }
     
-    self$`.values_log` <- log2(as.double(self$`.values_rescaled`))
+    self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
     if (aest == "y" && "group" %in% colnames(df)) {
       df$group <- as.integer(factor(df$x))
     }
-    df[[aest]] <- self$`.values_log`
+    df[[aest]] <- self$mic_values_log
     df
   }
+  
   scale$breaks <- function(..., self) {
-    if (!is.null(breaks_set)) {
+    if (!is.null(self$mic_breaks_set)) {
-      if (is.function(breaks_set)) {
+      if (is.function(self$mic_breaks_set)) {
-        breaks_set(...)
+        self$mic_breaks_set(...)
       } else {
-        log2(as.mic(breaks_set))
+        log2(as.mic(self$mic_breaks_set))
       }
     } else {
-      log2(as.mic(self$`.values_levels`))
+      log2(as.mic(self$mic_values_levels))
     }
   }
   scale$labels <- function(..., self) {
-    if (is.null(breaks_set)) {
+    if (is.null(self$mic_breaks_set)) {
-      self$`.values_levels`
+      self$mic_values_levels
     } else {
       breaks <- tryCatch(scale$breaks(), error = function(e) NULL)
       if (!is.null(breaks)) {
         # for when breaks are set by the user
         2 ^ breaks
       } else {
-        self$`.values_levels`
+        self$mic_values_levels
       }
     }
   }
+  
   scale$limits <- function(x, ..., self) {
-    rng <- range(log2(as.mic(self$`.values_levels`)))
+    if (!is.null(self$mic_limits_set)) {
+      if (is.function(self$mic_limits_set)) {
+        self$mic_limits_set(...)
+      } else {
+        log2(as.mic(self$mic_limits_set))
+      }
+    } else {
+      rng <- range(log2(as.mic(self$mic_values_levels)))
       # add 0.5 extra space
       rng <- c(rng[1] - 0.5, rng[2] + 0.5)
       if (!is.na(x[1]) && x[1] == 0) {
@@ -305,11 +318,12 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
       }
       rng
     }
+  }
+  
   scale
 }
 
 #' @export
-#' @inheritParams as.mic
 #' @rdname plot
 scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
   meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
@@ -318,7 +332,6 @@ scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
 }
 
 #' @export
-#' @inheritParams as.mic
 #' @rdname plot
 scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
   meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
@@ -327,7 +340,6 @@ scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
 }
 
 #' @export
-#' @inheritParams as.mic
 #' @rdname plot
 scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
   meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
@@ -341,7 +353,6 @@ scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
 scale_color_mic <- scale_colour_mic
 
 #' @export
-#' @inheritParams as.mic
 #' @rdname plot
 scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
   meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)

data-raw/gpt_training_text_v2.1.1.9153.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 2.1.1.9152. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9153. 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.
 ----------------------------------------------------------------------------------------------------
@@ -2893,7 +2893,7 @@ 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 prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{a manual range to rescale the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling 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{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}.}
 
@@ -7455,7 +7455,7 @@ 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 prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{A manual range to rescale the MIC values (using \code{\link[=rescale_mic]{rescale_mic()}}), e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling on one side, e.g., \code{mic_range = c(NA, 32)}. \strong{Note:} This rescales values but does not filter them - use the ggplot2 \code{limits} argument separately to exclude values from the plot.}
 
 \item{...}{arguments passed on to methods}
 

man/as.mic.Rd

@@ -27,7 +27,7 @@ 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 prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{a manual range to rescale the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling 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{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}.}
 

man/plot.Rd

@@ -111,7 +111,7 @@ 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 prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
+\item{mic_range}{A manual range to rescale the MIC values (using \code{\link[=rescale_mic]{rescale_mic()}}), e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling on one side, e.g., \code{mic_range = c(NA, 32)}. \strong{Note:} This rescales values but does not filter them - use the ggplot2 \code{limits} argument separately to exclude values from the plot.}
 
 \item{...}{arguments passed on to methods}