From 9d636983acde8112c1d7f906fc315a05a6340fa8 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Sat, 15 Feb 2025 12:38:29 +0100
Subject: [PATCH] (v2.1.1.9148) scale fix, antibiogram fix

---
 DESCRIPTION                                   |   4 +-
 NEWS.md                                       |   2 +-
 PythonPackage/AMR/AMR.egg-info/PKG-INFO       |   2 +-
 ...ny.whl => AMR-2.1.1.9148-py3-none-any.whl} | Bin 10254 -> 10252 bytes
 PythonPackage/AMR/dist/amr-2.1.1.9147.tar.gz  | Bin 10063 -> 0 bytes
 PythonPackage/AMR/dist/amr-2.1.1.9148.tar.gz  | Bin 0 -> 10060 bytes
 PythonPackage/AMR/setup.py                    |   2 +-
 R/aa_globals.R                                |   4 ++
 R/antibiogram.R                               |  46 +++++++++---------
 R/plotting.R                                  |  34 +++++++++++--
 ....txt => gpt_training_text_v2.1.1.9148.txt} |   2 +-
 tests/testthat/test-antibiogram.R             |   6 +--
 12 files changed, 68 insertions(+), 34 deletions(-)
 rename PythonPackage/AMR/dist/{AMR-2.1.1.9147-py3-none-any.whl => AMR-2.1.1.9148-py3-none-any.whl} (52%)
 delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9147.tar.gz
 create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9148.tar.gz
 rename data-raw/{gpt_training_text_v2.1.1.9147.txt => gpt_training_text_v2.1.1.9148.txt} (99%)

diff --git a/DESCRIPTION b/DESCRIPTION
index 967c91ccc..26182f899 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9147
-Date: 2025-02-14
+Version: 2.1.1.9148
+Date: 2025-02-15
 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
diff --git a/NEWS.md b/NEWS.md
index 67cbac601..151fa5e78 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9147
+# AMR 2.1.1.9148
 
 *(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).)*
 
diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO
index 50835e462..e17678be9 100644
--- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO
+++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9147
+Version: 2.1.1.9148
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends
diff --git a/PythonPackage/AMR/dist/AMR-2.1.1.9147-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9148-py3-none-any.whl
similarity index 52%
rename from PythonPackage/AMR/dist/AMR-2.1.1.9147-py3-none-any.whl
rename to PythonPackage/AMR/dist/AMR-2.1.1.9148-py3-none-any.whl
index ea82d530e4555fa6ebdcbb7fb46985ee71ca7a0a..768ffcf4bcc1b30786e8b1258f619e7e4a5a9b79 100644
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HcmV?d00001

diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py
index dc2ecc627..5d72d1b42 100644
--- a/PythonPackage/AMR/setup.py
+++ b/PythonPackage/AMR/setup.py
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9147',
+    version='2.1.1.9148',
     packages=find_packages(),
     install_requires=[
         'rpy2',
diff --git a/R/aa_globals.R b/R/aa_globals.R
index baa388825..479d56016 100755
--- a/R/aa_globals.R
+++ b/R/aa_globals.R
@@ -179,12 +179,16 @@ globalVariables(c(
   "microorganisms.codes",
   "mo",
   "n",
+  "n_susceptible",
+  "n_tested",
+  "n_total",
   "name",
   "new",
   "numerator",
   "observations",
   "old",
   "old_name",
+  "p_susceptible",
   "pattern",
   "R",
   "rank_index",
diff --git a/R/antibiogram.R b/R/antibiogram.R
index e122605f2..4bd4292da 100755
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -441,7 +441,7 @@ antibiogram.default <- function(x,
   x <- ascertain_sir_classes(x, "x")
   meet_criteria(wisca, allow_class = "logical", has_length = 1)
   if (isTRUE(wisca)) {
-    if (!missing(mo_transform)) {
+    if (!is.null(mo_transform)) {
       warning_("WISCA must be based on the species level as WISCA parameters are based on this. For that reason, `mo_transform` will be ignored.")
     }
     mo_transform <- function(x) suppressMessages(suppressWarnings(paste(mo_genus(x, keep_synonyms = TRUE, language = NULL), mo_species(x, keep_synonyms = TRUE, language = NULL))))
@@ -469,7 +469,7 @@ antibiogram.default <- function(x,
   
   # try to find columns based on type
   if (is.null(col_mo)) {
-    col_mo <- search_type_in_df(x = x, type = "mo", info = interactive())
+    col_mo <- search_type_in_df(x = x, type = "mo", info = info)
     stop_if(is.null(col_mo), "`col_mo` must be set")
   }
   # transform MOs
@@ -594,7 +594,7 @@ antibiogram.default <- function(x,
   }
   if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
     warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")
-    return(as_original_data_class(data.frame(), class(out), extra_class = "antibiogram"))
+    return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
   } else if (any(out$n_tested < minimum, na.rm = TRUE)) {
     out <- out %pm>%
       # also for WISCA, refrain from anything below 15 isolates:
@@ -612,7 +612,7 @@ antibiogram.default <- function(x,
   }
   
   if (NROW(out) == 0) {
-    return(as_original_data_class(data.frame(), class(out), extra_class = "antibiogram"))
+    return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
   }
   
   out$p_susceptible <- out$n_susceptible / out$n_tested
@@ -927,7 +927,6 @@ antibiogram.default <- function(x,
   rownames(out) <- NULL
   rownames(wisca_parameters) <- NULL
   rownames(long_numeric) <- NULL
-  
   structure(out,
             has_syndromic_group = has_syndromic_group,
             combine_SI = combine_SI,
@@ -943,7 +942,7 @@ antibiogram.default <- function(x,
 #' @export
 antibiogram.grouped_df <- function(x,
                                    antibiotics = where(is.sir),
-                                   mo_transform = function (...) "no_mo",
+                                   mo_transform = NULL,
                                    ab_transform = "name",
                                    syndromic_group = NULL,
                                    add_total_n = FALSE,
@@ -960,6 +959,7 @@ antibiogram.grouped_df <- function(x,
                                    conf_interval = 0.95,
                                    interval_side = "two-tailed",
                                    info = interactive()) {
+  stop_ifnot(is.null(mo_transform), "`mo_transform` must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes `mo_transform` redundant.", call = FALSE)
   stop_ifnot(is.null(syndromic_group), "`syndromic_group` must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making `syndromic_groups` redundant.", call = FALSE)
   groups <- attributes(x)$groups
   n_groups <- NROW(groups)
@@ -969,16 +969,19 @@ antibiogram.grouped_df <- function(x,
                               title = paste("Calculating AMR for", n_groups, "groups"))
   on.exit(close(progress))
   
+  out <- NULL
+  wisca_parameters <- NULL
+  long_numeric <- NULL
+  
   for (i in seq_len(n_groups)) {
-    if (i > 1) progress$tick()
+    progress$tick()
     rows <- unlist(groups[i, ]$.rows)
     if (length(rows) == 0) {
       next
     }
-    
     new_out <- antibiogram(as.data.frame(x)[rows, , drop = FALSE],
                            antibiotics = antibiotics,
-                           mo_transform = function(x) "no_mo",
+                           mo_transform = NULL,
                            ab_transform = ab_transform,
                            syndromic_group = NULL,
                            add_total_n = add_total_n,
@@ -994,17 +997,15 @@ antibiogram.grouped_df <- function(x,
                            simulations = simulations,
                            conf_interval = conf_interval,
                            interval_side = interval_side,
-                           info = i == 1 && info == TRUE)
+                           info = FALSE)
     new_wisca_parameters <- attributes(new_out)$wisca_parameters
     new_long_numeric <- attributes(new_out)$long_numeric
     
-    if (i == 1) progress$tick()
-    
     if (NROW(new_out) == 0) {
       next
     }
     
-    # remove first column 'Pathogen' (in whatever language)
+    # remove first column 'Pathogen' (in whatever language), except WISCA since that never has Pathogen column
     if (isFALSE(wisca)) {
       new_out <- new_out[, -1, drop = FALSE]
       new_long_numeric <- new_long_numeric[, -1, drop = FALSE]
@@ -1037,17 +1038,17 @@ antibiogram.grouped_df <- function(x,
       long_numeric <- rbind_AMR(long_numeric, new_long_numeric)
     }
   }
-
+  
   close(progress)
   
-  out <- structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
-                   has_syndromic_group = FALSE,
-                   combine_SI = isTRUE(combine_SI),
-                   wisca = isTRUE(wisca),
-                   conf_interval = conf_interval,
-                   formatting_type = formatting_type,
-                   wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
-                   long_numeric = as_original_data_class(long_numeric, class(x)))
+  structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
+            has_syndromic_group = FALSE,
+            combine_SI = isTRUE(combine_SI),
+            wisca = isTRUE(wisca),
+            conf_interval = conf_interval,
+            formatting_type = formatting_type,
+            wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
+            long_numeric = as_original_data_class(long_numeric, class(x)))
 }
 
 #' @export
@@ -1072,6 +1073,7 @@ wisca <- function(x,
   antibiogram(x = x,
               antibiotics = antibiotics,
               ab_transform = ab_transform,
+              mo_transform = NULL,
               syndromic_group = syndromic_group,
               add_total_n = add_total_n,
               only_all_tested = only_all_tested,
diff --git a/R/plotting.R b/R/plotting.R
index 691f99407..d7255e4e8 100755
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -227,10 +227,16 @@
 #' }
 NULL
 
-create_scale_mic <- function(aest, keep_operators, mic_range, ...) {
+create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
   ggplot_fn <- getExportedValue(paste0("scale_", aest, "_continuous"),
                                 ns = asNamespace("ggplot2"))
   args <- list(...)
+  breaks_set <- args$breaks
+  if (!is.null(args$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$limits
+  }
   # do not take these arguments into account, as they will be overwritten and seem to allow weird behaviour
   args[c("aesthetics", "trans", "transform", "transform_df", "breaks", "labels", "limits")] <- NULL
   scale <- do.call(ggplot_fn, args)
@@ -252,8 +258,30 @@ create_scale_mic <- function(aest, keep_operators, mic_range, ...) {
     df[[aest]] <- self$`.values_log`
     df
   }
-  scale$breaks <- function(..., self) log2(as.mic(self$`.values_levels`))
-  scale$labels <- function(..., self) self$`.values_levels`
+  scale$breaks <- function(..., self) {
+    if (!is.null(breaks_set)) {
+      if (is.function(breaks_set)) {
+        breaks_set(...)
+      } else {
+        log2(as.mic(breaks_set))
+      }
+    } else {
+      log2(as.mic(self$`.values_levels`))
+    }
+  }
+  scale$labels <- function(..., self) {
+    if (is.null(breaks_set)) {
+      self$`.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`
+      }
+    }
+  }
   scale$limits <- function(x, ..., self) {
     rng <- range(log2(as.mic(self$`.values_levels`)))
     # add 0.5 extra space
diff --git a/data-raw/gpt_training_text_v2.1.1.9147.txt b/data-raw/gpt_training_text_v2.1.1.9148.txt
similarity index 99%
rename from data-raw/gpt_training_text_v2.1.1.9147.txt
rename to data-raw/gpt_training_text_v2.1.1.9148.txt
index e50f29ceb..ab6abb81e 100644
--- a/data-raw/gpt_training_text_v2.1.1.9147.txt
+++ b/data-raw/gpt_training_text_v2.1.1.9148.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 2.1.1.9147. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9148. 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.
 ----------------------------------------------------------------------------------------------------
diff --git a/tests/testthat/test-antibiogram.R b/tests/testthat/test-antibiogram.R
index 8725436c1..853e1628c 100644
--- a/tests/testthat/test-antibiogram.R
+++ b/tests/testthat/test-antibiogram.R
@@ -104,7 +104,7 @@ ab8 <- suppressWarnings(antibiogram(example_isolates,
                                     wisca = TRUE))
 
 expect_inherits(ab8, "antibiogram")
-expect_equal(colnames(ab8), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
+expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
 
 # grouped tibbles
 
@@ -128,7 +128,7 @@ expect_silent(plot(ab5))
 expect_silent(plot(ab6))
 expect_silent(plot(ab7))
 expect_silent(plot(ab8))
-expect_error(plot(ab9))
+expect_silent(plot(ab9))
 
 if (AMR:::pkg_is_available("ggplot2")) {
   expect_inherits(ggplot2::autoplot(ab1), "gg")
@@ -139,5 +139,5 @@ if (AMR:::pkg_is_available("ggplot2")) {
   expect_inherits(ggplot2::autoplot(ab6), "gg")
   expect_inherits(ggplot2::autoplot(ab7), "gg")
   expect_inherits(ggplot2::autoplot(ab8), "gg")
-  expect_error(ggplot2::autoplot(ab9))
+  expect_inherits(ggplot2::autoplot(ab9), "gg")
 }