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(v3.0.0.9031) fix for ggplot2

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dr. M.S. (Matthijs) Berends
2025-09-12 16:52:59 +02:00
parent 5b99888151
commit e8c99f2775
4 changed files with 13 additions and 12 deletions
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6
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.0.9030 Version: 3.0.0.9031
Date: 2025-09-11 Date: 2025-09-12
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
@@ -70,5 +70,5 @@ BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE License: GPL-2 | file LICENSE
Encoding: UTF-8 Encoding: UTF-8
LazyData: true LazyData: true
RoxygenNote: 7.3.2 RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE, old_usage = TRUE) Roxygen: list(markdown = TRUE, old_usage = TRUE)

3
NEWS.md
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@@ -1,8 +1,9 @@
# AMR 3.0.0.9030 # AMR 3.0.0.9031
This is a bugfix release following the release of v3.0.0 in June 2025. This is a bugfix release following the release of v3.0.0 in June 2025.
### Changed ### Changed
* Allow support for newest `ggplot2` v4.0.0
* Fixed a bug in `antibiogram()` for when no antimicrobials are set * Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Fixed a bug in `antibiogram()` to allow column names containing the `+` character (#222) * Fixed a bug in `antibiogram()` to allow column names containing the `+` character (#222)
* Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space * Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space

14
R/plotting.R
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@@ -247,6 +247,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)) as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
} }
scale$transform_df <- function(self, df) { scale$transform_df <- function(self, df) {
out <- list()
if (!aest %in% colnames(df)) { if (!aest %in% colnames(df)) {
# support for geom_hline(), geom_vline(), etc # support for geom_hline(), geom_vline(), etc
other_x <- c("xintercept", "xmin", "xmax", "xend", "width") other_x <- c("xintercept", "xmin", "xmax", "xend", "width")
@@ -258,11 +259,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
} else { } else {
stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE)) stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
} }
out <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE) mics <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
if (!is.null(self$mic_values_rescaled) && any(out < min(self$mic_values_rescaled, na.rm = TRUE) | out > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) { if (!is.null(self$mic_values_rescaled) && any(mics < min(self$mic_values_rescaled, na.rm = TRUE) | mics > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.") warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
} }
df[[aest_val]] <- log2(as.double(out)) out[[aest_val]] <- log2(as.double(mics))
} else { } else {
self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE) self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
# create new breaks and labels here # create new breaks and labels here
@@ -286,11 +287,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
self$mic_values_log <- log2(as.double(self$mic_values_rescaled)) self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) { if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) {
df$group <- as.integer(factor(df$x)) out$group <- as.integer(factor(df$x))
} }
df[[aest]] <- self$mic_values_log out[[aest]] <- self$mic_values_log
} }
df out
} }
scale$breaks <- function(..., self) { scale$breaks <- function(..., self) {
@@ -317,7 +318,6 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
} }
} }
} }
scale$limits <- function(x, ..., self) { scale$limits <- function(x, ..., self) {
if (!is.null(self$mic_limits_set)) { if (!is.null(self$mic_limits_set)) {
if (is.function(self$mic_limits_set)) { if (is.function(self$mic_limits_set)) {

2
tests/testthat/test-_misc.R
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@@ -77,7 +77,7 @@ test_that("test-misc.R", {
if (!is_right) { if (!is_right) {
# otherwise, this is needed for older versions # otherwise, this is needed for older versions
df <- example_isolates[c(1:3), check_df("xx")] df <- example_isolates[c(1:3), check_df("xx")]
expect_true(is_right, info = "the environmental data cannot be found for base `x` or `xx`") expect_true(is_right, info = "the environmental data cannot be found for base `x` or `xx`")
} }
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {