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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
Version: 3.0.0.9030
Date: 2025-09-11
Version: 3.0.0.9031
Date: 2025-09-12
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
@@ -70,5 +70,5 @@ BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
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.
### 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()` 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

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