Merge branch 'main' into breakpoints

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.1.0.9019
+Version: 3.1.0.9020
 Date: 2026-11-09
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.1.0.9019
+# AMR 3.1.0.9020
 
 This version fixes a critical bug in WISCA that biased all coverage estimates of `wisca()` and `antibiogram(..., wisca = TRUE)` downwards since AMR 3.0.0. Users are strongly advised to re-run their WISCA analyses.
 
@@ -44,6 +44,8 @@ It also adds a `site` argument to `as.sir()`, stores EUCAST MIC breakpoints exac
   * Fixed punctuation being italicised along with taxonomic names, e.g., `"(S. aureus)"` now gives `"(*S. aureus*)"` instead of `"(S. *aureus)*"`
   * `NA` values now return `NA` instead of `"NA"`
   * Taxonomic names are now looked up once per session, making the function considerably faster for long vectors
+* `labels_sir_count()` and `ggplot_sir()`
+  * Fixed the data labels being placed on the wrong bars with `position = "dodge"` or `position = "stack"`. They are now grouped like the bars, using the new `fill` argument of `labels_sir_count()`, which `ggplot_sir()` sets automatically
 * `ggplot_pca()`
   * Fixed an error when setting `groups` together with `labels`, and setting `groups` without `labels` now colours the points by these groups instead of using them as labels, as documented
 * *Morganella* is interpreted as reported, with the breakpoints of Enterobacterales or Morganellaceae and not of *M. morganii*, which is now tested (#330)

R/ggplot_sir.R

@@ -33,7 +33,7 @@
 #' @param data A [data.frame] with column(s) of class [`sir`] (see [as.sir()]).
 #' @param position Position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`.
 #' @param x Variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable.
-#' @param fill Variable to categorise using the plots legend, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable.
+#' @param fill Variable to categorise using the plots legend, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable. For [labels_sir_count()], this must be the same as the `fill` of [geom_sir()], so that the labels are placed on the right bars.
 #' @param breaks A [numeric] vector of positions.
 #' @param limits A [numeric] vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum.
 #' @param facet Variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable.
@@ -261,6 +261,7 @@ ggplot_sir <- function(data,
     p <- p + labels_sir_count(
       position = position,
       x = x,
+      fill = fill,
       translate_ab = translate_ab,
       minimum = minimum,
       language = language,

R/plotting.R

@@ -1454,6 +1454,7 @@ labeller_taxonomy <- structure(
 #' @export
 labels_sir_count <- function(position = NULL,
                              x = "antibiotic",
+                             fill = "interpretation",
                              translate_ab = "name",
                              minimum = 30,
                              language = get_AMR_locale(),
@@ -1464,6 +1465,7 @@ labels_sir_count <- function(position = NULL,
   stop_ifnot_installed("ggplot2")
   meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
   meet_criteria(x, allow_class = "character", has_length = 1)
+  meet_criteria(fill, allow_class = "character", has_length = 1)
   meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
   language <- validate_language(language)
@@ -1474,18 +1476,29 @@ labels_sir_count <- function(position = NULL,
   if (is.null(position)) {
     position <- "fill"
   }
+  # labels are grouped like the bars of geom_sir(), so that they are placed on the right bar
+  vjust <- 0.5
   if (identical(position, "fill")) {
+    # centred in the bar segments
     position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
+  } else if (identical(position, "stack")) {
+    # centred in the bar segments
+    position <- ggplot2::position_stack(vjust = 0.5)
+  } else if (identical(position, "dodge")) {
+    # on top of the bars, with the default width of geom_col()
+    position <- ggplot2::position_dodge(width = 0.9)
+    vjust <- -0.5
   }
 
   x_name <- x
   ggplot2::geom_text(
-    mapping = utils::modifyList(ggplot2::aes(), list(label = str2lang("lbl"), x = str2lang(x), y = str2lang("value"))),
+    mapping = utils::modifyList(ggplot2::aes(), list(label = str2lang("lbl"), x = str2lang(x), y = str2lang("value"), group = str2lang(fill))),
     position = position,
     inherit.aes = FALSE,
     size = datalabels.size,
     colour = datalabels.colour,
     lineheight = 0.75,
+    vjust = vjust,
     data = function(x) {
       transformed <- sir_df(
         data = x,

man/ggplot_sir.Rd

@@ -48,6 +48,7 @@ geom_sir(
 labels_sir_count(
   position = NULL,
   x = "antibiotic",
+  fill = "interpretation",
   translate_ab = "name",
   minimum = 30,
   language = get_AMR_locale(),
@@ -64,7 +65,7 @@ labels_sir_count(
 
 \item{x}{Variable to show on x axis, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable.}
 
-\item{fill}{Variable to categorise using the plots legend, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable.}
+\item{fill}{Variable to categorise using the plots legend, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable. For \code{\link[=labels_sir_count]{labels_sir_count()}}, this must be the same as the \code{fill} of \code{\link[=geom_sir]{geom_sir()}}, so that the labels are placed on the right bars.}
 
 \item{facet}{Variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable.}
 

tests/testthat/test-ggplot_sir.R

@@ -160,5 +160,20 @@ test_that("test-ggplot_sir.R", {
         scale_sir_colours(aesthetics = "fill", Value4 = "S", Value5 = "I", Value6 = "R"))$data),
       "data.frame"
     )
+
+    # datalabels are placed on their own bar, also when dodged or stacked
+    for (pos in c("fill", "stack", "dodge")) {
+      built <- ggplot_build(ggplot_sir(example_isolates[, c("AMX", "CIP")], position = pos, guideline = NULL))
+      bars <- built$data[[1]]
+      labels <- built$data[[2]]
+      bars <- bars[order(bars$x, bars$group), , drop = FALSE]
+      labels <- labels[order(labels$x, labels$group), , drop = FALSE]
+      expect_equal(labels$x, bars$x)
+      if (pos == "dodge") {
+        expect_equal(labels$y, bars$ymax)
+      } else {
+        expect_equal(labels$y, (bars$ymin + bars$ymax) / 2)
+      }
+    }
   }
 })