add labels_rsi_count

2025-07-08 09:11:51 +02:00 · 2018-09-16 22:11:17 +02:00
parent b792a2754e
commit db14781593
16 changed files with 110 additions and 29 deletions
--- a/R/ab_property.R
+++ b/R/ab_property.R
@ -36,7 +36,7 @@
 #' ab_umcg("amcl")        # AMCL
 ab_property <- function(x, property = 'official') {
  property <- property[1]
-  if (!property %in% colnames(antibiotics)) {
+  if (!property %in% colnames(AMR::antibiotics)) {
    stop("invalid property: ", property, " - use a column name of the `antibiotics` data set")
  }
  if (!is.atc(x)) {
--- a/R/count.R
+++ b/R/count.R
@ -146,6 +146,10 @@ count_S <- function(...) {
 count_df <- function(data,
                     translate_ab = getOption("get_antibiotic_names", "official")) {

+  if (!"data.frame" %in% class(data)) {
+    stop("`count_df` must be called on a data.frame")
+  }
+
  if (data %>% select_if(is.rsi) %>% ncol() == 0) {
    stop("No columns with class 'rsi' found. See ?as.rsi.")
  }
@ -177,7 +181,7 @@ count_df <- function(data,

  res <- bind_rows(resS, resI, resR) %>%
    mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
-    tidyr::gather(Antibiotic, Count, -Interpretation, -data.groups)
+    tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)

  if (!translate_ab == FALSE) {
    if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
--- a/R/ggplot_rsi.R
+++ b/R/ggplot_rsi.R
@ -20,13 +20,16 @@
 #'
 #' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
 #' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
-#' @param position position adjustment of bars, either \code{"fill"}, \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})
+#' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
 #' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
 #' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
 #' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
 #' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.
-#' @param fun function to transform \code{data}, either \code{\link{portion_df}} (default) or \code{\link{count_df}}
+#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
 #' @param nrow (when using \code{facet}) number of rows
+#' @param datalabels show datalabels using \code{labels_rsi_count}, will at default only be shown when \code{fun = count_df}
+#' @param datalabels.size size of the datalabels
+#' @param datalabels.colour colour of the datalabels
 #' @param ... other parameters passed on to \code{geom_rsi}
 #' @details At default, the names of antibiotics will be shown on the plots using \code{\link{abname}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}.
 #'
@ -35,12 +38,14 @@
 #'
 #' \code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
 #'
-#' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range.
+#' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_y_continuous}}.
 #'
-#' \code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R.
+#' \code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_fill_brewer}}.
 #'
 #' \code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
 #'
+#' \code{labels_rsi_count} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2]{geom_text}}
+#'
 #' \code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
 #' @rdname ggplot_rsi
 #' @export
@ -58,6 +63,7 @@
 #'   geom_rsi() +
 #'   scale_y_percent() +
 #'   scale_rsi_colours() +
+#'   labels_rsi_count() +
 #'   theme_rsi()
 #'
 #' # or better yet, simplify this using the wrapper function - a single command:
@ -131,8 +137,11 @@ ggplot_rsi <- function(data,
                       # params = list(),
                       facet = NULL,
                       translate_ab = "official",
-                       fun = portion_df,
+                       fun = count_df,
                       nrow = NULL,
+                       datalabels = TRUE,
+                       datalabels.size = 3,
+                       datalabels.colour = "grey15",
                       ...) {

  if (!"ggplot2" %in% rownames(installed.packages())) {
@ -174,11 +183,22 @@ ggplot_rsi <- function(data,
    # set RSI colours
    p <- p + scale_rsi_colours()
  }
-  if (fun_name == "portion_df") {
+  if (is.null(position)) {
+    position <- "fill"
+  }
+  if (fun_name == "portion_df"
+      | (fun_name == "count_df" & position == "fill")) {
    # portions, so use y scale with percentage
    p <- p + scale_y_percent()
  }

+  if (fun_name == "count_df" & datalabels == TRUE) {
+    p <- p + labels_rsi_count(position = position,
+                              x = x,
+                              datalabels.size = datalabels.size,
+                              datalabels.colour = datalabels.colour)
+  }
+
  if (!is.null(facet)) {
    p <- p + facet_rsi(facet = facet, nrow = nrow)
  }
@ -192,20 +212,19 @@ geom_rsi <- function(position = NULL,
                     x = c("Antibiotic", "Interpretation"),
                     fill = "Interpretation",
                     translate_ab = "official",
-                     fun = portion_df,
+                     fun = count_df,
                     ...)  {

  fun_name <- deparse(substitute(fun))
  if (!fun_name %in% c("portion_df", "count_df", "fun")) {
    stop("`fun` must be portion_df or count_df")
  }
+  y <- "Value"
  if (identical(fun, count_df)) {
-    y <- "Count"
    if (missing(position) | is.null(position)) {
-      position <- "dodge"
+      position <- "fill"
    }
  } else {
-    y <- "Percentage"
    if (missing(position) | is.null(position)) {
      position <- "stack"
    }
@ -264,7 +283,6 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
 #' @export
 scale_y_percent <- function() {
  ggplot2::scale_y_continuous(breaks = seq(0, 1, 0.1),
-                              limits = c(0, 1),
                              labels = percent(seq(0, 1, 0.1)))
 }

@ -282,3 +300,35 @@ theme_rsi <- function() {
                   panel.grid.minor = ggplot2::element_blank(),
                   panel.grid.major.y = ggplot2::element_line(colour = "grey75"))
 }
+
+#' @rdname ggplot_rsi
+#' @export
+labels_rsi_count <- function(position = NULL,
+                             x = "Antibiotic",
+                             datalabels.size = 3,
+                             datalabels.colour = "grey15") {
+  if (is.null(position)) {
+    position <- "fill"
+  }
+  if (position == "fill") {
+    position <- ggplot2::position_fill(vjust = 0.5)
+  }
+  ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
+                                                   x = x,
+                                                   y = "Value"),
+                     position = position,
+                     data = getlbls,
+                     inherit.aes = FALSE,
+                     size = datalabels.size,
+                     colour = datalabels.colour)
+}
+
+#' @importFrom dplyr %>% group_by mutate
+getlbls <- function(data) {
+  data %>%
+    count_df() %>%
+    group_by(Antibiotic) %>%
+    mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
+                        " (n=", Value, ")")) %>%
+    mutate(lbl = ifelse(lbl == "0.0% (n=0)", "", lbl))
+}
--- a/R/globals.R
+++ b/R/globals.R
@ -22,7 +22,6 @@ globalVariables(c(".",
                  "antibiotics",
                  "cnt",
                  "count",
-                  "Count",
                  "cum_count",
                  "cum_percent",
                  "date_lab",
@ -37,6 +36,7 @@ globalVariables(c(".",
                  "key_ab",
                  "key_ab_lag",
                  "key_ab_other",
+                  "lbl",
                  "median",
                  "mic",
                  "microorganisms",
@ -46,7 +46,6 @@ globalVariables(c(".",
                  "other_pat_or_mo",
                  "Pasted",
                  "patient_id",
-                  "Percentage",
                  "prevalence",
                  "R",
                  "real_first_isolate",
@ -54,4 +53,5 @@ globalVariables(c(".",
                  "septic_patients",
                  "species",
                  "value",
+                  "Value",
                  "y"))
--- a/R/mo_property.R
+++ b/R/mo_property.R
@ -187,7 +187,7 @@ mo_aerobic <- function(x) {
 #' @export
 mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE, language = NULL) {
  property <- tolower(property[1])
-  if (!property %in% colnames(microorganisms)) {
+  if (!property %in% colnames(AMR::microorganisms)) {
    stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
  }
  result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
--- a/R/portion.R
+++ b/R/portion.R
@ -203,6 +203,10 @@ portion_df <- function(data,
                       minimum = 30,
                       as_percent = FALSE) {

+  if (!"data.frame" %in% class(data)) {
+    stop("`portion_df` must be called on a data.frame")
+  }
+
  if (data %>% select_if(is.rsi) %>% ncol() == 0) {
    stop("No columns with class 'rsi' found. See ?as.rsi.")
  }
@ -240,7 +244,7 @@ portion_df <- function(data,

  res <- bind_rows(resS, resI, resR) %>%
    mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
-    tidyr::gather(Antibiotic, Percentage, -Interpretation, -data.groups)
+    tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)

  if (!translate_ab == FALSE) {
    if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {