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add scale_x_mic()
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 2.1.1
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Date: 2023-10-20
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Version: 2.1.1.9001
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Date: 2023-12-03
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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@ -330,6 +330,7 @@ export(rsi_df)
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export(rsi_predict)
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export(scale_rsi_colours)
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export(scale_sir_colours)
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export(scale_x_mic)
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export(scale_y_percent)
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export(semi_join_microorganisms)
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export(set_AMR_locale)
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11
NEWS.md
11
NEWS.md
@ -1,3 +1,14 @@
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# AMR 2.1.1.9001
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## New
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* Function `scale_x_mic()`, an advanced function to use in ggplot, to allow plotting of MIC values on the x axis. It allow for manual range definition and plotting missing intermediate log2 levels.
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### Changed
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* For MICs:
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* Added 4096 and 5 powers of 192 as valid levels (192, 384, 576, 768, 960)
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* Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`.
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# AMR 2.1.1
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* Fix for selecting first isolates using the phenotype-based method
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@ -862,12 +862,20 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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object <- tolower(object)
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is_in <- tolower(is_in)
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}
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stop_ifnot(all(object %in% is_in, na.rm = TRUE), "argument `", obj_name, "` ",
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is_in.bak <- is_in
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if ("logical" %in% allow_class) {
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is_in <- is_in[!is_in %in% c("TRUE", "FALSE")]
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}
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or_values <- vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class)))
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if ("logical" %in% allow_class) {
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or_values <- paste0(or_values, ", or TRUE or FALSE")
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}
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stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument `", obj_name, "` ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"must be either ",
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"must only contain values "
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),
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vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class))),
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or_values,
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ifelse(allow_NA == TRUE, ", or NA", ""),
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call = call_depth
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)
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@ -1551,7 +1559,7 @@ readRDS_AMR <- function(file, refhook = NULL) {
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match <- function(x, table, ...) {
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if (!is.null(AMR_env$chmatch) && inherits(x, "character") && inherits(table, "character")) {
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# data.table::chmatch() is much faster than base::match() for character
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AMR_env$chmatch(x, table, ...)
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tryCatch(AMR_env$chmatch(x, table, ...), error = function(e) base::match(x, table, ...))
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} else {
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base::match(x, table, ...)
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}
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@ -1559,7 +1567,7 @@ match <- function(x, table, ...) {
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`%in%` <- function(x, table) {
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if (!is.null(AMR_env$chin) && inherits(x, "character") && inherits(table, "character")) {
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# data.table::`%chin%`() is much faster than base::`%in%`() for character
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AMR_env$chin(x, table)
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tryCatch(AMR_env$chin(x, table), error = function(e) base::`%in%`(x, table))
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} else {
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base::`%in%`(x, table)
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}
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44
R/mic.R
44
R/mic.R
@ -64,10 +64,10 @@ valid_mic_levels <- c(
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FUN.VALUE = character(45), operators,
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function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])
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))),
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c(t(vapply(
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FUN.VALUE = character(17), operators,
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function(x) paste0(x, sort(c(2^c(7:11), 192, 80 * c(2:12))))
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)))
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unique(c(t(vapply(
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FUN.VALUE = character(22), operators,
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function(x) paste0(x, sort(c(2^c(7:12), 192 * c(1:5), 80 * c(2:12))))
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))))
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)
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#' Transform Input to Minimum Inhibitory Concentrations (MIC)
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@ -76,6 +76,7 @@ valid_mic_levels <- c(
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#' @rdname as.mic
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#' @param x a [character] or [numeric] vector
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#' @param na.rm a [logical] indicating whether missing values should be removed
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#' @param keep_operators a [character] specifying how to handle operators (such as `>` and `<=`) in the input. Accepts one of three values: `"all"` (or `TRUE`) to keep all operators, `"none"` (or `FALSE`) to remove all operators, or `"edges"` to keep operators only at both ends of the range.
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#' @param ... arguments passed on to methods
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#' @details To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
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#'
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@ -161,15 +162,24 @@ valid_mic_levels <- c(
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#' if (require("ggplot2")) {
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#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
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#' }
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as.mic <- function(x, na.rm = FALSE) {
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as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(na.rm, allow_class = "logical", has_length = 1)
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if (is.mic(x)) {
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meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
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if (isTRUE(keep_operators)) {
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keep_operators <- "all"
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} else if (isFALSE(keep_operators)) {
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keep_operators <- "none"
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}
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if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
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x
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} else {
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x.bak <- NULL
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if (is.numeric(x)) {
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x <- format(x, scientific = FALSE)
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x.bak <- format(x, scientific = FALSE)
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# MICs never need more than 4 decimals, so:
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x <- format(round(x, 4), scientific = FALSE)
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} else {
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x <- as.character(unlist(x))
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}
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@ -177,7 +187,9 @@ as.mic <- function(x, na.rm = FALSE) {
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x <- x[!is.na(x)]
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}
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x[trimws2(x) == ""] <- NA
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x.bak <- x
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if (is.null(x.bak)) {
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x.bak <- x
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}
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# comma to period
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x <- gsub(",", ".", x, fixed = TRUE)
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@ -238,6 +250,16 @@ as.mic <- function(x, na.rm = FALSE) {
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call = FALSE
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)
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}
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if (keep_operators == "none" && !all(is.na(x))) {
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x <- gsub("[>=<]", "", x)
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} else if (keep_operators == "edges" && !all(is.na(x))) {
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dbls <- as.double(gsub("[>=<]", "", x))
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x[dbls == min(dbls, na.rm = TRUE)] <- paste0("<=", min(dbls, na.rm = TRUE))
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x[dbls == max(dbls, na.rm = TRUE)] <- paste0(">=", max(dbls, na.rm = TRUE))
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keep <- x[dbls == max(dbls, na.rm = TRUE) | dbls == min(dbls, na.rm = TRUE)]
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x[!x %in% keep] <- gsub("[>=<]", "", x[!x %in% keep])
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}
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set_clean_class(factor(x, levels = valid_mic_levels, ordered = TRUE),
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new_class = c("mic", "ordered", "factor")
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@ -302,8 +324,8 @@ pillar_shaft.mic <- function(x, ...) {
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operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
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out <- trimws(paste0(operators, trimws(format(crude_numbers))))
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out[is.na(x)] <- font_na(NA)
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# maketrailing zeroes almost invisible
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out[out %like% "[.]"] <- gsub("([.]?0+)$", font_white("\\1"), out[out %like% "[.]"], perl = TRUE)
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# make trailing zeroes less visible
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out[out %like% "[.]"] <- gsub("([.]?0+)$", font_silver("\\1"), out[out %like% "[.]"], perl = TRUE)
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create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
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}
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104
R/plot.R
104
R/plot.R
@ -29,8 +29,10 @@
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#' Plotting for Classes `sir`, `mic` and `disk`
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#'
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#' @description
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#' Functions to plot classes `sir`, `mic` and `disk`, with support for base \R and `ggplot2`.
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#'
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#' Especially [scale_x_mic()] is a relevant wrapper to plot MIC values for `ggplot2`. It allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
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#' @param x,object values created with [as.mic()], [as.disk()] or [as.sir()] (or their `random_*` variants, such as [random_mic()])
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#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
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#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
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@ -322,6 +324,89 @@ fortify.mic <- function(object, ...) {
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)
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}
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#' @export
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#' @inheritParams as.mic
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#' @param mic_range a manual range to plot the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to set no limit on one side, e.g., `mic_range = c(NA, 32)`.
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#' @param drop,guide,position,na.translate arguments passed on to [ggplot2::scale_x_discrete()]
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#' @rdname plot
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#' @examples
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#'
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#' # Plotting using scale_x_mic()
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#' \donttest{
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#' if (require("ggplot2")) {
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#' mic_plot <- ggplot(data.frame(mics = as.mic(c(0.125, "<=4", 4, 8, 32, ">=32")),
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#' counts = c(1, 1, 2, 2, 3, 3)),
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#' aes(mics, counts)) +
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#' geom_col()
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#' mic_plot +
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#' labs(title = "without scale_x_mic()")
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#' }
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#' if (require("ggplot2")) {
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#' mic_plot +
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#' scale_x_mic() +
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#' labs(title = "with scale_x_mic()")
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#' }
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#' if (require("ggplot2")) {
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#' mic_plot +
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#' scale_x_mic(keep_operators = "all") +
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#' labs(title = "with scale_x_mic() keeping all operators")
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#' }
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#' if (require("ggplot2")) {
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#' mic_plot +
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#' scale_x_mic(mic_range = c(1, 128)) +
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#' labs(title = "with scale_x_mic() using a manual range")
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#' }
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#' }
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scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, ..., drop = FALSE, guide = waiver(), position = "bottom", na.translate = TRUE) {
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meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
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meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
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stop_ifnot(all(mic_range %in% c(levels(as.mic(1)), NA)),
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"Values in `mic_range` must be valid MIC values")
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stop_ifnot_installed("ggplot2")
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ggplot2::ggproto(NULL, ggplot2::ScaleDiscretePosition,
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aesthetics = c("x", "xmin", "xmax", "xend"),
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na.translate = na.translate,
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drop = drop,
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guide = guide,
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position = position,
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transform = function(x, keep_ops = keep_operators, mic_rng = mic_range) {
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if (!is.null(mic_rng)) {
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min_mic <- mic_rng[1]
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max_mic <- mic_rng[2]
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if (!is.na(min_mic)) {
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x[x < as.mic(min_mic)] <- as.mic(min_mic)
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}
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if (!is.na(max_mic)) {
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x[x > as.mic(max_mic)] <- as.mic(max_mic)
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}
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}
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# transform MICs to only keep required operators
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x <- as.mic(x, keep_operators = ifelse(keep_ops == "edges", "none", keep_ops))
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# get range betwen min and max of MICs
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expanded <- plot_prepare_table(x,
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expand = TRUE,
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keep_operators = ifelse(keep_ops == "edges", "none", keep_ops),
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mic_range = mic_rng)
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if (keep_ops == "edges") {
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names(expanded)[1] <- paste0("<=", names(expanded)[1])
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names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)])
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}
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# MICs contain all MIC levels, so strip this to only existing levels and their intermediate values
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out <- factor(names(expanded),
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levels = names(expanded),
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ordered = TRUE)
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# and only keep the ones in the data
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if (keep_ops == "edges") {
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out <- out[match(x, as.double(as.mic(out, keep_operators = "all")))]
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} else {
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out <- out[match(x, out)]
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}
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out
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},
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...)
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}
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#' @method plot disk
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#' @export
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#' @importFrom graphics barplot axis mtext legend
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@ -714,15 +799,26 @@ fortify.sir <- function(object, ...) {
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)
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}
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plot_prepare_table <- function(x, expand) {
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plot_prepare_table <- function(x, expand, keep_operators = "all", mic_range = NULL) {
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x <- x[!is.na(x)]
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stop_if(length(x) == 0, "no observations to plot", call = FALSE)
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if (is.mic(x)) {
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x <- as.mic(x, keep_operators = keep_operators)
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if (expand == TRUE) {
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# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
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valid_lvls <- levels(x)
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extra_range <- max(x) / 2
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while (min(extra_range) / 2 > min(x)) {
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extra_range <- max(x)
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min_range <- min(x)
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if (!is.null(mic_range)) {
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if (!is.na(mic_range[2])) {
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extra_range <- as.mic(mic_range[2]) * 2
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}
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if (!is.na(mic_range[1])) {
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min_range <- as.mic(mic_range[1])
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}
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}
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extra_range <- extra_range / 2
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while (min(extra_range) / 2 > min_range) {
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extra_range <- c(min(extra_range) / 2, extra_range)
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}
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nms <- extra_range
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -9,7 +9,7 @@
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\alias{droplevels.mic}
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\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
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\usage{
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as.mic(x, na.rm = FALSE)
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as.mic(x, na.rm = FALSE, keep_operators = "all")
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NA_mic_
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@ -22,6 +22,8 @@ is.mic(x)
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\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
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\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
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\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
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\item{...}{arguments passed on to methods}
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46
man/plot.Rd
46
man/plot.Rd
@ -5,6 +5,7 @@
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\alias{plot.mic}
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\alias{autoplot.mic}
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\alias{fortify.mic}
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\alias{scale_x_mic}
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\alias{plot.disk}
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\alias{autoplot.disk}
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\alias{fortify.disk}
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@ -47,6 +48,16 @@
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\method{fortify}{mic}(object, ...)
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scale_x_mic(
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keep_operators = "edges",
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mic_range = NULL,
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...,
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drop = FALSE,
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guide = waiver(),
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position = "bottom",
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na.translate = TRUE
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)
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\method{plot}{disk}(
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x,
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main = deparse(substitute(x)),
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@ -126,6 +137,12 @@
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\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}.}
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\item{...}{arguments passed on to methods}
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\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
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\item{mic_range}{a manual range to plot the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
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\item{drop, guide, position, na.translate}{arguments passed on to \code{\link[ggplot2:scale_discrete]{ggplot2::scale_x_discrete()}}}
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}
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\value{
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The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
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@ -134,6 +151,8 @@ The \code{fortify()} functions return a \link{data.frame} as an extension for us
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}
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\description{
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Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
|
||||
|
||||
Especially \code{\link[=scale_x_mic]{scale_x_mic()}} is a relevant wrapper to plot MIC values for \code{ggplot2}. It allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
|
||||
}
|
||||
\details{
|
||||
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
|
||||
@ -167,4 +186,31 @@ if (require("ggplot2")) {
|
||||
autoplot(some_sir_values)
|
||||
}
|
||||
}
|
||||
|
||||
# Plotting using scale_x_mic()
|
||||
\donttest{
|
||||
if (require("ggplot2")) {
|
||||
mic_plot <- ggplot(data.frame(mics = as.mic(c(0.125, "<=4", 4, 8, 32, ">=32")),
|
||||
counts = c(1, 1, 2, 2, 3, 3)),
|
||||
aes(mics, counts)) +
|
||||
geom_col()
|
||||
mic_plot +
|
||||
labs(title = "without scale_x_mic()")
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
mic_plot +
|
||||
scale_x_mic() +
|
||||
labs(title = "with scale_x_mic()")
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
mic_plot +
|
||||
scale_x_mic(keep_operators = "all") +
|
||||
labs(title = "with scale_x_mic() keeping all operators")
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
mic_plot +
|
||||
scale_x_mic(mic_range = c(1, 128)) +
|
||||
labs(title = "with scale_x_mic() using a manual range")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user