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support for old rsi arguments

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dr. M.S. (Matthijs) Berends
2023-03-11 14:24:34 +01:00
parent 4416394e10
commit 262598b8d7
21 changed files with 327 additions and 199 deletions
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162
R/plot.R
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@ -88,8 +88,8 @@ plot.mic <- function(x,
ab = NULL,
guideline = "EUCAST",
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
@ -100,18 +100,14 @@ plot.mic <- function(x,
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
@ -158,7 +154,7 @@ plot.mic <- function(x,
legend_txt <- c(legend_txt, "(R) Resistant")
legend_col <- c(legend_col, colours_SIR[3])
}
legend("top",
x.intersp = 0.5,
legend = translate_into_language(legend_txt, language = language),
@ -180,8 +176,8 @@ barplot.mic <- function(height,
ab = NULL,
guideline = "EUCAST",
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
@ -192,18 +188,14 @@ barplot.mic <- function(height,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
plot(
@ -227,8 +219,8 @@ autoplot.mic <- function(object,
ab = NULL,
guideline = "EUCAST",
title = deparse(substitute(object)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
@ -240,18 +232,14 @@ autoplot.mic <- function(object,
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
if ("main" %in% names(list(...))) {
title <- list(...)$main
}
@ -278,12 +266,15 @@ autoplot.mic <- function(object,
df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"),
language = language
),
ordered = TRUE
levels = translate_into_language(
c(
"(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"
),
language = language
),
ordered = TRUE
)
p <- ggplot2::ggplot(df)
@ -328,8 +319,8 @@ fortify.mic <- function(object, ...) {
#' @rdname plot
plot.disk <- function(x,
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
mo = NULL,
ab = NULL,
guideline = "EUCAST",
@ -343,18 +334,14 @@ plot.disk <- function(x,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
@ -420,8 +407,8 @@ plot.disk <- function(x,
#' @noRd
barplot.disk <- function(height,
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
mo = NULL,
ab = NULL,
guideline = "EUCAST",
@ -435,18 +422,14 @@ barplot.disk <- function(height,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
plot(
@ -469,8 +452,8 @@ autoplot.disk <- function(object,
mo = NULL,
ab = NULL,
title = deparse(substitute(object)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
guideline = "EUCAST",
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
@ -483,18 +466,14 @@ autoplot.disk <- function(object,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
if ("main" %in% names(list(...))) {
title <- list(...)$main
}
@ -522,9 +501,12 @@ autoplot.disk <- function(object,
df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"),
levels = translate_into_language(
c(
"(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"
),
language = language
),
ordered = TRUE
@ -571,8 +553,8 @@ fortify.disk <- function(object, ...) {
#' @importFrom graphics plot text axis
#' @rdname plot
plot.sir <- function(x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
ylab = translate_AMR("Percentage", language = language),
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
main = deparse(substitute(x)),
language = get_AMR_locale(),
...) {
@ -580,14 +562,6 @@ plot.sir <- function(x,
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
data <- as.data.frame(table(x), stringsAsFactors = FALSE)
colnames(data) <- c("x", "n")
data$s <- round((data$n / sum(data$n)) * 100, 1)
@ -635,8 +609,8 @@ plot.sir <- function(x,
#' @noRd
barplot.sir <- function(height,
main = deparse(substitute(height)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
ylab = translate_AMR("Frequency", language = language),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
@ -644,18 +618,14 @@ barplot.sir <- function(height,
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
if ("colours_RSI" %in% names(list(...))) {
deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
colours_SIR <- list(...)$colours_RSI
}
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
@ -678,8 +648,8 @@ barplot.sir <- function(height,
# will be exported using s3_register() in R/zzz.R
autoplot.sir <- function(object,
title = deparse(substitute(object)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
ylab = translate_AMR("Frequency", language = language),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
...) {
@ -689,14 +659,6 @@ autoplot.sir <- function(object,
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_into_language(xlab, language = language)
}
if ("main" %in% names(list(...))) {
title <- list(...)$main
}