P281424/AMR
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language updates

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-08-19 12:33:14 +02:00
parent 4b19c3dc5e
commit 3f2f60ab77
23 changed files with 543 additions and 506 deletions
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63
R/plot.R
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@ -98,10 +98,10 @@ plot.mic <- function(x,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_RSI) == 1) {
@ -149,7 +149,7 @@ plot.mic <- function(x,
legend("top",
x.intersp = 0.5,
legend = translate_AMR(legend_txt, language = language),
legend = translate_into_language(legend_txt, language = language),
fill = legend_col,
horiz = TRUE,
cex = 0.75,
@ -185,10 +185,10 @@ barplot.mic <- function(height,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
@ -211,7 +211,7 @@ autoplot.mic <- function(object,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
title = paste("MIC values of", deparse(substitute(object))),
title = deparse(substitute(object)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -231,10 +231,10 @@ autoplot.mic <- function(object,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
if ("main" %in% names(list(...))) {
@ -259,8 +259,8 @@ autoplot.mic <- function(object,
df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols <- factor(translate_AMR(df$cols, language = language),
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language),
ordered = TRUE)
p <- ggplot2::ggplot(df)
@ -270,7 +270,7 @@ autoplot.mic <- function(object,
"Susceptible" = colours_RSI[2],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3])
names(vals) <- translate_AMR(names(vals), language = language)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
@ -321,10 +321,10 @@ plot.disk <- function(x,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_RSI) == 1) {
@ -372,7 +372,7 @@ plot.disk <- function(x,
}
legend("top",
x.intersp = 0.5,
legend = translate_AMR(legend_txt, language = language),
legend = translate_into_language(legend_txt, language = language),
fill = legend_col,
horiz = TRUE,
cex = 0.75,
@ -408,10 +408,10 @@ barplot.disk <- function(height,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
@ -433,7 +433,7 @@ barplot.disk <- function(height,
autoplot.disk <- function(object,
mo = NULL,
ab = NULL,
title = paste("Disk zones of", deparse(substitute(object))),
title = deparse(substitute(object)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
guideline = "EUCAST",
@ -454,10 +454,10 @@ autoplot.disk <- function(object,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
if ("main" %in% names(list(...))) {
@ -483,8 +483,8 @@ autoplot.disk <- function(object,
df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols <- factor(translate_AMR(df$cols, language = language),
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language),
ordered = TRUE)
p <- ggplot2::ggplot(df)
@ -494,7 +494,7 @@ autoplot.disk <- function(object,
"Susceptible" = colours_RSI[2],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3])
names(vals) <- translate_AMR(names(vals), language = language)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
@ -526,11 +526,20 @@ plot.rsi <- function(x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = deparse(substitute(x)),
language = get_AMR_locale(),
...) {
meet_criteria(ylab, allow_class = "character", has_length = 1)
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)
@ -592,10 +601,10 @@ barplot.rsi <- function(height,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_RSI) == 1) {
@ -620,7 +629,7 @@ barplot.rsi <- function(height,
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.rsi <- function(object,
title = paste("Resistance Overview of", deparse(substitute(object))),
title = deparse(substitute(object)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -634,10 +643,10 @@ autoplot.rsi <- function(object,
# translate if not specifically set
if (missing(ylab)) {
ylab <- translate_AMR(ylab, language = language)
ylab <- translate_into_language(ylab, language = language)
}
if (missing(xlab)) {
xlab <- translate_AMR(xlab, language = language)
xlab <- translate_into_language(xlab, language = language)
}
if ("main" %in% names(list(...))) {