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(v2.1.1.9144) new MIC scales and fix for rescale_mic()

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dr. M.S. (Matthijs) Berends
2025-02-11 08:48:37 +01:00
parent 2171f05951
commit 07757c933c
13 changed files with 191 additions and 79 deletions
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4
man/as.mic.Rd
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@ -27,9 +27,9 @@ rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
\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.}
\item{mic_range}{a manual range to limit 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)}.}
\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{TRUE} for \code{\link[=rescale_mic]{rescale_mic()}} and \code{FALSE} for \code{\link[=droplevels]{droplevels()}}. When setting this to \code{FALSE} in \code{\link[=rescale_mic]{rescale_mic()}}, the output will have factor levels that acknowledge \code{mic_range}.}
\item{...}{arguments passed on to methods}
}

54
man/plot.Rd
View File

@ -5,6 +5,7 @@
\alias{scale_x_mic}
\alias{scale_y_mic}
\alias{scale_colour_mic}
\alias{scale_color_mic}
\alias{scale_fill_mic}
\alias{plot.mic}
\alias{autoplot.mic}
@ -22,17 +23,15 @@
\alias{labels_sir_count}
\title{Plotting Helpers for AMR Data Analysis}
\usage{
scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
...)
scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
...)
scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_colour_mic(keep_operators = "edges", mic_range = NULL,
drop = FALSE, ...)
scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
...)
scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
\method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
@ -103,9 +102,7 @@ labels_sir_count(position = NULL, x = "antibiotic",
\arguments{
\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.}
\item{mic_range}{a manual range to limit 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)}.}
\item{drop}{a \link{logical} to remove intermediate MIC values, defaults to \code{FALSE}}
\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{...}{arguments passed on to methods}
@ -196,7 +193,7 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
# Plotting using scale_x_mic() ---------------------------------------------
# Plotting using scale_x_mic() -----------------------------------------
\donttest{
if (require("ggplot2")) {
mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
@ -227,6 +224,37 @@ if (require("ggplot2")) {
labs(title = "with scale_x_mic() using a manual 'outside' range")
}
# Plotting using scale_y_mic() -----------------------------------------
some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
if (require("ggplot2")) {
ggplot(data.frame(mic = some_mic_values,
group = some_groups),
aes(group, mic)) +
geom_boxplot() +
geom_violin(linetype = 2, colour = "grey", fill = NA) +
scale_y_mic()
}
if (require("ggplot2")) {
ggplot(data.frame(mic = some_mic_values,
group = some_groups),
aes(group, mic)) +
geom_boxplot() +
geom_violin(linetype = 2, colour = "grey", fill = NA) +
scale_y_mic(mic_range = c(NA, 2))
}
# Plotting using scale_fill_mic() -----------------------------------------
some_counts <- as.integer(runif(20, 5, 50))
if (require("ggplot2")) {
ggplot(data.frame(mic = some_mic_values,
group = some_groups,
counts = some_counts,
aes(group, counts, fill = mic)) +
geom_col() +
scale_fill_mic(mic_range = c(0.5, 16))
}
# Auto plotting --------------------------------------------------------
if (require("ggplot2")) {
autoplot(some_mic_values)
}
@ -237,7 +265,7 @@ if (require("ggplot2")) {
autoplot(some_sir_values)
}
# Plotting using scale_y_percent() -----------------------------------------
# Plotting using scale_y_percent() -------------------------------------
if (require("ggplot2")) {
p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
counts = c(1, 1, 2, 2, 3, 3)),