mirror of
https://github.com/msberends/AMR.git
synced 2026-11-16 00:10:57 +01:00
(v3.0.1.9151) Fix inconsistencies in the plotting functions and correct the translations of the interpretation categories
Plotting: - Base colours and legends of interpreted MIC and disk values on the interpretation itself instead of matching colours - Fix SDD in autoplot() for disks, the colours of barplot() for SIR values, and barplot() for MICs ignoring language and expand - Match a named colours_SIR by name; let keep_operators = TRUE/FALSE in scale_*_mic() behave as "all"/"none" - Let a named values in scale_*_sir() replace the colours it names, warn in scale_x_sir(), and pass other arguments on - Let the default of eucast_I follow the guideline option, also for EUCAST before 2019 - Support unquoted column names in facet_sir() without evaluating them - Correct the documentation and examples Translations: - Add SDD, NS, WT and NWT, and correct S, I, R and NI in 18 languages - Sources of the terms for 'I': NAK via German laboratories (de), SZU national reference laboratory (cs), lex.dk (da), Karolinska University Hospital (sv), COESANT (es), Nordlab (fi), CA-SFM (fr); no by analogy with da and sv - Not verified against an official source: ar, bn, el, hi, id, ja, ko, pl, ro, ru, sw, tr, uk, ur, vi, zh Tests: - Let the grouped antibiogram test use English so it passes in other locales
This commit is contained in:
dr. M.S. (Matthijs) Berends committed
1 parent
b63263cc56
commit
43accd35d1
9 files changed
+333
-359
No files matched your search
+14
-14
@@ -35,21 +35,21 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
|
||||
scale_x_sir(
|
||||
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
|
||||
language = get_AMR_locale(),
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
|
||||
eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
|
||||
...
|
||||
)
|
||||
|
||||
scale_colour_sir(
|
||||
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
|
||||
language = get_AMR_locale(),
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
|
||||
eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
|
||||
...
|
||||
)
|
||||
|
||||
scale_fill_sir(
|
||||
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
|
||||
language = get_AMR_locale(),
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
|
||||
eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
|
||||
...
|
||||
)
|
||||
|
||||
@@ -158,11 +158,11 @@ theme_sir()
|
||||
|
||||
\item{...}{Arguments passed on to methods.}
|
||||
|
||||
\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.}
|
||||
\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with at least the names S, I and R. With three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.}
|
||||
|
||||
\item{language}{Language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the package option \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} to prevent translation.}
|
||||
|
||||
\item{eucast_I}{A \link{logical} to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be \code{TRUE} if the default \link[=as.sir]{AMR interpretation guideline} is set to EUCAST (which is the default). With \code{FALSE}, it will be interpreted as "Intermediate".}
|
||||
\item{eucast_I}{A \link{logical} to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be \code{TRUE} if the default \link[=as.sir]{AMR interpretation guideline} is set to EUCAST 2019 or later (which is the default). With \code{FALSE}, it will be interpreted as "Intermediate".}
|
||||
|
||||
\item{x, object}{Values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.sir]{as.sir()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}}).}
|
||||
|
||||
@@ -198,12 +198,12 @@ The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} mo
|
||||
\description{
|
||||
Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
|
||||
|
||||
Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
|
||||
Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allow custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
|
||||
}
|
||||
\details{
|
||||
\subsection{The \verb{scale_*_mic()} Functions}{
|
||||
|
||||
The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale.
|
||||
The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale.
|
||||
|
||||
There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class \link[=as.mic]{mic}.
|
||||
|
||||
@@ -212,7 +212,7 @@ When manually added though, they allow to rescale the MIC range with an 'inside'
|
||||
|
||||
\subsection{The \verb{scale_*_sir()} Functions}{
|
||||
|
||||
The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI < WT < NWT < NS).
|
||||
The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI < WT < NWT < NS).
|
||||
|
||||
There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class \link[=as.sir]{sir}.
|
||||
|
||||
@@ -227,10 +227,10 @@ This package contains more functions that extend the \code{ggplot2} package, to
|
||||
\item \code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_y_continuous]{ggplot2::scale_y_continuous()}}.
|
||||
\item \code{\link[=scale_sir_colours]{scale_sir_colours()}} allows to set colours to any aesthetic, even for \code{shape} or \code{linetype}.
|
||||
\item \code{\link[=theme_sir]{theme_sir()}} is a \link[ggplot2:theme]{ggplot2 theme} with minimal distraction.
|
||||
\item \code{\link[=labels_sir_count]{labels_sir_count()}} print datalabels on the bars with percentage and number of isolates, using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
|
||||
\item \code{\link[=labels_sir_count]{labels_sir_count()}} prints data labels on the bars with percentage and number of isolates, using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
|
||||
}
|
||||
|
||||
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
|
||||
The interpretation of "I" will be named "Susceptible, incr. exp." (susceptible, increased exposure) for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
|
||||
|
||||
For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2026, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
|
||||
}
|
||||
@@ -254,7 +254,7 @@ if (require("ggplot2")) {
|
||||
}
|
||||
|
||||
if (require("ggplot2")) {
|
||||
# support for 27 languages, various guidelines, and many options
|
||||
# support for all languages in ?translate, various guidelines, and many options
|
||||
autoplot(some_disk_values,
|
||||
mo = "Escherichia coli", ab = "cipro",
|
||||
guideline = "CLSI", language = "no",
|
||||
@@ -351,8 +351,8 @@ if (require("ggplot2")) {
|
||||
) +
|
||||
theme_minimal() +
|
||||
geom_boxplot(fill = NA, colour = "grey30") +
|
||||
geom_jitter(width = 0.25)
|
||||
labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
|
||||
geom_jitter(width = 0.25) +
|
||||
labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
|
||||
|
||||
mic_sir_plot
|
||||
}
|
||||
@@ -361,7 +361,7 @@ if (require("ggplot2")) {
|
||||
scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
|
||||
scale_colour_sir(
|
||||
language = "pt", # Portuguese
|
||||
name = "Support in 28 languages"
|
||||
name = "Support in many languages"
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
Reference in new issue
Block a user