AMR/man/plot.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotting.R
\name{plot}
\alias{plot}
\alias{scale_x_mic}
\alias{scale_y_mic}
\alias{scale_colour_mic}
\alias{scale_color_mic}
\alias{scale_fill_mic}
\alias{scale_x_sir}
\alias{scale_colour_sir}
\alias{scale_color_sir}
\alias{scale_fill_sir}
\alias{plot.mic}
\alias{autoplot.mic}
\alias{plot.disk}
\alias{autoplot.disk}
\alias{plot.sir}
\alias{autoplot.sir}
\alias{facet_sir}
\alias{scale_y_percent}
\alias{scale_sir_colours}
\alias{scale_sir_colors}
\alias{theme_sir}
\alias{labels_sir_count}
\title{Plotting Helpers for AMR Data Analysis}
\usage{
scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)

scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)

scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)

scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)

scale_x_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
  language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
  "EUCAST") == "EUCAST", ...)

scale_colour_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
  language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
  "EUCAST") == "EUCAST", ...)

scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
  language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
  "EUCAST") == "EUCAST", ...)

\method{plot}{mic}(x, mo = NULL, ab = NULL,
  guideline = getOption("AMR_guideline", "EUCAST"),
  main = deparse(substitute(x)), 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,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)

\method{autoplot}{mic}(object, mo = NULL, ab = NULL,
  guideline = getOption("AMR_guideline", "EUCAST"),
  title = deparse(substitute(object)), 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,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)

\method{plot}{disk}(x, main = deparse(substitute(x)),
  ylab = translate_AMR("Frequency", language = language),
  xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
  mo = NULL, ab = NULL, guideline = getOption("AMR_guideline", "EUCAST"),
  colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
  language = get_AMR_locale(), expand = TRUE,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)

\method{autoplot}{disk}(object, mo = NULL, ab = NULL,
  title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
  language = language), xlab = translate_AMR("Disk diffusion diameter (mm)",
  language = language), guideline = getOption("AMR_guideline", "EUCAST"),
  colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
  language = get_AMR_locale(), expand = TRUE,
  include_PKPD = getOption("AMR_include_PKPD", TRUE),
  breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)

\method{plot}{sir}(x, ylab = translate_AMR("Percentage", language =
  language), xlab = translate_AMR("Antimicrobial Interpretation", language =
  language), main = deparse(substitute(x)), language = get_AMR_locale(),
  ...)

\method{autoplot}{sir}(object, title = deparse(substitute(object)),
  xlab = translate_AMR("Antimicrobial Interpretation", language = language),
  ylab = translate_AMR("Frequency", language = language),
  colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
  language = get_AMR_locale(), ...)

facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)

scale_y_percent(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
  limits = c(0, NA))

scale_sir_colours(..., aesthetics, colours_SIR = c("#3CAEA3", "#F6D55C",
  "#ED553B"))

theme_sir()

labels_sir_count(position = NULL, x = "antibiotic",
  translate_ab = "name", minimum = 30, language = get_AMR_locale(),
  combine_SI = TRUE, datalabels.size = 3, datalabels.colour = "grey15")
}
\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 rescale the MIC values (using \code{\link[=rescale_mic]{rescale_mic()}}), e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling on one side, e.g., \code{mic_range = c(NA, 32)}. \strong{Note:} This rescales values but does not filter them - use the ggplot2 \code{limits} argument separately to exclude values from the plot.}

\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{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{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()}}).}

\item{mo}{Any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}.}

\item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}

\item{guideline}{Interpretation guideline to use - the default is the latest included EUCAST guideline, see \emph{Details}.}

\item{main, title}{Title of the plot.}

\item{xlab, ylab}{Axis title.}

\item{expand}{A \link{logical} to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.}

\item{include_PKPD}{A \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}

\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 package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}

\item{facet}{Variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable.}

\item{nrow}{(when using \code{facet}) number of rows.}

\item{breaks}{A \link{numeric} vector of positions.}

\item{limits}{A \link{numeric} vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum.}

\item{aesthetics}{Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size".}

\item{position}{Position adjustment of bars, either \code{"fill"}, \code{"stack"} or \code{"dodge"}.}

\item{translate_ab}{A column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}.}

\item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}

\item{combine_SI}{A \link{logical} to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}.}

\item{datalabels.size}{Size of the datalabels.}

\item{datalabels.colour}{Colour of the datalabels.}
}
\value{
The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
}
\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.
}
\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. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as \code{>=}) if desired. Missing intermediate log2 levels will be plotted too.
}

\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). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 20 supported languages (use \code{language = NULL} to keep S/I/R). Also, except for \code{\link[=scale_x_sir]{scale_x_sir()}}, they set colour-blind friendly colours to the \code{colour} and \code{fill} aesthetics.
}

\subsection{Additional \code{ggplot2} Functions}{

This package contains more functions that extend the \code{ggplot2} package, to help in visualising AMR data results. All these functions are internally used by \code{\link[=ggplot_sir]{ggplot_sir()}} too.
\itemize{
\item \code{\link[=facet_sir]{facet_sir()}} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}}.
\item \code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_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()}}.
}

The interpretation of "I" will be named "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 2025, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
}
}
\examples{
some_mic_values <- random_mic(size = 100)
some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))

\donttest{
# Plotting using ggplot2's autoplot() for MIC, disk, and SIR -----------
if (require("ggplot2")) {
  autoplot(some_mic_values)
}
if (require("ggplot2")) {
  # when providing the microorganism and antibiotic, colours will show interpretations:
  autoplot(some_mic_values, mo = "Escherichia coli", ab = "cipro")
}
if (require("ggplot2")) {
  # support for 20 languages, various guidelines, and many options
  autoplot(some_disk_values,
    mo = "Escherichia coli", ab = "cipro",
    guideline = "CLSI 2024", language = "no",
    title = "Disk diffusion from the North"
  )
}


# Plotting using scale_x_mic() -----------------------------------------
if (require("ggplot2")) {
  mic_plot <- ggplot(
    data.frame(
      mics = as.mic(c(0.25, "<=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, 16)) +
    labs(title = "with scale_x_mic() using a manual 'within' range")
}
if (require("ggplot2")) {
  mic_plot +
    scale_x_mic(mic_range = c(0.032, 256)) +
    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, 0.25))
}


# Plotting using scale_x_sir() -----------------------------------------
if (require("ggplot2")) {
  ggplot(
    data.frame(
      x = c("I", "R", "S"),
      y = c(45, 323, 573)
    ),
    aes(x, y)
  ) +
    geom_col() +
    scale_x_sir()
}


# Plotting using scale_y_mic() and scale_colour_sir() ------------------
if (require("ggplot2")) {
  plain <- ggplot(
    data.frame(
      mic = some_mic_values,
      group = some_groups,
      sir = as.sir(some_mic_values,
        mo = "E. coli",
        ab = "cipro"
      )
    ),
    aes(x = group, y = mic, colour = sir)
  ) +
    theme_minimal() +
    geom_boxplot(fill = NA, colour = "grey") +
    geom_jitter(width = 0.25)

  plain
}
if (require("ggplot2")) {
  # and now with our MIC and SIR scale functions:
  plain +
    scale_y_mic() +
    scale_colour_sir()
}
if (require("ggplot2")) {
  plain +
    scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
    scale_colour_sir(
      language = "pt",
      name = "Support in 20 languages"
    )
}
}

# Plotting using base R's plot() ---------------------------------------

plot(some_mic_values)
# when providing the microorganism and antibiotic, colours will show interpretations:
plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")

plot(some_disk_values)
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")

plot(some_sir_values)
}