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# Plotting Helpers for AMR Data Analysis

Source: `R/plotting.R`
`plot.Rd`

Functions to plot classes `sir`, `mic` and `disk`, with support for base R and `ggplot2`.

Especially the `scale_*_mic()` functions are relevant wrappers to plot MIC values for `ggplot2`. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.

## 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(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
      language = get_AMR_locale(),
      eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
      ...
    )

    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",
      ...
    )

    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",
      ...
    )

    # S3 method for class 'mic'
    plot(
      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(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
      language = get_AMR_locale(),
      expand = TRUE,
      include_PKPD = getOption("AMR_include_PKPD", TRUE),
      breakpoint_type = getOption("AMR_breakpoint_type", "human"),
      ...
    )

    # S3 method for class 'mic'
    autoplot(
      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(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
      language = get_AMR_locale(),
      expand = TRUE,
      include_PKPD = getOption("AMR_include_PKPD", TRUE),
      breakpoint_type = getOption("AMR_breakpoint_type", "human"),
      ...
    )

    # S3 method for class 'disk'
    plot(
      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(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
      language = get_AMR_locale(),
      expand = TRUE,
      include_PKPD = getOption("AMR_include_PKPD", TRUE),
      breakpoint_type = getOption("AMR_breakpoint_type", "human"),
      ...
    )

    # S3 method for class 'disk'
    autoplot(
      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(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
      language = get_AMR_locale(),
      expand = TRUE,
      include_PKPD = getOption("AMR_include_PKPD", TRUE),
      breakpoint_type = getOption("AMR_breakpoint_type", "human"),
      ...
    )

    # S3 method for class 'sir'
    plot(
      x,
      ylab = translate_AMR("Percentage", language = language),
      xlab = translate_AMR("Antimicrobial Interpretation", language = language),
      main = deparse(substitute(x)),
      language = get_AMR_locale(),
      ...
    )

    # S3 method for class 'sir'
    autoplot(
      object,
      title = deparse(substitute(object)),
      xlab = translate_AMR("Antimicrobial Interpretation", language = language),
      ylab = translate_AMR("Frequency", language = language),
      colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#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(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#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

keep_operators

  A character specifying how to handle operators (such as `>` and `<=`) in the input. Accepts one of three values: `"all"` (or `TRUE`) to keep all operators, `"none"` (or `FALSE`) to remove all operators, or `"edges"` to keep operators only at both ends of the range.

mic_range

  A manual range to rescale the MIC values (using `rescale_mic()`), e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent rescaling on one side, e.g., `mic_range = c(NA, 32)`. Note: This rescales values but does not filter them - use the ggplot2 `limits` argument separately to exclude values from the plot.

...

  Arguments passed on to methods.

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.

language

  Language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see `get_AMR_locale()`) and can be overwritten by setting the package option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see translate. Use `language = NULL` to prevent translation.

eucast_I

  A logical to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be `TRUE` if the default AMR interpretation guideline is set to EUCAST (which is the default). With `FALSE`, it will be interpreted as "Intermediate".

x, object

  Values created with `as.mic()`, `as.disk()` or `as.sir()` (or their `random_*` variants, such as `random_mic()`).

mo

  Any (vector of) text that can be coerced to a valid microorganism code with `as.mo()`.

ab

  Any (vector of) text that can be coerced to a valid antimicrobial drug code with `as.ab()`.

guideline

  Interpretation guideline to use - the default is the latest included EUCAST guideline, see Details.

main, title

  Title of the plot.

xlab, ylab

  Axis title.

expand

  A 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.

include_PKPD

  A logical to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`. Can also be set with the package option `AMR_include_PKPD`.

breakpoint_type

  The type of breakpoints to use, either `"ECOFF"`, `"animal"`, or `"human"`. ECOFF stands for Epidemiological Cut-Off values. The default is `"human"`, which can also be set with the package option `AMR_breakpoint_type`. If `host` is set to values of veterinary species, this will automatically be set to `"animal"`.

facet

  Variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable.

nrow

  (when using `facet`) number of rows.

breaks

  A numeric vector of positions.

limits

  A numeric vector of length two providing limits of the scale, use `NA` to refer to the existing minimum or maximum.

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".

position

  Position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`.

translate_ab

  A column name of the antimicrobials data set to translate the antibiotic abbreviations to, using `ab_property()`.

minimum

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

combine_SI

  A 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 `TRUE`.

datalabels.size

  Size of the datalabels.

datalabels.colour

  Colour of the datalabels.

## Value

The `autoplot()` functions return a `ggplot` model that is extendible with any `ggplot2` function.

## Details

### The `scale_*_mic()` Functions

The functions `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()`, and `scale_fill_mic()` functions allow to plot the 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 mic.

When manually added though, they allow to rescale the MIC range with an 'inside' or 'outside' range if required, and provide the option to retain the operators in MIC values (such as `>=`). Missing intermediate log2 levels will always be plotted too.

### The `scale_*_sir()` Functions

The functions `scale_x_sir()`, `scale_colour_sir()`, and `scale_fill_sir()` functions allow to plot the 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 sir.

At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 28 supported languages (use `language = NULL` to keep S/I/R). Also, except for `scale_x_sir()`, they set colour-blind friendly colours to the `colour` and `fill` aesthetics.

### Additional `ggplot2` Functions

This package contains more functions that extend the `ggplot2` package, to help in visualising AMR data results. All these functions are internally used by `ggplot_sir()` too.

- `facet_sir()` creates 2d plots (at default based on S/I/R) using `ggplot2::facet_wrap()`.

- `scale_y_percent()` transforms the y axis to a 0 to 100% range using `ggplot2::scale_y_continuous()`.

- `scale_sir_colours()` allows to set colours to any aesthetic, even for `shape` or `linetype`.

- `theme_sir()` is a ggplot2 theme with minimal distraction.

- `labels_sir_count()` print datalabels on the bars with percentage and number of isolates, using `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 2026, unless the package option `AMR_guideline` is set. See `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")) {
      autoplot(some_mic_values, mo = "Staph aureus", ab = "Ceftaroline", guideline = "CLSI")
    }

    if (require("ggplot2")) {
      # support for 27 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 = "scale_x_mic() automatically applied")
    }

    if (require("ggplot2")) {
      mic_plot +
        scale_x_mic(keep_operators = "none") +
        labs(title = "with scale_x_mic() keeping no 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 = "grey30", fill = NA) +
        labs(title = "scale_y_mic() automatically applied")
    }

    if (require("ggplot2")) {
      ggplot(
        data.frame(
          mic = some_mic_values,
          group = some_groups
        ),
        aes(group, mic)
      ) +
        geom_boxplot() +
        geom_violin(linetype = 2, colour = "grey30", 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")) {
      mic_sir_plot <- 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 = "grey30") +
        geom_jitter(width = 0.25)
      labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")

      mic_sir_plot
    }

    if (require("ggplot2")) {
      mic_sir_plot +
        scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
        scale_colour_sir(
          language = "pt", # Portuguese
          name = "Support in 28 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")
    #> ℹ No EUCAST 2026 MIC interpretations found for ampicillin in Staphylococcus
    #>   aureus

    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)