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https://github.com/msberends/AMR.git
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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper
This commit is contained in:
133
man/plot.Rd
133
man/plot.Rd
@@ -22,128 +22,83 @@
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\alias{labels_sir_count}
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\title{Plotting Helpers for AMR Data Analysis}
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\usage{
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scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
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...)
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scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
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...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL,
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drop = FALSE, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
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...)
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\method{plot}{mic}(
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x,
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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main = deparse(substitute(x)),
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ylab = translate_AMR("Frequency", language = language),
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xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(),
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expand = TRUE,
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\method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
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main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
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= language),
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xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
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language), colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), expand = TRUE,
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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...
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)
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{autoplot}{mic}(
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object,
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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title = deparse(substitute(object)),
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\method{autoplot}{mic}(object, mo = NULL, ab = NULL,
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guideline = "EUCAST", title = deparse(substitute(object)),
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ylab = translate_AMR("Frequency", language = language),
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xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(),
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expand = TRUE,
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xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
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language), colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(), expand = TRUE,
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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...
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)
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{fortify}{mic}(object, ...)
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\method{plot}{disk}(
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x,
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main = deparse(substitute(x)),
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\method{plot}{disk}(x, main = deparse(substitute(x)),
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ylab = translate_AMR("Frequency", language = language),
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xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
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mo = NULL,
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ab = NULL,
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guideline = "EUCAST",
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mo = NULL, ab = NULL, guideline = "EUCAST",
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(),
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expand = TRUE,
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language = get_AMR_locale(), expand = TRUE,
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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...
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)
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{autoplot}{disk}(
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object,
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mo = NULL,
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ab = NULL,
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title = deparse(substitute(object)),
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ylab = translate_AMR("Frequency", language = language),
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xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
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guideline = "EUCAST",
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(),
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expand = TRUE,
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\method{autoplot}{disk}(object, mo = NULL, ab = NULL,
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title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
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language = language), xlab = translate_AMR("Disk diffusion diameter (mm)",
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language = language), guideline = "EUCAST", colours_SIR = c("#3CAEA3",
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"#F6D55C", "#ED553B"), language = get_AMR_locale(), expand = TRUE,
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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...
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)
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
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\method{fortify}{disk}(object, ...)
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\method{plot}{sir}(
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x,
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ylab = translate_AMR("Percentage", language = language),
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xlab = translate_AMR("Antimicrobial Interpretation", language = language),
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main = deparse(substitute(x)),
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language = get_AMR_locale(),
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...
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)
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\method{plot}{sir}(x, ylab = translate_AMR("Percentage", language =
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language), xlab = translate_AMR("Antimicrobial Interpretation", language =
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language), main = deparse(substitute(x)), language = get_AMR_locale(),
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...)
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\method{autoplot}{sir}(
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object,
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title = deparse(substitute(object)),
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\method{autoplot}{sir}(object, title = deparse(substitute(object)),
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xlab = translate_AMR("Antimicrobial Interpretation", language = language),
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ylab = translate_AMR("Frequency", language = language),
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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language = get_AMR_locale(),
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...
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)
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language = get_AMR_locale(), ...)
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\method{fortify}{sir}(object, ...)
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facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
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scale_y_percent(
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breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
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limits = c(0, NA)
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)
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scale_y_percent(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
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limits = c(0, NA))
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scale_sir_colours(
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...,
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aesthetics = "fill",
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colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B")
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)
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scale_sir_colours(..., aesthetics = "fill", colours_SIR = c("#3CAEA3",
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"#F6D55C", "#ED553B"))
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theme_sir()
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labels_sir_count(
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position = NULL,
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x = "antibiotic",
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translate_ab = "name",
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minimum = 30,
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language = get_AMR_locale(),
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combine_SI = TRUE,
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datalabels.size = 3,
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datalabels.colour = "grey15"
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)
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labels_sir_count(position = NULL, x = "antibiotic",
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translate_ab = "name", minimum = 30, language = get_AMR_locale(),
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combine_SI = TRUE, datalabels.size = 3, datalabels.colour = "grey15")
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}
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\arguments{
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\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.}
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