mirror of https://github.com/msberends/AMR.git
225 lines
9.6 KiB
R
225 lines
9.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/ggplot_rsi.R
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\name{ggplot_rsi}
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\alias{ggplot_rsi}
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\alias{geom_rsi}
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\alias{facet_rsi}
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\alias{scale_y_percent}
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\alias{scale_rsi_colours}
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\alias{theme_rsi}
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\alias{labels_rsi_count}
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\title{AMR Plots with \code{ggplot2}}
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\usage{
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ggplot_rsi(
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data,
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position = NULL,
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x = "antibiotic",
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fill = "interpretation",
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facet = NULL,
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breaks = seq(0, 1, 0.1),
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limits = NULL,
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translate_ab = "name",
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combine_SI = TRUE,
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combine_IR = FALSE,
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minimum = 30,
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language = get_locale(),
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nrow = NULL,
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colours = c(S = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R =
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"#ED553B"),
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datalabels = TRUE,
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datalabels.size = 2.5,
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datalabels.colour = "grey15",
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title = NULL,
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subtitle = NULL,
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caption = NULL,
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x.title = "Antimicrobial",
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y.title = "Proportion",
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...
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)
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geom_rsi(
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position = NULL,
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x = c("antibiotic", "interpretation"),
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fill = "interpretation",
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translate_ab = "name",
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minimum = 30,
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language = get_locale(),
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combine_SI = TRUE,
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combine_IR = FALSE,
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...
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)
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facet_rsi(facet = c("interpretation", "antibiotic"), nrow = NULL)
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scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)
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scale_rsi_colours(..., aesthetics = "fill")
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theme_rsi()
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labels_rsi_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_locale(),
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combine_SI = TRUE,
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combine_IR = FALSE,
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datalabels.size = 3,
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datalabels.colour = "grey15"
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)
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}
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\arguments{
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\item{data}{a \link{data.frame} with column(s) of class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}})}
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\item{position}{position adjustment of bars, either \code{"fill"}, \code{"stack"} or \code{"dodge"}}
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\item{x}{variable to show on x axis, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable}
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\item{fill}{variable to categorise using the plots legend, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable}
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\item{facet}{variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable}
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\item{breaks}{numeric vector of positions}
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\item{limits}{numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum}
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\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
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\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
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\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see argument \code{combine_SI}.}
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\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}.}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{nrow}{(when using \code{facet}) number of rows}
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\item{colours}{a named vactor with colour to be used for filling. The default colours are colour-blind friendly.}
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\item{datalabels}{show datalabels using \code{\link[=labels_rsi_count]{labels_rsi_count()}}}
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\item{datalabels.size}{size of the datalabels}
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\item{datalabels.colour}{colour of the datalabels}
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\item{title}{text to show as title of the plot}
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\item{subtitle}{text to show as subtitle of the plot}
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\item{caption}{text to show as caption of the plot}
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\item{x.title}{text to show as x axis description}
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\item{y.title}{text to show as y axis description}
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\item{...}{other arguments passed on to \code{\link[=geom_rsi]{geom_rsi()}} or, in case of \code{\link[=scale_rsi_colours]{scale_rsi_colours()}}, named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See \emph{Examples}.}
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\item{aesthetics}{aesthetics to apply the colours to, defaults to "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"}
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}
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\description{
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Use these functions to create bar plots for AMR data analysis. All functions rely on \link[ggplot2:ggplot]{ggplot2} functions.
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}
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\details{
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At default, the names of antibiotics will be shown on the plots using \code{\link[=ab_name]{ab_name()}}. This can be set with the \code{translate_ab} argument. See \code{\link[=count_df]{count_df()}}.
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\subsection{The Functions}{
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\code{\link[=geom_rsi]{geom_rsi()}} will take any variable from the data that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) using \code{\link[=rsi_df]{rsi_df()}} and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
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\code{\link[=facet_rsi]{facet_rsi()}} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}}.
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\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()}}.
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\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.
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\code{\link[=theme_rsi]{theme_rsi()}} is a [ggplot2 theme][\code{\link[ggplot2:theme]{ggplot2::theme()}} with minimal distraction.
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\code{\link[=labels_rsi_count]{labels_rsi_count()}} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
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\code{\link[=ggplot_rsi]{ggplot_rsi()}} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\verb{\%>\%}). See \emph{Examples}.
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}
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}
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\section{Maturing Lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
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}
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\section{Read more on Our Website!}{
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On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
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}
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\examples{
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if (require("ggplot2") & require("dplyr")) {
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# get antimicrobial results for drugs against a UTI:
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ggplot(example_isolates \%>\% select(AMX, NIT, FOS, TMP, CIP)) +
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geom_rsi()
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# prettify the plot using some additional functions:
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df <- example_isolates \%>\% select(AMX, NIT, FOS, TMP, CIP)
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ggplot(df) +
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geom_rsi() +
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scale_y_percent() +
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scale_rsi_colours() +
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labels_rsi_count() +
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theme_rsi()
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# or better yet, simplify this using the wrapper function - a single command:
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example_isolates \%>\%
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select(AMX, NIT, FOS, TMP, CIP) \%>\%
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ggplot_rsi()
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# get only proportions and no counts:
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example_isolates \%>\%
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select(AMX, NIT, FOS, TMP, CIP) \%>\%
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ggplot_rsi(datalabels = FALSE)
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# add other ggplot2 arguments as you like:
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example_isolates \%>\%
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select(AMX, NIT, FOS, TMP, CIP) \%>\%
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ggplot_rsi(width = 0.5,
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colour = "black",
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size = 1,
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linetype = 2,
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alpha = 0.25)
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example_isolates \%>\%
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select(AMX) \%>\%
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ggplot_rsi(colours = c(SI = "yellow"))
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}
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\donttest{
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# resistance of ciprofloxacine per age group
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example_isolates \%>\%
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mutate(first_isolate = first_isolate(.)) \%>\%
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filter(first_isolate == TRUE,
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mo == as.mo("E. coli")) \%>\%
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# age_groups() is also a function in this AMR package:
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group_by(age_group = age_groups(age)) \%>\%
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select(age_group,
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CIP) \%>\%
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ggplot_rsi(x = "age_group")
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# a shorter version which also adjusts data label colours:
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example_isolates \%>\%
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select(AMX, NIT, FOS, TMP, CIP) \%>\%
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ggplot_rsi(colours = FALSE)
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# it also supports groups (don't forget to use the group var on `x` or `facet`):
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example_isolates \%>\%
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select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\%
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group_by(hospital_id) \%>\%
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ggplot_rsi(x = "hospital_id",
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facet = "antibiotic",
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nrow = 1,
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title = "AMR of Anti-UTI Drugs Per Hospital",
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x.title = "Hospital",
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datalabels = FALSE)
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}
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}
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