% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggplot_rsi.R
\name{ggplot_rsi}
\alias{ggplot_rsi}
\alias{geom_rsi}
\alias{facet_rsi}
\alias{scale_y_percent}
\alias{scale_rsi_colours}
\alias{theme_rsi}
\title{AMR bar plots with \code{ggplot}}
\usage{
ggplot_rsi(data, x = "Antibiotic", facet = NULL)

geom_rsi(position = "stack", x = c("Antibiotic", "Interpretation"))

facet_rsi(facet = c("Interpretation", "Antibiotic"))

scale_y_percent()

scale_rsi_colours()

theme_rsi()
}
\arguments{
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}

\item{x}{parameter to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"}}

\item{facet}{parameter to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"}}

\item{position}{position adjustment of bars, either \code{"stack"} (default) or \code{"dodge"}}
}
\description{
Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
}
\details{
At default, the names of antibiotics will be shown on the plots using \code{\link{abname}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}.

\strong{The functions}\cr
\code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{\link{portion_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.

\code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.

\code{scale_y_percent} transforms the y axis to a 0 to 100% range.

\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R.

\code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.

\code{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 (\code{\%>\%}). See Examples.
}
\examples{
library(dplyr)
library(ggplot2)

# get antimicrobial results for drugs against a UTI:
ggplot(septic_patients \%>\% select(amox, nitr, fosf, trim, cipr)) +
  geom_rsi()

# prettify it using some additional functions
df <- septic_patients[, c("amox", "nitr", "fosf", "trim", "cipr")]
ggplot(df) +
  geom_rsi(x = "Interpretation") +
  facet_rsi(facet = "Antibiotic") +
  scale_y_percent() +
  scale_rsi_colours() +
  theme_rsi()

# or better yet, simplify this using the wrapper function - a single command:
septic_patients \%>\%
  select(amox, nitr, fosf, trim, cipr) \%>\%
  ggplot_rsi()

septic_patients \%>\%
  select(amox, nitr, fosf, trim, cipr) \%>\%
  ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
}