mirror of https://github.com/msberends/AMR.git
90 lines
3.3 KiB
R
90 lines
3.3 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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\title{AMR bar plots with \code{ggplot}}
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\usage{
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ggplot_rsi(data, position = "stack", x = "Antibiotic",
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fill = "Interpretation", facet = NULL)
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geom_rsi(position = "stack", x = c("Antibiotic", "Interpretation"),
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fill = "Interpretation")
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facet_rsi(facet = c("Interpretation", "Antibiotic"))
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scale_y_percent()
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scale_rsi_colours()
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theme_rsi()
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}
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\arguments{
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\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
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\item{position}{position adjustment of bars, either \code{"stack"} (default) or \code{"dodge"}}
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\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"}}
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\item{fill}{variable to categorise using the plots legend}
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\item{facet}{variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"}}
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}
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\description{
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Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} 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{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)}.
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\strong{The functions}\cr
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\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.
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\code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
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\code{scale_y_percent} transforms the y axis to a 0 to 100% range.
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\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R.
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\code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
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\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.
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}
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\examples{
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library(dplyr)
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library(ggplot2)
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# get antimicrobial results for drugs against a UTI:
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ggplot(septic_patients \%>\% select(amox, nitr, fosf, trim, cipr)) +
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geom_rsi()
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# prettify it using some additional functions
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df <- septic_patients[, c("amox", "nitr", "fosf", "trim", "cipr")]
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ggplot(df) +
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geom_rsi(x = "Interpretation") +
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facet_rsi(facet = "Antibiotic") +
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scale_y_percent() +
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scale_rsi_colours() +
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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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septic_patients \%>\%
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select(amox, nitr, fosf, trim, cipr) \%>\%
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ggplot_rsi()
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septic_patients \%>\%
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select(amox, nitr, fosf, trim, cipr) \%>\%
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ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
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# it also supports groups (don't forget to use facet on the group):
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septic_patients \%>\%
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select(hospital_id, amox, cipr) \%>\%
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group_by(hospital_id) \%>\%
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ggplot_rsi() +
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facet_grid("hospital_id") +
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labs(title = "AMR of Amoxicillin And Ciprofloxacine Per Hospital")
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}
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