P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

re added nrow

This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-08-29 16:35:32 +02:00
parent d9e68e0a50
commit d654444c8e
2 changed files with 9 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
R/ggplot_rsi.R
View File

@ -26,6 +26,7 @@
#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.
#' @param fun function to transform \code{data}, either \code{\link{portion_df}} (default) or \code{\link{count_df}}
#' @param nrow (when using \code{facet}) number of rows
#' @param ... other parameters passed on to \code{geom_rsi}
#' @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)}.
#'
@ -129,6 +130,7 @@ ggplot_rsi <- function(data,
facet = NULL,
translate_ab = "official",
fun = portion_df,
nrow = NULL,
...) {
if (!"ggplot2" %in% rownames(installed.packages())) {
@ -154,7 +156,7 @@ ggplot_rsi <- function(data,
}
if (!is.null(facet)) {
p <- p + facet_rsi(facet = facet)
p <- p + facet_rsi(facet = facet, nrow = nrow)
}
p
@ -202,7 +204,7 @@ geom_rsi <- function(position = NULL,
#' @rdname ggplot_rsi
#' @export
facet_rsi <- function(facet = c("Interpretation", "Antibiotic")) {
facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
facet <- facet[1]
if (tolower(facet) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) {
@ -211,7 +213,7 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic")) {
facet <- "Antibiotic"
}
ggplot2::facet_wrap(facets = facet, scales = "free_x")
ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow)
}
#' @rdname ggplot_rsi

6
man/ggplot_rsi.Rd
View File

@ -11,13 +11,13 @@
\usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, translate_ab = "official",
fun = portion_df, ...)
fun = portion_df, nrow = NULL, ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
fill = "Interpretation", translate_ab = "official",
fun = portion_df, ...)
facet_rsi(facet = c("Interpretation", "Antibiotic"))
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
scale_y_percent()
@ -40,6 +40,8 @@ theme_rsi()
\item{fun}{function to transform \code{data}, either \code{\link{portion_df}} (default) or \code{\link{count_df}}}
\item{nrow}{(when using \code{facet}) number of rows}
\item{...}{other parameters passed on to \code{geom_rsi}}
}
\description{