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Added support for 'html' in italicize_taxonomy() (#134)

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Emil Rossing 2024-02-13 13:47:07 +01:00 committed by GitHub
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commit 74ea6c8c60
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3 changed files with 16 additions and 9 deletions
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13
R/italicise_taxonomy.R
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@ -31,11 +31,11 @@
#' #'
#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic. #' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.
#' @param string a [character] (vector) #' @param string a [character] (vector)
#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details* #' @param type type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see *Details*
#' @details #' @details
#' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set. #' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set.
#' #'
#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur. #' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or `<i>` and `</i>` when using html. When using 'ansi', ANSI colours will be added using `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
#' #'
#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae". #' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
#' @export #' @export
@ -44,18 +44,21 @@
#' italicise_taxonomy("An overview of S. aureus isolates") #' italicise_taxonomy("An overview of S. aureus isolates")
#' #'
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi")) #' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
italicise_taxonomy <- function(string, type = c("markdown", "ansi")) { italicise_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
if (missing(type)) { if (missing(type)) {
type <- "markdown" type <- "markdown"
} }
meet_criteria(string, allow_class = "character") meet_criteria(string, allow_class = "character")
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi")) meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi", "html"))
add_MO_lookup_to_AMR_env() add_MO_lookup_to_AMR_env()
if (type == "markdown") { if (type == "markdown") {
before <- "*" before <- "*"
after <- "*" after <- "*"
} else if (type == "html") {
before <- "<i>"
after <- "</i>"
} else if (type == "ansi") { } else if (type == "ansi") {
if (!has_colour() && !identical(Sys.getenv("IN_PKGDOWN"), "true")) { if (!has_colour() && !identical(Sys.getenv("IN_PKGDOWN"), "true")) {
return(string) return(string)
@ -134,7 +137,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
#' @rdname italicise_taxonomy #' @rdname italicise_taxonomy
#' @export #' @export
italicize_taxonomy <- function(string, type = c("markdown", "ansi")) { italicize_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
if (missing(type)) { if (missing(type)) {
type <- "markdown" type <- "markdown"
} }

4
inst/tinytest/test-italicise_taxonomy.R
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@ -41,3 +41,7 @@ if (AMR:::has_colour()) {
"test for \033[3mE. coli\033[23m" "test for \033[3mE. coli\033[23m"
) )
} }
expect_identical(
italicise_taxonomy("test for E. coli", "html"),
"test for <i>E. coli</i>"
)

8
man/italicise_taxonomy.Rd
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@ -5,14 +5,14 @@
\alias{italicize_taxonomy} \alias{italicize_taxonomy}
\title{Italicise Taxonomic Families, Genera, Species, Subspecies} \title{Italicise Taxonomic Families, Genera, Species, Subspecies}
\usage{ \usage{
italicise_taxonomy(string, type = c("markdown", "ansi")) italicise_taxonomy(string, type = c("markdown", "ansi", "html"))
italicize_taxonomy(string, type = c("markdown", "ansi")) italicize_taxonomy(string, type = c("markdown", "ansi", "html"))
} }
\arguments{ \arguments{
\item{string}{a \link{character} (vector)} \item{string}{a \link{character} (vector)}
\item{type}{type of conversion of the taxonomic names, either "markdown" or "ansi", see \emph{Details}} \item{type}{type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see \emph{Details}}
} }
\description{ \description{
According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic. According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.
@ -20,7 +20,7 @@ According to the binomial nomenclature, the lowest four taxonomic levels (family
\details{ \details{
This function finds the taxonomic names and makes them italic based on the \link{microorganisms} data set. This function finds the taxonomic names and makes them italic based on the \link{microorganisms} data set.
The taxonomic names can be italicised using markdown (the default) by adding \code{*} before and after the taxonomic names, or using ANSI colours by adding \verb{\\033[3m} before and \verb{\\033[23m} after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur. The taxonomic names can be italicised using markdown (the default) by adding \code{*} before and after the taxonomic names, or \verb{<i>} and \verb{</i>} when using html. When using 'ansi', ANSI colours will be added using \verb{\\033[3m} before and \verb{\\033[23m} after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae". This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
} }