AMR/R/italicise_taxonomy.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2022 Berends MS, Luz CF et al.                              #
# Developed at the University of Groningen, the Netherlands, in        #
# collaboration with non-profit organisations Certe Medical            #
# Diagnostics & Advice, and University Medical Center Groningen.       # 
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
# We created this package for both routine data analysis and academic  #
# research and it was publicly released in the hope that it will be    #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                      #
# Visit our website for the full manual and a complete tutorial about  #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
# ==================================================================== #

#' Italicise Taxonomic Families, Genera, Species, Subspecies
#' 
#' 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 type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
#' @details 
#' 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.
#' 
#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
#' @export
#' @examples
#' italicise_taxonomy("An overview of Staphylococcus aureus isolates")
#' italicise_taxonomy("An overview of S. aureus isolates")
#' 
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
  if (missing(type)) {
    type <- "markdown"
  }
  meet_criteria(string, allow_class = "character")
  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
  
  if (type == "markdown") {
    before <- "*"
    after <- "*"
  } else if (type == "ansi") {
    if (!has_colour()) {
      return(string)
    }
    before <- "\033[3m"
    after <- "\033[23m"
  }
  
  vapply(FUN.VALUE = character(1),
         string,
         function(s) {
           s_split <- unlist(strsplit(s, " "))
           
           search_strings <- gsub("[^a-zA-Z-]", "", s_split)
           
           ind_species <- search_strings != "" &
             search_strings %in% MO_lookup[which(MO_lookup$rank %in% c("family",
                                                                       "genus",
                                                                       "species",
                                                                       "subspecies",
                                                                       "infraspecies",
                                                                       "subsp.")),
                                           "species",
                                           drop = TRUE]
           
           ind_fullname <- search_strings != "" &
             search_strings %in% c(MO_lookup[which(MO_lookup$rank %in% c("family",
                                                                         "genus",
                                                                         "species",
                                                                         "subspecies",
                                                                         "infraspecies",
                                                                         "subsp.")),
                                             "fullname",
                                             drop = TRUE],
                                   MO_lookup[which(MO_lookup$rank %in% c("family",
                                                                         "genus",
                                                                         "species",
                                                                         "subspecies",
                                                                         "infraspecies",
                                                                         "subsp.")),
                                             "subspecies",
                                             drop = TRUE])

           # also support E. coli, add "E." to indices
           has_previous_genera_abbr <- s_split[which(ind_species) - 1] %like_case% "^[A-Z][.]?$"
           ind_species <- c(which(ind_species), which(ind_species)[has_previous_genera_abbr] - 1)
           
           ind <- c(ind_species, which(ind_fullname))
           
           s_split[ind] <- paste0(before, s_split[ind], after)
           s_paste <- paste(s_split, collapse = " ")
           
           # clean up a bit
           s_paste <- gsub(paste0(after, " ", before), " ", s_paste, fixed = TRUE)
           
           s_paste
         },
         USE.NAMES = FALSE)
}

#' @rdname italicise_taxonomy
#' @export
italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
  if (missing(type)) {
    type <- "markdown"
  }
  italicise_taxonomy(string = string, type = type)
}