# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 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 italic. This function finds taxonomic names within strings and makes them italic. #' @inheritSection lifecycle Maturing Lifecycle #' @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". #' @inheritSection AMR Read more on Our Website! #' @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")) #' #' # since ggplot2 supports no markdown (yet), use #' # italicise_taxonomy() and the `ggtext` pkg for titles: #' #' if (require("ggplot2") && require("ggtext")) { #' ggplot(example_isolates$AMC, #' title = italicise_taxonomy("Amoxi/clav in E. coli")) + #' theme(plot.title = ggtext::element_markdown()) #' } italicise_taxonomy <- function(string, type = c("markdown", "ansi")) { if (missing(type)) { type <- "markdown" } meet_criteria(string, allow_class = "character") meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi")) if (type == "markdown") { before <- "*" after <- "*" } else if (type == "ansi") { if (!has_colour()) { return(string) } before <- "\033[3m" after <- "\033[23m" } vapply(FUN.VALUE = character(1), string, function(s) { s_split <- unlist(strsplit(s, " ")) search_strings <- gsub("[^a-zA-Z-]", "", s_split) ind_species <- search_strings != "" & search_strings %in% MO_lookup[which(MO_lookup$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) }