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# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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# # |
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# SOURCE # |
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# https://github.com/msberends/AMR # |
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# # |
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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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# # |
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# This R package is free software; you can freely use and distribute # |
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# it for both personal and commercial purposes under the terms of the # |
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# GNU General Public License version 2.0 (GNU GPL-2), as published by # |
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# the Free Software Foundation. # |
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# We created this package for both routine data analysis and academic # |
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# research and it was publicly released in the hope that it will be # |
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # |
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# # |
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# Visit our website for the full manual and a complete tutorial about # |
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # |
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# ==================================================================== # |
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#' Italicise Taxonomic Families, Genera, Species, Subspecies |
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#' |
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#' 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. |
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#' @inheritSection lifecycle Maturing Lifecycle |
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#' @param string a character (vector) |
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#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details* |
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#' @details |
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#' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set. |
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#' |
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#' 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. |
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#' |
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#' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae". |
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#' @inheritSection AMR Read more on Our Website! |
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#' @export |
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#' @examples |
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#' italicise_taxonomy("An overview of Staphylococcus aureus isolates") |
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#' italicise_taxonomy("An overview of S. aureus isolates") |
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#' |
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#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi")) |
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italicise_taxonomy <- function(string, type = c("markdown", "ansi")) { |
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if (missing(type)) { |
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type <- "markdown" |
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} |
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meet_criteria(string, allow_class = "character") |
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi")) |
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if (type == "markdown") { |
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before <- "*" |
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after <- "*" |
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} else if (type == "ansi") { |
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if (!has_colour()) { |
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return(string) |
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} |
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before <- "\033[3m" |
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after <- "\033[23m" |
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} |
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vapply(FUN.VALUE = character(1), |
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string, |
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function(s) { |
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s_split <- unlist(strsplit(s, " ")) |
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search_strings <- gsub("[^a-zA-Z-]", "", s_split) |
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ind_species <- search_strings != "" & |
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search_strings %in% MO_lookup[which(MO_lookup$rank %in% c("family", |
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"genus", |
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"species", |
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"subspecies", |
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"infraspecies", |
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"subsp.")), |
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"species", |
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drop = TRUE] |
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ind_fullname <- search_strings != "" & |
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search_strings %in% c(MO_lookup[which(MO_lookup$rank %in% c("family", |
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"genus", |
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"species", |
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"subspecies", |
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"infraspecies", |
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"subsp.")), |
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"fullname", |
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drop = TRUE], |
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MO_lookup[which(MO_lookup$rank %in% c("family", |
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"genus", |
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"species", |
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"subspecies", |
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"infraspecies", |
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"subsp.")), |
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"subspecies", |
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drop = TRUE]) |
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# also support E. coli, add "E." to indices |
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has_previous_genera_abbr <- s_split[which(ind_species) - 1] %like_case% "^[A-Z][.]?$" |
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ind_species <- c(which(ind_species), which(ind_species)[has_previous_genera_abbr] - 1) |
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ind <- c(ind_species, which(ind_fullname)) |
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s_split[ind] <- paste0(before, s_split[ind], after) |
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s_paste <- paste(s_split, collapse = " ") |
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# clean up a bit |
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s_paste <- gsub(paste0(after, " ", before), " ", s_paste, fixed = TRUE) |
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s_paste |
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}, |
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USE.NAMES = FALSE) |
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} |
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#' @rdname italicise_taxonomy |
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#' @export |
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italicize_taxonomy <- function(string, type = c("markdown", "ansi")) { |
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italicise(string = string, type = type) |
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} |
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