Here is a function that will take a character string in R and return an expression for fancy formatting in plots that properly italicize scientific names. The syntax for doing this is truly quite horrible, but this is how R does it.
scientific_name_formatter <- function(raw_name) {
# strsplit returns a list but we are passing in only
# one name so we just take the first element of the list
words = strsplit(raw_name, ' ', fixed = TRUE)[[1]]
# some sort of acronym or bin name, leave it alone
if(length(words) < 2) { return(raw_name) }
else if (length(words) > 2) {
if (words[1] == 'Candidatus') {
# for candidatus names, only the Candidatus part is italicised # name shortening it for brevity
unitalic <- paste(words[2:length(words)], collapse = ' ') return(bquote(paste(italic(Ca.) ~ .(unitalic)))) }
else if (grepl('^\[A-Z\]+$', words[1])) {
# If the first word is in all caps then it is an abreviation
# so we don't want to italicize that at all
return(raw_name) }
else {
# assume that everything after the second word is strain name # which should not get italicised
unitalic <- paste(words[3:length(words)], collapse = ' ') return(bquote(paste(italic(.(words[1])) ~ italic(.(words[2])) ~ .(unitalic) )))
}
} else {
return(bquote(paste(italic(.(words[1])) ~ italic(.(words[2])))))
}
}
I use it like the following in ggplot by setting the labels in scale_y_discrete.
scale_y_discrete(limits = df$organism_name, labels = sapply(df$organism_name, scientific_name_formatter ))