View source: R/graph_species_names.R
graph_species_names | R Documentation |
Italicise species names for graphing Producing mixed italics for species names in plots is tricky. This function will do it for the species in the mandatory surveillance collections
graph_species_names(x)
x |
a character vector giving the data collection |
A factor variable with labels that will control italicisation
graph_species_names("Klebsiella spp")
graph_species_names("MRSA")
graph_species_names(x = c("Klebsiella spp", "MRSA"))
graph_species_names <- function(x){
assertthat::assert_that(is.character(x), msg = "x must be a character")
x <- trimws(x)
assertthat::assert_that(
all(x %in% c("C. difficile", "E. coli","Klebsiella spp", "MRSA", "MSSA",
"P. aeruginosa", "Pseudomonas aeruginosa")),
msg = "Please make sure that x is one of C. difficile, E. coli,
Klebsiella spp, MRSA, MSSA, P. aeruginosa or Pseudomonas aeruginosa,
S. aureus or Staphylococcus aureus"
)
x <- ifelse(x == "Pseudomonas aeruginosa", "P. aeruginosa", x)
x <- factor(x)
levels(x) = c("C. difficile" = expression(italic("C. difficile")),
"E. coli" = expression(italic("E. coli")),
"Klebsiella spp" = expression(paste(italic("Klebsiella "), " spp.")),
"MRSA" = "MRSA",
"MSSA" = "MSSA",
"P. aeruginosa" = expression(italic("P. aeruginosa")),
"S. aureus" = expression(italic("S. aureus"))
)
x <- droplevels(x)
return(x)
}
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