R/data.R

In ontologyPlot: Visualising Sets of Ontological Terms

#' Capitalise words in character vector
#'
#' @param x Character vector 
#' @return Character vector
#' @examples
#' simple_cap(c("a simple test", "Another-test"))
#' @export
simple_cap <- function(x) {
	s <- strsplit(x, " ")
	sapply(
		s,
		function(x) paste(
			toupper(substring(x, 1,1)), 
			substring(x, 2),
			sep="", collapse=" "
		)
	)
}

#' Get human readable, shortened (where possible) ontological term names
#'
#' @template ontology
#' @template terms
#' @return Character vector
#' @examples
#' library(ontologyIndex)
#' data(hpo)
#' get_shortened_names(hpo, c("HP:0001873", "HP:0011877"))
#' @export
get_shortened_names <- function(ontology, terms) sapply(FUN=simple_cap, gsub(x=gsub(
	"Impaired |(Abnormality of (the )?)|(Abnormal )", 
	"", 
	ontology$name[terms]
), pattern="^\\s+|\\s+$", replacement=""))