R/make_file_links.R

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

#' Make file links for R Markdown
#'
#' Make file links for R Markdown.
#'
#' @inheritParams base::dir
#' @return Vector of file links.
#' @export

make_file_links <- function(path=".", pattern=NULL, recursive=FALSE, full.names=TRUE) {
  full.path <- dir(path=path, pattern=pattern, recursive=recursive, full.names=full.names)
  if (length(full.path) == 0) stop("No file found.")

  file.nm <- full.path
  idxs <- gregexpr("/", file.nm)
  mx <- max(sapply(idxs, length))

  for(i in seq_len(mx)){
    file.nm.tmp <- sub("[^/]*/", "", file.nm)
    if (sum(duplicated(file.nm.tmp)) > 0) break
    file.nm <- file.nm.tmp
  }

  links <- paste(paste0("[", file.nm, "](", full.path, ")"), collapse = " & ")
  return(links)
}