R/new_exp.R

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

#' Create a template folder for flow cytometry experiments
#'
#' @param path path to the parent directory where the experiment folder is to be initiated
#' @param name name of the experiment folder
#' @param date_prefix logical if the folder name should be prefixed with the current date
#'
#' @return No return value. Instead a folder with template files is written to disk.
#' @export
#'
#' @examples
#' \dontrun{
#' new_exp(path = '/Users/CMS/Documents/experiments', name = 'CD3_titration')
#' }
new_exp <- function(path = NULL, name = NULL, date_prefix = T) {

    if (base::is.null(path)) {
        stop("Please provide a directory (path) to create the folder in.")
    }

    if (date_prefix) {
        if (base::is.null(name)) {
            name <- base::paste0(base::gsub("-", "", base::Sys.Date()), "_experiment")
        } else {
            name <- base::paste0(base::gsub("-", "", base::Sys.Date()), "_", name)
        }
    } else {
        if (base::is.null(name)) {
            name <- "experiment"
        }
    }

    if (dir.exists(base::file.path(path, name))) {
        stop(paste0(base::file.path(path, name), " already exists."))
    }

    utils::untar(base::system.file("extdata", "template_folder.tgz", package = "fcexpr"), exdir = path)
    base::file.rename(base::file.path(path, "template_folder"), base::file.path(path, name))

    if (getOS() == "Windows") {
        files <- list.files(base::file.path(path, name), all.files = T, recursive = T, full.names = T)
        file.remove(files[which(grepl("^\\.", basename(files)))])
    }

    base::message(base::paste0(base::file.path(path, name), " created."))
}


getOS <- function() {
    machine <- switch(Sys.info()[["sysname"]],
                      Windows= "Windows",
                      Linux  = "Linux",
                      Darwin = "Mac")
    return(machine)
}