R/gl.list.reports.r

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#' @name gl.list.reports
#' @title Prints dartR reports saved in tempdir
#' @return Prints a table with all reports saved in tempdir. Currently the style
#' cannot be changed.
#' @export
#' @author Bernd Gruber & Luis Mijangos (bugs? Post to
#' \url{https://groups.google.com/d/forum/dartr})
#' @seealso \code{\link{gl.print.reports}}
#' @examples
#' \dontrun{
#' gl.report.callrate(testset.gl,save2tmp=TRUE)
#' gl.list.reports()
#' }

gl.list.reports <- function() {
    files_tempdir_temp <- list.files(tempdir())
    files_tempdir_plot <-
        files_tempdir_temp[which(str_match(files_tempdir_temp, "Plot") == "Plot")]
    files_tempdir_table <-
        files_tempdir_temp[which(str_match(files_tempdir_temp, "Table") == "Table")]
    files_tempdir_blast <-
        files_tempdir_temp[which(str_match(files_tempdir_temp, "Blast") == "Blast")]
    files_tempdir_files <-
        files_tempdir_temp[which(str_match(files_tempdir_temp, "File") == "File")]
    
    files_tempdir <-
        c(files_tempdir_plot,
          files_tempdir_table,
          files_tempdir_blast)
    
    nh <- length(files_tempdir)
    if (nh == 0) {
        cat(warn("There are no dartR reports saved in the current tempdir."))
    } else {
        dd <-
            data.frame(
                nr = 1:nh,
                reports = files_tempdir,
                time = file.info(paste0(tempdir(), "/", files_tempdir))$atime
            )
        dd$function_call <- NA
        for (i in 1:length(files_tempdir)) {
            dd$function_call[i] <-
                readRDS(paste0(tempdir(), "/", files_tempdir[i]))[[1]]
        }
        
        dd$function_call <- substr(dd$function_call, 2, 999)
        dd$function_call <- crayon::yellow(dd$function_call)
        dd$time <- crayon::magenta(dd$time)
        tables <- which(str_match(dd$reports, "Table") == "Table")
        plots <- which(str_match(dd$reports, "Plot") == "Plot")
        dd[tables, "reports"] <- crayon::blue(dd[tables, "reports"])
        dd[plots, "reports"] <- crayon::cyan(dd[plots, "reports"])
        dd <- dd[order(dd$time),]
        dd$nr <- 1:nrow(dd)
        dd$nr <- crayon::green(dd$nr)
        
        colnames(dd) <- crayon::bold(colnames(dd))
        print(knitr::kable(
            dd,
            align = c("c", "l", "l"),
            format = "simple",
            width = 80,
            row.names = FALSE
        ))
        
    }
}