R/K2dashboard.R

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

#' Generate interactive dashboard of K2 Taxonomer results
#'
#' This function will generate an interactive dashboard of the annotated K=2
#' clustering results in a specified directory.
#' @param K2res Object of class K2.
#' @param analysis_name Character string of the name of analysis to write files
#' and generate title of report.
#' @param about Logical. Whether to create an 'about' tab in the dashboard.
#' @param output_dir Base directory to put report.
#' @return Nothing.  Writes files to a specified directory.
#' @references
#'  \insertRef{reed_2020}{K2Taxonomer}
#' @keywords clustering
#' @export
#' @examples
#'
#' ## Read in K2 Taxonomer results
#' data(K2res)
#'
#' ## Generate interactive dashboard
#' K2dashboard(K2res, output_dir=tempdir())
#'

K2dashboard <- function(K2res, analysis_name="K2Taxonomer",
    about=TRUE, output_dir=".") {

    ## Run checks
    .isK2(K2res)

    ## Check K2 object
    k2Check <- .checkK2(K2res)

    ## K2 algorithm
    if (length(K2results(K2res)) == 0) {
        stop("No results found. Please run K2tax() or runK2Taxonomer().\n")
    }

    ## DGE
    if (is.null(K2results(K2res)[[1]]$dge)) {
        stop("No differential analysis results found. Please run runDGEmods().\n")
    }

    ## GSE
    if (is.null(K2results(K2res)[[1]]$gse)) {
        stop("No enrichment results found. Please run runDGEmods().\n")
    }

    ## GSVA
    if (ncol(K2gSet(K2res)) == 0) {
        stop("No ssGSEA data found. Please run runGSVAmods().\n")
    }

    ## DSSE
    if (is.null(K2results(K2res)[[1]]$dsse)) {
        stop("No differential enrichment results found. Please run runDSSEmods().\n")
    }

    ## DSSE
    if (is.null(K2results(K2res)[[1]]$dsse)) {
        stop("No differential enrichment results found. Please run runDSSEmods().\n")
    }

    ## Create file paths
    analysis_name_nospace <- gsub(" ", "_", analysis_name)

    ## Directory to print
    dirPath <- file.path(output_dir, paste(analysis_name_nospace,
        gsub("-| |:", "_", Sys.time()), sample(1e+07, 1), sep="_"))
    ## RMD file
    RMDpath <- file.path(dirPath, paste0(analysis_name_nospace,
        ".Rmd"))

    ## Create folder to put report and results file
    dir.create(dirPath)

    ## Save K2results to this folder
    saveRDS(K2res, file.path(dirPath, "K2results.rds"))

    ## Get rmd file location
    K2rmd <- system.file("dashboard", "K2Dashboard.Rmd", package =
        "K2Taxonomer")

    ## Write RMD file
    K2rmdLines <- readLines(K2rmd)

    # Add title
    K2rmdLines[2] <- gsub("K2TITLEPLACEHOLDER", analysis_name,
        K2rmdLines[2])

    # Add about document
    if (about) {
        file.copy(system.file("dashboard", "about.md", package="K2Taxonomer"),
            dirPath, overwrite=TRUE)
    }

    # Write document
    writeLines(K2rmdLines, RMDpath)

    ## Print success message
    cat("Dashboard created in '", dirPath, "'.\n", sep="")

    invisible(NULL)
}