R/report.R

In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

#' RLSeq Report
#'
#' Builds an HTML report to showcase the results available in the supplied
#' [RLRanges] object (see also [RLResults]).
#'
#' @param object An RLRanges object.
#' @param reportPath A path indicating the report output HTML file.
#'  Default: "rlreport.html"
#' @param intermediates_dir A directory indicating where intermediate
#'  files should be stored during report building. If not set,
#'  a random directory in `tmp/` will be used. Default: NULL.
#' @param quiet If TRUE, messages are suppressed. Default: FALSE.
#' @param ... Arguments passed to `rmarkdown::render()`
#' @return TRUE
#' @examples
#'
#' # Example data with RLSeq() already run.
#' rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))
#'
#' # Get a TMP file (only for example usae)
#' tmp <- tempfile()
#'
#' # Generate the report
#' report(rlr, reportPath = tmp)
#' @export
report <- function(object,
    reportPath = "rlreport.html",
    intermediates_dir = NULL,
    quiet = FALSE,
    ...) {

    # Check for missing packages and stop if found
    pkgs <- vapply(
        X = c("kableExtra", "DT", "rmarkdown"),
        FUN = requireNamespace,
        quietly = TRUE,
        FUN.VALUE = logical(1)
    )
    if (any(!pkgs)) {
        pks <- paste0(names(pkgs)[which(!pkgs)], collapse = '", "')
        stop(
            'Packages needed for report() but not installed: "',
            pks, '"'
        )
    }

    # Get the template
    template <- system.file("Rmd", "report.Rmd", package = "RLSeq")

    # Render template
    # note: We use callr::r here because if you don't, then you get
    # this issue:
    # https://community.rstudio.com/t/
    # rmarkdown-displays-a-plot-when-its-not-supposed-to/93757/2
    intermediates_dir <- ifelse(
        is.null(intermediates_dir),
        tempdir(check = TRUE),
        intermediates_dir
    )
    callr::r(
        function(template, object, reportPath, intermediates_dir, quiet, ...) {
            rmarkdown::render(
                template,
                params = list(
                    "object" = object
                ),
                output_format = "html_document",
                output_dir = normalizePath(dirname(reportPath)),
                intermediates_dir = intermediates_dir,
                output_file = reportPath,
                quiet = quiet,
                ...
            )
        },
        args = list(
            template = template,
            object = object,
            reportPath = reportPath,
            intermediates_dir = intermediates_dir,
            quiet = quiet,
            ...
        ),
        show = !quiet
    )

    # Return
    return(TRUE)
}