R/run_shiny_app.R

In tmakowski/iaoreader: A Web Application for Analysing IAO Peptide Files

#' @title Run IAO Peptide Reader App
#'
#' @description This function is responsible for starting the core application
#'  of this package. The application itself is located inside the
#'  \code{IAOPeptideReader} package files.
#'
#' @param port a port on which the Shiny application will be hosted.
#' @param run_app when \code{FALSE} the app object is returned and the
#'  application is not started. This is mainly used for deployment of the
#'  Shiny application to services such as \url{https://www.shinyapps.io/}.
#'
#' @rawNamespace import(shiny, except = c(dataTableOutput, renderDataTable))
#' @importFrom DT dataTableOutput renderDataTable
#' @importFrom data.table fread rbindlist
#'
#' @export
run_shiny_app <- function(port = 8080, run_app = TRUE) {
    if (!is.logical(run_app) || is.na(run_app)) {
        stop("run_app argument has to be either TRUE or FALSE", call. = FALSE)
    }

    pkg_name <- "IAOPeptideReader"
    ui_path <- system.file(pkg_name, "ui.R", package = pkg_name)
    server_path <- system.file(pkg_name, "server.R", package = pkg_name)
    www_path <- system.file(pkg_name, "www", package = pkg_name)

    if (ui_path == "" || server_path == "" || www_path == "") {
        stop(
            paste(
                "Internal package files are missing.",
                "Consider re-installing the", pkg_name, " package."
            ),
            call. = FALSE
        )
    }

    # Note: sourcing those files allows avoiding namespace issues. If the app
    #       would be run directly with:
    #       runApp(system.file("IAOPeptideReader", package = "IAOPeptideReader"))
    #       then the functions imported by the package could not be used within
    #       the application due to the Shiny creating its own namespace.
    #       By sourcing those files all functions imported by the package are
    #       available within the application.
    source(ui_path, local = TRUE, chdir = TRUE)
    source(server_path, local = TRUE, chdir = TRUE)

    # Manually attaching the resources to /www static URL.
    addResourcePath("www", www_path)
    app <- shinyApp(ui(), server)

    if (!run_app) {
        return(app)
    }

    runApp(app, port)
}