Feature/prune gui

DESCRIPTION

@@ -1,61 +1,57 @@
 Package: HaDeX
-Title: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data 
+Title: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass
+    Spectrometry Data
 Version: 1.2.1
-Authors@R: c(person("Weronika", "Puchala", 
-           email = "[email protected]", 
-           comment = c(ORCID = "0000-0003-2163-1429"),
-           role = c("cre", "aut")),
-           person("Michal", "Burdukiewicz", 
-           email = "[email protected]", 
-           comment = c(ORCID = "0000-0001-8926-582X"),
-           role = c("aut")),
-           person("Dominik", "Rafacz", 
-           email = "[email protected]",
-           role = c("ctb")),
-           person("Krystyna", "Grzesiak", 
-           email = "[email protected]",
-           role = c("ctb")))
-Description: Functions for processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by 
-             Mass Spectrometry experiments (HDX-MS). 'HaDeX' <10.1093/bioinformatics/btaa587> introduces a new 
-             standardized and reproducible workflow for the analysis of the HDX-MS data, including novel uncertainty 
-             intervals. Additionally, it covers data exploration, quality control and generation of publication-quality 
-             figures. All functionalities are also available in the in-built 'Shiny' app.
-Depends: R (>= 3.0)
+Authors@R: c(
+    person("Weronika", "Puchala", , "[email protected]", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0003-2163-1429")),
+    person("Michal", "Burdukiewicz", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0001-8926-582X")),
+    person("Dominik", "Rafacz", , "[email protected]", role = "ctb"),
+    person("Krystyna", "Grzesiak", , "[email protected]", role = "ctb")
+  )
+Description: Functions for processing, analysis and visualization of
+    Hydrogen Deuterium eXchange monitored by Mass Spectrometry experiments
+    (HDX-MS). 'HaDeX' <10.1093/bioinformatics/btaa587> introduces a new
+    standardized and reproducible workflow for the analysis of the HDX-MS
+    data, including novel uncertainty intervals. Additionally, it covers
+    data exploration, quality control and generation of
+    publication-quality figures. All functionalities are also available in
+    the in-built 'Shiny' app.
 License: GPL-3
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.0
+Depends: 
+    R (>= 3.0)
 Imports: 
     checkmate,
-    cowplot,
     data.table,
-  	dplyr,
-  	DT,
-  	ggplot2,
-  	gsubfn,
-  	latex2exp,
-  	magick,
-  	plyr,
-  	reshape2,
-  	readr,
-  	readxl,
-  	shiny,
-  	stringr,
-  	stringi,
-  	tidyr
+    dplyr,
+    ggplot2,
+    grid,
+    HaDeXGUI,
+    httpuv,
+    magick,
+    plyr,
+    readr,
+    readxl,
+    remotes,
+    shiny,
+    stats,
+    stringi,
+    stringr,
+    tidyr,
+    tools,
+    utils
 Suggests:
-    spelling, 
-    covr,
-    digest,
-    gridExtra,
+    DT,
     knitr,
-    pander,
-    renv,
+    magrittr,
     rmarkdown,
-    shinycustomloader,
-    shinyhelper,
-    shinyjs,
+    spelling,
     testthat,
     vdiffr
-VignetteBuilder: knitr
+VignetteBuilder: 
+    knitr
+Encoding: UTF-8
 Language: en-US
+LazyData: true
+RoxygenNote: 7.2.0

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(HaDeX_gui)
+export(HaDeX_GUI)
 export(HaDeXify)
 export(add_stat_dependency)
 export(calculate_MHP)
@@ -30,6 +30,7 @@ export(get_n_replicates)
 export(get_peptide_sequence)
 export(get_protein_coverage)
 export(get_protein_redundancy)
+export(install_GUI)
 export(plot_amino_distribution)
 export(plot_butterfly)
 export(plot_chiclet)
@@ -150,6 +151,7 @@ importFrom(readr,parse_number)
 importFrom(readr,read_csv)
 importFrom(readr,read_tsv)
 importFrom(readxl,read_excel)
+importFrom(remotes,install_github)
 importFrom(shiny,runApp)
 importFrom(stats,qt)
 importFrom(stringi,stri_count)

R/HaDeX_gui.R

@@ -1,14 +1,63 @@
+#' Checks if GUI package is installed
+#' 
+#' Indicates presence or absence of HaDeXGUI package.
+#' 
+#' @return logical value indicating availability of GUI package
+is_GUI_installed <- function()
+  length(find.package("HaDeXGUI", quiet = TRUE)) > 0
+
+#' Installs GUI package from GitHub
+#' 
+#' @importFrom remotes install_github
+#' @export
+install_GUI <- function()
+  remotes::install_github("hadexversum/HaDeXGUI")
+
+handle_missing_GUI <- function() {
+  if (interactive()) {
+    response <- menu(
+      c("yes", "no"), 
+      title = "To be able to run HaDeX Graphical User Interface, you have to have the 'HaDeXGUI' package installed. It is available via GitHub. Install?")
+    switch (
+      response, 
+      yes = tryCatch(
+        install_GUI(),
+        finally = if (!is_GUI_installed()) {
+          warning("There was an error during an attempt to install 'HaDeXGUI' package.", call. = FALSE)
+        } else {
+          message("Package installed successfully. You can run the app now calling 'HaDeX_GUI()' once again.")
+        }
+      ),
+      no = message("You cannot run the GUI without having installed 'HaDeXGUI'. You can do it by calling 'HaDeX::install_GUI()'."),
+    )
+  } else {
+    message("To be able to run HaDeX Graphical User Interface, you have to have the 'HaDeXGUI' package installed. You can do it by calling 'HaDeX::install_GUI()'.")
+  }
+}
+
 #' HaDeX Graphical User Interface
 #'
-#' @description Launches graphical user interface.
+#' @description Launches graphical user interface from HaDeXGUI package. If the
+#'   GUI package is not installed, it asks user whether to install it
 #' 
 #' @importFrom shiny runApp
 #' 
-#' @param port The TCP port. See \code{\link[shiny]{runApp}}.
+#' @param ... arguments to pass to \code{HaDeXGUI::run_app()}. 
+#'    See \code{\link[HaDeXGUI]{run_app}}.
+#' @param port number of port for the app to run on.
+#' @param prod should the app run in production mode (TRUE) or development (FALSE)?
 #' 
 #' @section Warning : Any ad-blocking software may cause malfunctions.
 #' 
-#' @export HaDeX_gui
-
-HaDeX_gui <- function(port = getOption("shiny.port"))
-  runApp(system.file("HaDeX", package = "HaDeX"), port = port)
+#' @export
+HaDeX_GUI <- function(port = httpuv::randomPort(), prod = TRUE, ...) {
+  if (is_GUI_installed()) {
+    opts <- options()
+    on.exit(options(opts))
+    options(
+      shiny.port = port,
+      golem.app.prod = prod
+    )
+    HaDeXGUI::run_app(options = options, ...)
+  } else handle_missing_GUI()
+}