added launch.browser option

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: premessa
 Type: Package
 Title: R package for pre-processing of flow and mass cytometry data
-Version: 0.2.1
+Version: 0.2.2
 Author: "Pier Federico Gherardini <pfgherardini@parkerici.org> [aut, cre]"
 Description: This package includes panel editing/renaming for FCS files, bead-based normalization and debarcoding.
 Imports: shiny (>= 0.14), flowCore, reshape, ggplot2, hexbin, gridExtra, rhandsontable, jsonlite

R/normalize_cytof.R

@@ -264,6 +264,12 @@ normalize_folder <- function(wd, output.dir.name, beads.gates, beads.type, basel
         beads.data <- m[beads.events,]
 
         norm.res <- correct_data_channels(m, beads.data, baseline.data, beads.cols.names)
+
+        # Do some cleanup to save memory
+        fcs <- flowCore::read.FCS(file.path(wd, f.name), which.lines = 1) # We only need the keywords
+        m <- NULL
+        gc()
+
         m.normed <- norm.res$m.normed
         m.normed <- cbind(m.normed,
                         beadDist = get_mahalanobis_distance_from_beads(m.normed, beads.events, beads.cols.names))

R/shiny_helpers.R

@@ -52,24 +52,38 @@ get_initial_beads_gates <- function(fcs) {
 #' the working directory for the software.
 #' To stop the software simply hit the "ESC" key in your R session.
 #'
+#' @param launch.browser Whether to open the GUI in a separate browser window
+#'   (recommended)
 #' @param ... Additional arguments to be passed to \code{shiny::runApp}
 #' @export
-normalizer_GUI <- function(...) {
-    shiny::runApp(appDir = file.path(system.file(package = "premessa"), "normalizer_shinyGUI"), ...)
+normalizer_GUI <- function(launch.browser = TRUE, ...) {
+    shiny::runApp(appDir = file.path(system.file(package = "premessa"), "normalizer_shinyGUI"),
+                  launch.browser = launch.browser, ...)
 }
 
 #' Starts the debarcoder GUI
 #'
 #' To stop the software simply hit the "ESC" key in your R session.
 #'
-#' @param ... Additional arguments to be passed to \code{shiny::runApp}
+#' @inheritParams normalizer_GUI
 #' @export
-debarcoder_GUI <- function(...) {
-    shiny::runApp(appDir = file.path(system.file(package = "premessa"), "debarcoder_shinyGUI"), ...)
+debarcoder_GUI <- function(launch.browser = TRUE, ...) {
+    shiny::runApp(appDir = file.path(system.file(package = "premessa"), "debarcoder_shinyGUI"),
+                  launch.browser = launch.browser, ...)
 }
 
+#' Starts the panel editor GUI
+#'
+#' Upon starting, a file selection window will appear from your R session. You should use
+#' this window to navigate to the directory containing the data you want to analyze,
+#' and select any file in that directory. The directory itself will then become
+#' the working directory for the software.
+#' To stop the software simply hit the "ESC" key in your R session.
+#'
+#' @inheritParams normalizer_GUI
 #' @export
-paneleditor_GUI <- function(...) {
-    shiny::runApp(appDir = file.path(system.file(package = "premessa"), "paneleditor_shinyGUI"), ...)
+paneleditor_GUI <- function(launch.browser = TRUE, ...) {
+    shiny::runApp(appDir = file.path(system.file(package = "premessa"), "paneleditor_shinyGUI"),
+                  launch.browser = launch.browser, ...)
 }