closes #2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: grappolo
 Type: Package
 Title: Feature generation from single-cell data
-Version: 0.4.2
+Version: 0.4.3
 Authors@R: "Pier Federico Gherardini <[email protected]> [aut, cre]"
 Description: This is a package to cluster single-cell flow data and generate
     features that can be used for model building

inst/shinyGUI/server.R

@@ -8,7 +8,7 @@ get_cluster_groups_table <- function(v, key) {
                 tags$span(class = "glyphicon glyphicon-trash")
             )
         )),
-        ifelse(length(v > 1), 
+        ifelse(length(v > 1),
             tagList(lapply(tail(v, n = -1), function(x) {tags$tr(tags$td(x))})),
             tagList()
         )
@@ -24,7 +24,7 @@ render_clustering_ui <- function(working.directory, ...) {renderUI({
                 selectInput("clusteringui_markers", "Choose the markers for clustering", choices = c(""), multiple = T, width = "100%")
             )
         ),
-        
+
         conditionalPanel(
             condition = "input.clusteringui_clustering_mode == 'Pooled'",
             fluidRow(
@@ -44,12 +44,12 @@ render_clustering_ui <- function(working.directory, ...) {renderUI({
             )
         ),
         fluidRow(
-            column(12,    
-               
+            column(12,
+
                 numericInput("clusteringui_num_clusters", "Number of clusters", value = 200, min = 1, max = 2000),
-                numericInput("clusteringui_num_samples", "Number of samples (lower numbers lead to faster but less accurate results)", value = 50, min = 2), 
-                numericInput("clusteringui_asinh_cofactor", "Cofactor for asinh transformation", value = 5), 
-                numericInput("clusteringui_num_cores", "Number of CPU cores to use", value = 1), 
+                numericInput("clusteringui_num_samples", "Number of samples (lower numbers lead to faster but less accurate results)", value = 50, min = 2),
+                numericInput("clusteringui_asinh_cofactor", "Cofactor for asinh transformation", value = 5),
+                numericInput("clusteringui_num_cores", "Number of CPU cores to use", value = 1),
                 actionButton("clusteringui_start", "Start clustering")
             )
         )
@@ -59,7 +59,7 @@ render_clustering_ui <- function(working.directory, ...) {renderUI({
 shinyServer(function(input, output, session) {
     working.directory <- dirname(file.choose())
     output$clusteringUI <- render_clustering_ui(working.directory, input, output, session)
-    
+
     observe({
         if(!is.null(input$clusteringui_file_for_markers) && grepl("*.fcs$", input$clusteringui_file_for_markers)) {
             v <- grappolo:::get_fcs_col_names(file.path(working.directory, input$clusteringui_file_for_markers))
@@ -76,7 +76,7 @@ shinyServer(function(input, output, session) {
 
     observe({
         key <- input$clusteringui_remove_clustering_group$key
-        if(!is.null(key) && key != "") 
+        if(!is.null(key) && key != "")
             isolate({
                 clusteringui_reactive_values$clustering_groups[key] <- NULL
             })
@@ -87,43 +87,53 @@ shinyServer(function(input, output, session) {
         clusteringui_reactive_values$clustering_groups <- c(clusteringui_reactive_values$clustering_groups,
                                                             setNames(list(files_list), files_list[1])
         )
-        print(clusteringui_reactive_values$clustering_groups)  
     })
 
-    observeEvent(input$clusteringui_start, 
+    observeEvent(input$clusteringui_start,
         isolate({
             showModal(modalDialog(
                 sprintf("Clustering started with markers %s ",  paste(input$clusteringui_markers, collapse = " ")), br(),
                 "please wait..."
             ))
-
+
+            # This calls to force are necessary because the clustering functions will spawn
+            # a different process, see https://github.com/rstudio/shiny/issues/2163
+
+            num.cores <- force(input$clusteringui_num_cores)
+            col.names <- force(input$clusteringui_markers)
+            num.clusters <- force(input$clusteringui_num_clusters)
+            asinh.cofactor <- force(input$clusteringui_asinh_cofactor)
+            num.samples <- force(input$clusteringui_num_samples)
+            downsample.to <- force(input$clusteringui_downsample_to)
+            output.dir <- force(working.directory)
+
             if(input$clusteringui_clustering_mode == "Pooled") {
                 input.files <- lapply(clusteringui_reactive_values$clustering_groups, function(s) {file.path(working.directory, s)})
-                grappolo::cluster_fcs_files_groups(input.files, 
-                    num.cores = input$clusteringui_num_cores, 
-                    col.names = input$clusteringui_markers,
-                    num.clusters = input$clusteringui_num_clusters, 
-                    asinh.cofactor = input$clusteringui_asinh_cofactor, 
-                    num.samples = input$clusteringui_num_samples, 
-                    downsample.to = input$clusteringui_downsample_to,
-                    output.dir = working.directory
+                grappolo::cluster_fcs_files_groups(input.files,
+                    num.cores = num.cores,
+                    col.names = col.names,
+                    num.clusters = num.clusters,
+                    asinh.cofactor = asinh.cofactor,
+                    num.samples = num.samples,
+                    downsample.to = downsample.to,
+                    output.dir = output.dir
                 )
             } else {
-                grappolo::cluster_fcs_files_in_dir(working.directory,
-                    num.cores = input$clusteringui_num_cores, 
-                    col.names = input$clusteringui_markers,
-                    num.clusters = input$clusteringui_num_clusters, 
-                    asinh.cofactor = input$clusteringui_asinh_cofactor, 
-                    num.samples = input$clusteringui_num_samples,   
-                    output.dir = working.directory 
+                grappolo::cluster_fcs_files_in_dir(output.dir,
+                    num.cores = num.cores,
+                    col.names = col.names,
+                    num.clusters = num.clusters,
+                    asinh.cofactor = asinh.cofactor,
+                    num.samples = num.samples,
+                    output.dir = output.dir
                 )
             }
-            
+
             showModal(modalDialog(
                 sprintf("Clustering completed. The output files can be found in %s", working.directory)
 
             ))
         })
     )
 
-})
+})