first working version of full scmap (cluster+cell)

server.R

@@ -79,16 +79,16 @@ server <- function(input, output) {
         return(res)
     }
 
-    getIndex <- function() {
+    scmapCluster_index <- function() {
         if (input$data_type == "existing") {
             # load indexes
-            files <- list.files(paste0("www/refs/", input$organism), pattern = ".csv")
+            files <- list.files(paste0("www/scmap-cluster/", input$organism), pattern = ".csv")
             index <- list()
             for (f in files) {
                 name <- strsplit(f, "\\.")[[1]][1]
                 tmp <- read.csv(
                     paste0(
-                        "www/refs/", 
+                        "www/scmap-cluster/", 
                         input$organism, "/", f
                     )
                 )
@@ -114,29 +114,74 @@ server <- function(input, output) {
         return(index)
     }
 
+    scmapCell_index <- function() {
+        if (input$data_type == "existing") {
+            # load indexes
+            files <- list.files(paste0("www/scmap-cell/", input$organism), pattern = ".rds")
+            index <- list()
+            for (f in files) {
+                name <- strsplit(f, "\\.")[[1]][1]
+                tmp <- readRDS(
+                    paste0(
+                        "www/scmap-cell/", 
+                        input$organism, "/", f
+                    )
+                )
+                index[[name]] <- tmp
+            }
+        } else {
+            # compute the index
+            dataset <- values$reference_data()
+            if(values$features) {
+                rowData(dataset)$scmap_features <- values$scmap_features
+                rowData(dataset)$scmap_scores <- values$scmap_scores
+            } else {
+                dataset <- selectFeatures(dataset)
+            }
+            index <- indexCell(
+                dataset
+            )
+            index <- list(metadata(index)$scmap_cell_index)
+        }
+        return(index)
+    }
+
     scmap <- function() {
 
-        # compute index
-        index <- getIndex()
-
         # run scmap-cluster
+        index_cluster <- scmapCluster_index()
         scmapCluster_results <- scmapCluster(
             values$projection_data(),
-            index_list = index
+            index_list = index_cluster
         )
 
         if(!"SingleCellExperiment" %in% is(scmapCluster_results)) {
             # summarise results of scmap-cluster
-            values$scmap_cluster_siml <- scmapCluster_results$scmap_cluster_siml
-            values$scmap_cluster_labs <- scmapCluster_results$scmap_cluster_labs
-            values$scmap_cluster_comb <- scmapCluster_results$combined_labs
+            values$scmap_cluster_res <- scmapCluster_results
             values$scmap_cluster_all <- 
-                scmapClusterResults2table(index, scmapCluster_results$scmap_cluster_labs)
+                scmapClusterResults2table(index_cluster, scmapCluster_results$scmap_cluster_labs)
             values$scmap_cluster_combined <- 
-                scmapClusterResults2table(index, data.frame(scmapCluster_results$combined_labs))
+                scmapClusterResults2table(index_cluster, data.frame(scmapCluster_results$combined_labs))
         } else {
             values$scmap_cluster_worked <- FALSE
         }
+
+        if(input$run_scmap_cell == "Yes") {
+            # run scmap-cell
+            index_cell <- scmapCell_index()
+            scmapCell_results <- scmapCell(
+                values$projection_data(),
+                index_list = index_cell
+            )
+            if("list" %in% is(scmapCell_results)) {
+                # summarise results of scmap-cell
+                values$scmap_cell_all <- scmapCell_results
+            } else {
+                print(class(scmapCell_results))
+                values$scmap_cell_worked <- FALSE
+            }
+        }
+
         return()
     }
 
@@ -205,35 +250,50 @@ server <- function(input, output) {
         )
     })
 
-    output$results_cluster <- renderUI({
+    output$results <- renderUI({
         switch(input$data_type,
                "own" = list(
+                   fluidRow(
                         box(width = 12,
-                            title = "Results",
+                            title = "scmap-cluster",
                             DT::dataTableOutput('results_table'),
-                            downloadButton("scmap_cluster_labs", 'Download All Assignments'),
-                            downloadButton("scmap_cluster_siml", 'Download All Similarities'),
+                            downloadButton("scmap_cluster_all", 'Download'),
                             solidHeader = TRUE,
                             status = "success"
+                        ),
+                        conditionalPanel("input.run_scmap_cell == 'Yes'", 
+                             box(width = 12,
+                                 title = "scmap-cell",
+                                 downloadButton("scmap_cell_all", 'Download'),
+                                 solidHeader = TRUE,
+                                 status = "success"
+                             )
                         )
+                   )
                ),
                "existing" = list(
                    fluidRow(
                        box(width = 12,
-                           title = "Individual Results",
+                           title = "scmap-cluster",
                            DT::dataTableOutput('results_table'),
-                           downloadButton("scmap_cluster_labs", 'Download All Assignments'),
-                           downloadButton("scmap_cluster_siml", 'Download All Similarities'),
+                           downloadButton("scmap_cluster_all", 'Download'),
                            solidHeader = TRUE,
                            status = "success"
                        ),
                        box(width = 12,
-                           title = "Consensus Results",
+                           title = "scmap-cluster (combined)",
                            DT::dataTableOutput('consensus_results_table'),
-                           downloadButton("consensus_results_assignments", 'Download Consensus Assignments'),
                            solidHeader = TRUE,
                            status = "success"
-                       )
+                       ),
+                       conditionalPanel("input.run_scmap_cell == 'Yes'", 
+                            box(width = 12,
+                                title = "scmap-cell",
+                                downloadButton("scmap_cell_all", 'Download'),
+                                solidHeader = TRUE,
+                                status = "success"
+                            )
+                        )
                    )
                )
         )
@@ -331,30 +391,21 @@ server <- function(input, output) {
         values$feature_table <- row_data
     })
 
-    output$scmap_cluster_labs <- downloadHandler(
+    output$scmap_cluster_all <- downloadHandler(
         filename = function() {
-            paste('scmap_results_assignments.csv', sep='')
+            'scmap-cluster.rds'
         },
         content = function(con) {
-            write.csv(values$scmap_cluster_labs, con, quote = FALSE)
+            saveRDS(values$scmap_cluster_res, con)
         }
     )
 
-    output$scmap_cluster_siml <- downloadHandler(
+    output$scmap_cell_all <- downloadHandler(
         filename = function() {
-            paste('scmap_results_similarities.csv', sep='')
+            'scmap-cell.rds'
         },
         content = function(con) {
-            write.csv(values$scmap_cluster_siml, con, quote = FALSE)
-        }
-    )
-
-    output$consensus_results_assignments <- downloadHandler(
-        filename = function() {
-            paste('scmap_results_consensus.csv', sep='')
-        },
-        content = function(con) {
-            write.csv(values$scmap_cluster_comb, con, quote = FALSE)
+            saveRDS(values$scmap_cell_all, con)
         }
     )
 
@@ -367,10 +418,12 @@ server <- function(input, output) {
     })
     output$reference_data <- reactive({
         values$scmap_cluster_worked <- TRUE
+        values$scmap_cell_worked <- TRUE
         return(!is.null(values$reference_data()))
     })
     output$projection_data <- reactive({
         values$scmap_cluster_worked <- TRUE
+        values$scmap_cell_worked <- TRUE
         return(!is.null(values$projection_data()))
     })
     output$reference_feature_symbol <- reactive({
@@ -404,6 +457,10 @@ server <- function(input, output) {
         return(values$scmap_cluster_worked)
     })
 
+    output$scmap_cell_worked <- reactive({
+        return(values$scmap_cell_worked)
+    })
+
     # make output variables visible for the client side
     outputOptions(output, "projection_file", suspendWhenHidden = FALSE)
     outputOptions(output, "reference_file", suspendWhenHidden = FALSE)
@@ -414,4 +471,5 @@ server <- function(input, output) {
     outputOptions(output, "pdata_cell_types", suspendWhenHidden = FALSE)
     outputOptions(output, "features", suspendWhenHidden = FALSE)
     outputOptions(output, "scmap_cluster_worked", suspendWhenHidden = FALSE)
+    outputOptions(output, "scmap_cell_worked", suspendWhenHidden = FALSE)
 }

ui.R

@@ -25,7 +25,7 @@ dashboardPage(
                      menuItem("About", tabName = "about", icon = icon("bank")),
                      menuItem("Datasets", tabName = "datasets", icon = icon("cloud-upload")),
                      menuItem("Features", tabName = "features", icon = icon("gears")),
-                     menuItem("scmap-cluster", tabName = "results_cluster", icon = icon("area-chart"))
+                     menuItem("Results", tabName = "results", icon = icon("area-chart"))
                  )
             )
         ),
@@ -40,7 +40,7 @@ dashboardPage(
                   sidebarMenu(
                       menuItem("About", tabName = "about", icon = icon("bank")),
                       menuItem("Datasets", tabName = "datasets", icon = icon("cloud-upload")),
-                      menuItem("scmap-cluster", tabName = "results_cluster", icon = icon("area-chart"))
+                      menuItem("Results", tabName = "results", icon = icon("area-chart"))
                   )
              )
         )
@@ -155,6 +155,14 @@ dashboardPage(
                                  solidHeader = TRUE
                              )
                         ),
+                        box(width = 12,
+                            HTML("<p class='lead'>Would you like to run scmap-cell? (may take some time)</p>"),
+                            radioButtons("run_scmap_cell", NULL,
+                                         c("No" = "No",
+                                           "Yes" = "Yes"),
+                                         selected = "No"),
+                            solidHeader = TRUE
+                        ),
                         solidHeader = TRUE,
                         status = "primary"
                     )
@@ -206,39 +214,20 @@ dashboardPage(
                     )
                 )
             ),
-            tabItem(tabName = "results_cluster",
+            tabItem(tabName = "results",
                 fluidRow(
-                    conditionalPanel("input.data_type == 'own'",
-                         box(width = 12,
-                             title = "Cell Projection",
-                             HTML("<p><b>scmap</b> projects all cells
-                                  of the Projection dataset to the
-                                  reference calculated from the Reference dataset. 
-                                  The Reference is computed by calculating
-                                  the median expression in each of 500 
-                                  selected features across all
-                                  cells in each cell type."),
-                             solidHeader = TRUE,
-                             status = "primary"
-                         )
-                    ),
-                    conditionalPanel("input.data_type == 'existing'",
-                        box(width = 12,
-                            title = "Cell Projection",
-                            HTML("<p><b>scmap</b> projects all cells
-                                 of the Projection dataset to the precomputed
-                                 References. The references were computed by
-                                 selecting 500 most informative features of each
-                                 Reference dataset and calculating
-                                 the median expression in each of 500 features across all
-                                 cells in each cell type."),
-                            solidHeader = TRUE,
-                            status = "primary"
-                        )
-                    )
+                  box(width = 12,
+                     title = "Cell Projection",
+                     HTML("<p><b>scmap</b> projects all cells
+                          of the Projection dataset to the
+                          either cell clusters (<b>scmap-cluster</b>) or
+                          each individual cell (<b>scmap-cell</b>) of the Reference dataset."),
+                     solidHeader = TRUE,
+                     status = "primary"
+                 )
                 ),
-                conditionalPanel(condition="!$('html').hasClass('shiny-busy') & output.scmap_cluster_worked",
-                    uiOutput("results_cluster")
+                conditionalPanel(condition="!$('html').hasClass('shiny-busy') & output.scmap_cluster_worked & output.scmap_cell_worked",
+                    uiOutput("results")
                 ),
                 conditionalPanel(condition="$('html').hasClass('shiny-busy')",
                     fluidRow(
@@ -252,11 +241,11 @@ dashboardPage(
                             offset = 2)
                     )
                 ),
-                conditionalPanel("!output.scmap_cluster_worked",
+                conditionalPanel("!output.scmap_cluster_worked || !output.scmap_cell_worked",
                     box(width = 12,
                      HTML("
                           <div class='alert alert-danger'>
-                          <p class = 'lead'>scmap-cluster did not work! Most probably
+                          <p class = 'lead'>scmap did not work! Most probably
                             Reference and Projection come from different organisms, 
                             please check your inputs!</p>
                           </div>"),