@@ -22,17 +22,22 @@ nonLinearWorkflow <- function(input, output, session, parent,

   ns <- session$ns

   output$ui <- renderUI({

-    bsCollapsePanel(tagList(icon("chevron-circle-down"), "Downstream Analysis"), 

-                    uiOutput(ns("de")),

-                    uiOutput(ns("pa")),

-                    uiOutput(ns("qcf")),

-                    uiOutput(ns("nbc")),

-                    uiOutput(ns("cw")),

-                    uiOutput(ns("dr")),

-                    uiOutput(ns("fs")),

-                    uiOutput(ns("cl")),

-                    uiOutput(ns("cv")),

-                    style = "success")

+    bsCollapse(

+      open = "Next Steps",

+      bsCollapsePanel("Next Steps", 

+                               uiOutput(ns("de")),

+                               uiOutput(ns("pa")),

+                               uiOutput(ns("qcf")),

+                               uiOutput(ns("nbc")),

+                               uiOutput(ns("cw")),

+                               uiOutput(ns("dr")),

+                               uiOutput(ns("fs")),

+                               uiOutput(ns("cl")),

+                               uiOutput(ns("cv")),

+                               style = "success"

+                      )

+      )

+    

   })

   if(de){

@@ -142,11 +142,32 @@ shinyServer(function(input, output, session) {

   }

   updateFeatureAnnots <- function(){

+    

     selectRowData <- colnames(rowData(vals$counts))

+    my_list <- data.frame()

+    for(i in selectRowData) {

+      my_list[i,1] <- paste0(i, " (e.g. ", paste(head(rowData(vals$counts)[,i], n = 3), collapse = ","), ")")    

+    }

+    selectRowDataWithExamples <- as.character(my_list[,1])

+    

+    

+    selectNonNARowData <- names(apply(rowData(vals$counts), 2, anyNA)[apply(rowData(vals$counts), 2, anyNA) == FALSE])

+    my_list2 <- data.frame()

+    for(j in selectNonNARowData) {

+      my_list2[j,1] <- paste0(j, " (e.g. ", paste(head(rowData(vals$counts)[,j], n = 3), collapse = ","), ")")    

+    }

+    selectNonNARowDataWithExamples <- as.character(my_list2[,1])

+    

+    Default <- paste0("Default (e.g. ", paste(head(rownames(vals$counts), n = 3), collapse = ","), ")")

+    

     updateSelectInput(session, "gsByParam",

                       choices = c("rownames", selectRowData))

     updateSelectInput(session, "importFeatureDispOpt",

-                      choices = c("Rownames (Default)", selectRowData))

+                      choices = c(Default, 

+                                  selectRowDataWithExamples))

+    updateSelectInput(session, "importFeatureNamesOpt",

+                      choices = c(Default, 

+                                  selectNonNARowDataWithExamples))

     updateSelectInput(session, "filteredFeature",

                       choices = c("none", selectRowData))

     updateSelectInput(session, "hvgPlotFeatureDisplay",

@@ -441,7 +462,7 @@ shinyServer(function(input, output, session) {

         count <- 0

         if (!is.na(path)) {

           # Add Reference selection for cellRangerV2

-          if (input$algoChoice == "cellRanger2") {

+          if (input$uploadChoice == "cellRanger2") {

             ## Identify available reference

             firstSampleDir <- list.dirs(path, recursive = FALSE)[1]

             refPath <- file.path(firstSampleDir, "outs/filtered_gene_bc_matrices")

@@ -498,7 +519,7 @@ shinyServer(function(input, output, session) {

                                                  collapse = .Platform$file.sep))

         path <- dirPaths$sDirectory

         if (!is.na(path)) {

-          if (input$algoChoice == "cellRanger2") {

+          if (input$uploadChoice == "cellRanger2") {

             ## Identify available reference

             refPath <- file.path(path, "outs/filtered_gene_bc_matrices")

             refList <- basename(list.dirs(refPath, recursive = FALSE))

@@ -588,7 +609,7 @@ shinyServer(function(input, output, session) {

     } else {

       allDirs <- list.dirs(basePath, recursive = FALSE)

       # if we are adding a new CellRangerV2 sample

-      if (input$algoChoice == "cellRanger2") {

+      if (input$uploadChoice == "cellRanger2") {

         allUI <- vector()

         allIDs <- vector()

         count <- 0

@@ -677,6 +698,7 @@ shinyServer(function(input, output, session) {

       )

       removeModal()

     }

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

   })

   # event listeners for Cell Ranger import modals' OK buttons

@@ -688,7 +710,7 @@ shinyServer(function(input, output, session) {

       showModal(importCRSDir(failed = TRUE))

     } else {

       # add the files to the appropriate reactiveValues

-      if (input$algoChoice == "cellRanger2") {

+      if (input$uploadChoice == "cellRanger2") {

         id <- paste0("snewSampleCR2", allImportEntries$id_count)

         entry <- list(type="cellRanger2", id=id, 

                       params=list(cellRangerDirs = dirname(samplePath), 

@@ -704,7 +726,7 @@ shinyServer(function(input, output, session) {

         allImportEntries$id_count <- allImportEntries$id_count + 1

       }

       # add new row to table

-      addToGeneralSampleTable(input$algoChoice, id, samplePath, input$sSampleID)

+      addToGeneralSampleTable(input$uploadChoice, id, samplePath, input$sSampleID)

       # handler to remove the sample that was just added

       observeEvent(input[[paste0("remove", id)]],{

         removeUI(

@@ -722,6 +744,8 @@ shinyServer(function(input, output, session) {

       })

       removeModal()

     }

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

+    

   })

   # data directory

@@ -730,7 +754,7 @@ shinyServer(function(input, output, session) {

     if ((!nzchar(input$dSampleID)) || (identical(dataPath, character(0)))) {

       showModal(importCRDDir(failed = TRUE))

     } else {

-      if (input$algoChoice == "cellRanger2") {

+      if (input$uploadChoice == "cellRanger2") {

         id <- paste0("dnewSampleCR2", allImportEntries$id_count)

         entry <- list(type="cellRanger2", id=id, 

                       params=list(dataDir = dataPath, 

@@ -744,7 +768,7 @@ shinyServer(function(input, output, session) {

         allImportEntries$id_count <- allImportEntries$id_count + 1

       }

       # add new row to table

-      addToGeneralSampleTable(input$algoChoice, id, dataPath, input$dSampleID)

+      addToGeneralSampleTable(input$uploadChoice, id, dataPath, input$dSampleID)

       observeEvent(input[[paste0("remove", id)]],{

         removeUI(

           selector = paste0("#", id)

@@ -761,6 +785,8 @@ shinyServer(function(input, output, session) {

       })

       removeModal()

     }

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

+    

   })

   # event handler for pressing OK on the import modal

@@ -771,29 +797,29 @@ shinyServer(function(input, output, session) {

       showModal(importModal(failed = TRUE))

     } else {

       entry <- list()

-      if (input$algoChoice == "starSolo") {

+      if (input$uploadChoice == "starSolo") {

         id <- paste0("newSampleSS", allImportEntries$id_count)

         entry <- list(type="starSolo", id = id, params=list(STARsoloDirs = basePath, samples = input$sampleName))

         allImportEntries$samples <- c(allImportEntries$samples, list(entry))

         allImportEntries$id_count <- allImportEntries$id_count+1

-      } else if (input$algoChoice == "busTools") {

+      } else if (input$uploadChoice == "busTools") {

         id <- paste0("newSampleBUS", allImportEntries$id_count)

         entry <- list(type="busTools", id = id, params=list(BUStoolsDirs = basePath, samples = input$sampleName))

         allImportEntries$samples <- c(allImportEntries$samples, list(entry))

         allImportEntries$id_count <- allImportEntries$id_count+1

-      } else if (input$algoChoice == "seqc") {

+      } else if (input$uploadChoice == "seqc") {

         id <- paste0("newSampleSEQ", allImportEntries$id_count)

         entry <- list(type="seqc", id = id, params=list(seqcDirs = basePath, prefix = input$sampleID, samples = input$sampleName))

         updateTextInput(session, "sampleID", value = "")

         allImportEntries$samples <- c(allImportEntries$samples, list(entry))

         allImportEntries$id_count <- allImportEntries$id_count+1

-      } else if (input$algoChoice == "optimus") {

+      } else if (input$uploadChoice == "optimus") {

         id <- paste0("newSampleOpt", allImportEntries$id_count)

         entry <- list(type="optimus", id = id, params=list(OptimusDirs = basePath, samples = input$sampleName))

         allImportEntries$samples <- c(allImportEntries$samples, list(entry))

         allImportEntries$id_count <- allImportEntries$id_count+1

       }

-      addToGeneralSampleTable(input$algoChoice, id, basePath, input$sampleName)

+      addToGeneralSampleTable(input$uploadChoice, id, basePath, input$sampleName)

       observeEvent(input[[paste0("remove", id)]],{

         removeUI(

           selector = paste0("#", id)

@@ -810,6 +836,8 @@ shinyServer(function(input, output, session) {

       })

       removeModal()

     }

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

+    

   })

   # Event handler to import a file input

@@ -850,6 +878,8 @@ shinyServer(function(input, output, session) {

       }

       allImportEntries$samples <- allImportEntries$samples[toRemove]

     })

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

+    

   })

   # Event handler to import an example input

@@ -885,6 +915,8 @@ shinyServer(function(input, output, session) {

       }

       allImportEntries$samples <- allImportEntries$samples[toRemove]

     })

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

+    

   })

   # Event handler to import an RDS input

@@ -910,6 +942,8 @@ shinyServer(function(input, output, session) {

       }

       allImportEntries$samples <- allImportEntries$samples[toRemove]

     })

+    updateCollapse(session = session, "importUI", style = list("1. Add sample to import:" = "success"))

+    

   })

   # Event handler for "Upload" button on import page

@@ -1018,6 +1052,8 @@ shinyServer(function(input, output, session) {

       # datasets. Otherwise, errors may pop out when Shiny listens to the new

       # object but cannot find the old result.

     })

+    updateCollapse(session = session, "importUI", style = list("2. Create dataset:" = "success"))

+    

     callModule(module = nonLinearWorkflow, id = "nlw-import", parent = session, qcf = TRUE)

     .loadClose() # close the notification spinner and console log

@@ -1343,13 +1379,20 @@ shinyServer(function(input, output, session) {

     if (!is.null(vals$counts)) {

       withBusyIndicatorServer("importFeatureDipSet", {

         selected <- NULL

-        if (!input$importFeatureDispOpt == "Rownames (Default)") {

-          selected <- input$importFeatureDispOpt

+        

+        if (!stringr::word(input$importFeatureDispOpt, 1) == "Default") {

+          featureName <- word(input$importFeatureDispOpt, 1) 

+          selected <- featureName

+        }

+        if (!stringr::word(input$importFeatureNamesOpt, 1) == "Default") {

+          featureID <- word(input$importFeatureNamesOpt, 1) 

+          rownames(vals$counts) <- rowData(vals$counts)[[featureID]]

         }

         vals$counts <- setSCTKDisplayRow(vals$counts, selected)

         updateFeatureDisplaySelect(selected = selected)

       })

     }

+    updateCollapse(session = session, "importUI", style = list("3. Data summary:" = "success"))

   })

   updateFeatureDisplaySelect <- function(selected = NULL, updateOptions = FALSE) 

   {

@@ -2144,7 +2187,7 @@ shinyServer(function(input, output, session) {

   }, striped = TRUE, border = TRUE, align = "c", spacing = "l")

   #Render summary table

-  output$summarycontents <- renderTable({

+  output$summarycontents <- DT::renderDataTable({

       req(vals$counts)

       if ("Sample" %in% names(colData(vals$counts))) {

         sampleVar <- "Sample"

@@ -2157,7 +2200,7 @@ shinyServer(function(input, output, session) {

       singleCellTK::summarizeSCE(inSCE = vals$counts,

                                  useAssay = NULL,

                                  sampleVariableName = sampleVar)

-  }, striped = TRUE, border = TRUE, align = "c", spacing = "l")

+  })

   #Reset the data to the original uploaded dataset

@@ -16,6 +16,7 @@ if ("scRNAseq" %in% rownames(installed.packages())){

                        "NestorowaHSC (Nestorowa et al, 2016)" = "NestorowaHSCData")

 }

+# User Interface for import Workflow ---

 shinyPanelImport <- fluidPage(

   useShinyjs(),

   tags$style(appCSS),

@@ -33,26 +34,36 @@ shinyPanelImport <- fluidPage(

     )

   ),

   tags$br(),

-  tags$div(

-    class = "container",

-    h1("Import"),

-    h5(tags$a(href = paste0(docs.artPath, "import_data.html"),

-              "(help)", target = "_blank")),

-    tags$hr(),

-    h3("1. Choose data source:"),

-    radioButtons("uploadChoice", label = NULL, c("Import from a preprocessing tool" = 'directory',

-                                                 "Import from flat files (.csv, .txt, .mtx)" = "files",

-                                                 "Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds",

-                                                 "Import example datasets" = "example")

-    ),

-    tags$hr(),

-    conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),

-                     h3("2. Upload data in tab separated text format:"),

-                     fluidRow(

-                       column(width = 4,

-                              wellPanel(

-                                h4("Example count file:"),

-                                HTML('<table class="table"><thead><tr class="header"><th>Gene</th>

+  

+  h1("Import"),

+  h5(tags$a(href = paste0(docs.artPath, "import_data.html"),

+            "(help)", target = "_blank")),

+  tags$hr(),

+  

+  bsCollapse(

+    id = "importUI", 

+    open = "1. Add sample to import:",

+    bsCollapsePanel(

+      "1. Add sample to import:",

+      radioButtons("uploadChoice", label = NULL, c("Cell Ranger (Version 3 or above)" = "cellRanger3",

+                                                   "Cell Ranger (Version 2)" = "cellRanger2",

+                                                   "STARsolo" = "starSolo",

+                                                   "BUStools" = "busTools",

+                                                   "SEQC" = "seqc",

+                                                   "Optimus" = "optimus",

+                                                   #"Import from a preprocessing tool" = 'directory',

+                                                   "Import from flat files (.csv, .txt, .mtx)" = "files",

+                                                   "Upload SingleCellExperiment or Seurat object stored in an RDS File" = "rds",

+                                                   "Import example datasets" = "example")

+      ),

+      tags$hr(),

+      conditionalPanel(condition = sprintf("input['%s'] == 'files'", "uploadChoice"),

+                       h3("Upload data in tab separated text format:"),

+                       fluidRow(

+                         column(width = 4,

+                                wellPanel(

+                                  h4("Example count file:"),

+                                  HTML('<table class="table"><thead><tr class="header"><th>Gene</th>

                  <th>Cell1</th><th>Cell2</th><th>&#x2026;</th><th>CellN</th>

                  </tr></thead><tbody><tr class="odd"><td>Gene1</td><td>0</td>

                  <td>0</td><td>&#x2026;</td><td>0</td></tr><tr class="even">

@@ -63,257 +74,264 @@ shinyPanelImport <- fluidPage(

                  <td>&#x2026;</td><td>&#x2026;</td></tr><tr class="odd">

                  <td>GeneM</td><td>10</td><td>10</td><td>&#x2026;</td><td>10</td>

                  </tr></tbody></table>'),

-            tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",

-                   "Download an example count file here.", target = "_blank"),

-            tags$br(),

-            tags$br(),

-            fileInput(

-              "countsfile",

-              HTML(

-                paste("Input assay (eg. counts, required):",

-                tags$span(style = "color:red", "*", sep = ""))

-              ),

-              accept = c(

-                "text/csv", "text/comma-separated-values", "mtx",

-                "text/tab-separated-values", "text/plain", ".csv", ".tsv"

-              )

-            )

-          ),

-          h4("Input Assay Type:"),

-          selectInput("inputAssayType", label = NULL,

-                      c("counts", "normcounts", "logcounts", "cpm",

-                        "logcpm", "tpm", "logtpm")

-          )

-        ),

-        column(width = 4,

-          wellPanel(

-            h4("Example cell annotation file:"),

-            HTML('<table class="table"><thead><tr class="header"><th>Cell</th>

+                                  tags$a(href = "https://drive.google.com/open?id=1n0CtM6phfkWX0O6xRtgPPg6QuPFP6pY8",

+                                         "Download an example count file here.", target = "_blank"),

+                                  tags$br(),

+                                  tags$br(),

+                                  fileInput(

+                                    "countsfile",

+                                    HTML(

+                                      paste("Input assay (eg. counts, required):",

+                                            tags$span(style = "color:red", "*", sep = ""))

+                                    ),

+                                    accept = c(

+                                      "text/csv", "text/comma-separated-values", "mtx",

+                                      "text/tab-separated-values", "text/plain", ".csv", ".tsv"

+                                    )

+                                  )

+                                ),

+                                h4("Input Assay Type:"),

+                                selectInput("inputAssayType", label = NULL,

+                                            c("counts", "normcounts", "logcounts", "cpm",

+                                              "logcpm", "tpm", "logtpm")

+                                )

+                         ),

+                         column(width = 4,

+                                wellPanel(

+                                  h4("Example cell annotation file:"),

+                                  HTML('<table class="table"><thead><tr class="header"><th>Cell</th>

                  <th>Annot1</th><th>&#x2026;</th></tr></thead><tbody><tr class="odd">

                  <td>Cell1</td><td>a</td><td>&#x2026;</td></tr><tr class="even">

                  <td>Cell2</td><td>a</td><td>&#x2026;</td></tr><tr class="odd">

                  <td>Cell3</td><td>b</td><td>&#x2026;</td></tr><tr class="even">

                  <td>&#x2026;</td><td>&#x2026;</td><td>&#x2026;</td></tr><tr class="odd"><td>CellN</td>

                  <td>b</td><td>&#x2026;</td></tr></tbody></table>'),

-                                tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",

-                                       "Download an example annotation file here.", target = "_blank"),

-                                tags$br(),

-                                tags$br(),

-                                fileInput(

-                                  "annotFile", "Cell annotations (optional):",

-                                  accept = c(

-                                    "text/csv", "text/comma-separated-values",

-                                    "text/tab-separated-values", "text/plain", ".csv", ".tsv"

+                                  tags$a(href = "https://drive.google.com/open?id=10IDmZQUiASN4wnzO4-WRJQopKvxCNu6J",

+                                         "Download an example annotation file here.", target = "_blank"),

+                                  tags$br(),

+                                  tags$br(),

+                                  fileInput(

+                                    "annotFile", "Cell annotations (optional):",

+                                    accept = c(

+                                      "text/csv", "text/comma-separated-values",

+                                      "text/tab-separated-values", "text/plain", ".csv", ".tsv"

+                                    )

                                   )

                                 )

-                              )

-                       ),

-                       column(width = 4,

-                              wellPanel(

-                                h4("Example feature file:"),

-                                HTML('<table class="table"><thead><tr class="header"><th>Gene</th>

+                         ),

+                         column(width = 4,

+                                wellPanel(

+                                  h4("Example feature file:"),

+                                  HTML('<table class="table"><thead><tr class="header"><th>Gene</th>

                <th>Annot2</th><th>&#x2026;</th></tr></thead><tbody><tr class="odd">

                  <td>Gene1</td><td>a</td><td>&#x2026;</td></tr><tr class="even">

                  <td>Gene2</td><td>a</td><td>&#x2026;</td></tr><tr class="odd">

                  <td>Gene3</td><td>b</td><td>&#x2026;</td></tr><tr class="even">

                  <td>&#x2026;</td><td>&#x2026;</td><td>&#x2026;</td></tr><tr class="odd"><td>GeneM</td>

                  <td>b</td><td>&#x2026;</td></tr></tbody></table>'),

-                                tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",

-                                       "Download an example feature file here.", target = "_blank"),

-                                tags$br(),

-                                tags$br(),

-                                fileInput(

-                                  "featureFile", "Feature annotations (optional):",

-                                  accept = c(

-                                    "text/csv", "text/comma-separated-values",

-                                    "text/tab-separated-values", "text/plain", ".csv", ".tsv"

+                                  tags$a(href = "https://drive.google.com/open?id=1gxXaZPq5Wrn2lNHacEVaCN2a_FHNvs4O",

+                                         "Download an example feature file here.", target = "_blank"),

+                                  tags$br(),

+                                  tags$br(),

+                                  fileInput(

+                                    "featureFile", "Feature annotations (optional):",

+                                    accept = c(

+                                      "text/csv", "text/comma-separated-values",

+                                      "text/tab-separated-values", "text/plain", ".csv", ".tsv"

+                                    )

                                   )

                                 )

-                              )

-                       )

-                     ),

-        actionButton("addFilesImport", "Add To Sample List")

-    ),

-    conditionalPanel(

-      condition = sprintf("input['%s'] == 'example'", "uploadChoice"),

-      h3("2. Choose Example Dataset:"),

-      selectInput("selectExampleData", label = NULL, exampleDatasets),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),

-        h3(tags$a(href = "http://dx.doi.org/10.1038/nbt.2967", "130 cells from (Pollen et al. 2014), 65 at high coverage and 65 at low coverage", target = "_blank")),

-        "Transcriptomes of cell populations in both of low-coverage (~0.27 million reads per cell) and high-coverage (~5 million reads per cell) to identify cell-type-specific biomarkers, and to compare gene expression across samples specifically for cells of a given type as well as to reconstruct developmental lineages of related cell types. Data was loaded from the 'scRNASeq' package.",

-        tags$br(),

-        tags$br()

-      ),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'allen_tasic'", "selectExampleData"),

-        h3(tags$a(href = "http://dx.doi.org/10.1038/nn.4216", "Mouse visual cortex cells from (Tasic et al. 2016)", target = "_blank")),

-        "Subset of 379 cells from the mouse visual cortex. Data was loaded from the 'scRNASeq' package.",

-        tags$br(),

-        tags$br()

-      ),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'NestorowaHSCData'", "selectExampleData"),

-        h3(tags$a(href = "https://www.nature.com/articles/nbt.2967", "1920 Mouse haematopoietic stem cells from (Nestorowa et al. 2015).", target= "_blank")),

-        "Data was loaded from the 'scRNASeq' package.",

-        tags$br(),

-        tags$br()

-      ),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),

-        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

-        "Data was loaded with the 'TENxPBMCData' package.",

-        tags$br(),

-        tags$br()

-      ),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'pbmc4k'", "selectExampleData"),

-        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "4,430 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

-        "Data was loaded with the 'TENxPBMCData' package.",

-        tags$br(),

-        tags$br()

-      ),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'pbmc6k'", "selectExampleData"),

-        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

-        "Data was loaded with the 'TENxPBMCData' package.",

-        tags$br(),

-        tags$br()

-      ),

-      conditionalPanel(

-        condition = sprintf("input['%s'] == 'pbmc8k'", "selectExampleData"),

-        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

-        "Data was loaded with the 'TENxPBMCData' package.",

-        tags$br(),

-        tags$br()

+                         )

+                       ),

+                       actionButton("addFilesImport", "Add To Dataset List")

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'pbmc33k'", "selectExampleData"),

-        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

-        "Data was loaded with the 'TENxPBMCData' package.",

-        tags$br(),

-        tags$br()

+        condition = sprintf("input['%s'] == 'example'", "uploadChoice"),

+        h3("Choose Example Dataset:"),

+        selectInput("selectExampleData", label = NULL, exampleDatasets),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'fluidigm_pollen'", "selectExampleData"),

+          h3(tags$a(href = "http://dx.doi.org/10.1038/nbt.2967", "130 cells from (Pollen et al. 2014), 65 at high coverage and 65 at low coverage", target = "_blank")),

+          "Transcriptomes of cell populations in both of low-coverage (~0.27 million reads per cell) and high-coverage (~5 million reads per cell) to identify cell-type-specific biomarkers, and to compare gene expression across samples specifically for cells of a given type as well as to reconstruct developmental lineages of related cell types. Data was loaded from the 'scRNASeq' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'allen_tasic'", "selectExampleData"),

+          h3(tags$a(href = "http://dx.doi.org/10.1038/nn.4216", "Mouse visual cortex cells from (Tasic et al. 2016)", target = "_blank")),

+          "Subset of 379 cells from the mouse visual cortex. Data was loaded from the 'scRNASeq' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'NestorowaHSCData'", "selectExampleData"),

+          h3(tags$a(href = "https://www.nature.com/articles/nbt.2967", "1920 Mouse haematopoietic stem cells from (Nestorowa et al. 2015).", target= "_blank")),

+          "Data was loaded from the 'scRNASeq' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'pbmc3k'", "selectExampleData"),

+          h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

+          "Data was loaded with the 'TENxPBMCData' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'pbmc4k'", "selectExampleData"),

+          h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "4,430 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

+          "Data was loaded with the 'TENxPBMCData' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'pbmc6k'", "selectExampleData"),

+          h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

+          "Data was loaded with the 'TENxPBMCData' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'pbmc8k'", "selectExampleData"),

+          h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

+          "Data was loaded with the 'TENxPBMCData' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'pbmc33k'", "selectExampleData"),

+          h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

+          "Data was loaded with the 'TENxPBMCData' package.",

+          tags$br(),

+          tags$br()

+        ),

+        conditionalPanel(

+          condition = sprintf("input['%s'] == 'pbmc68k'", "selectExampleData"),

+          h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

+          "Data was loaded with the 'TENxPBMCData' package.",

+          tags$br(),

+          tags$br()

+        ),

+        actionButton("addExampleImport", "Add To Sample List")

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'pbmc68k'", "selectExampleData"),

-        h3(tags$a(href = "https://doi.org/10.1038/ncomms14049", "68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics", target = "_blank")),

-        "Data was loaded with the 'TENxPBMCData' package.",

-        tags$br(),

-        tags$br()

-      ),

-      actionButton("addExampleImport", "Add To Sample List")

-    ),

-    conditionalPanel(

-      condition = sprintf("input['%s'] == 'rds'", "uploadChoice"),

-      h3("2. Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),

-      fileInput(

-        "rdsFile", "SingleCellExperiment or Seurat RDS file:", accept = c(".rds", ".RDS")

-      ),

-      actionButton("addRDSImport", "Add To Sample List")

-    ),

-    conditionalPanel(

-      condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),

-      tags$style(HTML("

-      div {

-        word-wrap: break-word;

-      }

-      ")),

-      h3("2. Choose a Preprocessing Tool:"),

-      radioButtons("algoChoice", label = NULL, c("Cell Ranger v2" = "cellRanger2",

-                                                 "Cell Ranger v3" = "cellRanger3",

-                                                 "STARsolo" = "starSolo",

-                                                 "BUStools" = "busTools",

-                                                 "SEQC" = "seqc",

-                                                 "Optimus" = "optimus")

+        condition = sprintf("input['%s'] == 'rds'", "uploadChoice"),

+        h3("Choose an RDS file that contains a SingleCellExperiment or Seurat object:"),

+        fileInput(

+          "rdsFile", "SingleCellExperiment or Seurat RDS file:", accept = c(".rds", ".RDS")

+        ),

+        actionButton("addRDSImport", "Add To Sample List")

       ),

-      tags$br(),

+      #conditionalPanel(

+      #condition = sprintf("input['%s'] == 'directory'", "uploadChoice"),

+      #tags$style(HTML("

+      #div {

+      #  word-wrap: break-word;

+      #}

+      #")),

+      #h3("2. Choose a Preprocessing Tool:"),

+      #radioButtons("algoChoice", label = NULL, c("Cell Ranger v2" = "cellRanger2",

+      #                                          "Cell Ranger v3" = "cellRanger3",

+      #                                         "STARsolo" = "starSolo",

+      #                                        "BUStools" = "busTools",

+      #                                       "SEQC" = "seqc",

+      #                                      "Optimus" = "optimus")

+      #),

+      #tags$br(),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'cellRanger2'", "algoChoice"),

+        condition = sprintf("input['%s'] == 'cellRanger2'", "uploadChoice"),

         actionButton("addCR2Sample", "Add a Sample"),

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'cellRanger3'", "algoChoice"),

+        condition = sprintf("input['%s'] == 'cellRanger3'", "uploadChoice"),

         actionButton("addCR3Sample", "Add a Sample"),

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'starSolo'", "algoChoice"),

+        condition = sprintf("input['%s'] == 'starSolo'", "uploadChoice"),

         wellPanel(

           h5("Please select the directory that contains your /Gene directory as your base directory. ")

         ),

         actionButton("addSSSample", "Add a Sample"),

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'busTools'", "algoChoice"),

+        condition = sprintf("input['%s'] == 'busTools'", "uploadChoice"),

         wellPanel(

           h5("Please select your /genecount directory as your base directory.")

         ),

         actionButton("addBUSSample", "Add a Sample"),

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'seqc'", "algoChoice"),

+        condition = sprintf("input['%s'] == 'seqc'", "uploadChoice"),

         wellPanel(

           h5("Please select the directory that contains your sample files as your base directory.")

         ),

         actionButton("addSEQSample", "Add a Sample"),

       ),

       conditionalPanel(

-        condition = sprintf("input['%s'] == 'optimus'", "algoChoice"),

+        condition = sprintf("input['%s'] == 'optimus'", "uploadChoice"),

         wellPanel(

           h5("Please select the directory that contains the following four directories - call-MergeCountFiles, call-MergeCellMetrics, call-MergeGeneMetrics, call-RunEmptyDrops - as your base directory.")

         ),

         actionButton("addOptSample", "Add a Sample"),

       ),

+      style = "primary"

     ),

-    tags$hr(),

-    h3("3. Import:"),

-    wellPanel(

-      h4("Samples to Import:"),

-      fluidRow(

-        column(3, tags$b("Type")),

-        column(3, tags$b("Location")),

-        column(3, tags$b("Sample Name")),

-        column(3, tags$b("Remove"))

+    

+    bsCollapsePanel(

+      "2. Create dataset:",

+      wellPanel(

+        h4("Samples to Import:"),

+        fluidRow(

+          column(3, tags$b("Type")),

+          column(3, tags$b("Location")),

+          column(3, tags$b("Sample Name")),

+          column(3, tags$b("Remove"))

+        ),

+        tags$div(id = "newSampleImport"),

+        tags$br(),

+        tags$br(),

+        actionButton("clearAllImport", "Clear Samples")

+      ),

+      shinyjs::hidden(

+        tags$div(

+          id = "combineOptions",

+          radioButtons("combineSCEChoice", label = NULL, c("Add to existing dataset" = 'addToExistingSCE',

+                                                           "Overwrite existing dataset" = "overwriteSCE")

+          )

+        )

       ),

-      tags$div(id = "newSampleImport"),

+      actionButton("uploadData", "Create"),

+      

       tags$br(),

       tags$br(),

-      actionButton("clearAllImport", "Clear Samples")

+      style = "primary"

     ),

-    shinyjs::hidden(

-      tags$div(

-        id = "combineOptions",

-        radioButtons("combineSCEChoice", label = NULL, c("Add to existing SCE object" = 'addToExistingSCE',

-                                                         "Overwrite existing SCE object" = "overwriteSCE")

+    

+    bsCollapsePanel(

+      "3. Data summary:",

+      hidden(

+        wellPanel(

+          id = "annotationData",

+          h3("Data summary"),

+          DT::dataTableOutput("summarycontents"),

+          

+          tags$hr(),

+          

+          h3("Dataset options:"),

+          selectInput("importFeatureNamesOpt",

+                      "Set feature ID (only showing annotations without the NAs)",

+                      c("Default", featureChoice)),

+          selectInput("importFeatureDispOpt",

+                      "Set feature names to be displayed in downstream visualization",

+                      c("Default", featureChoice)),

+          

+          withBusyIndicatorUI(actionButton("importFeatureDipSet", "Set")),

         )

-      )

-    ),

-    actionButton("uploadData", "Import"),

-  

-    tags$br(),

-    tags$br(),

-    hidden(

-      wellPanel(

-        id = "annotationData",

-        h3("Data summary"),

-        tableOutput("summarycontents"),

-

-        tags$hr(),

-

-        h3("Set Feature for Display:"),

-        selectInput("importFeatureDispOpt",

-                    "Select the feature ID type that should be displayed in downstream visualization",

-                    c("Rownames (Default)", featureChoice)),

-        withBusyIndicatorUI(actionButton("importFeatureDipSet", "Set")),

-      )

-    ),

-

-    tags$div(

-      class = "container",

-      p("")

-    ),

-

-    nonLinearWorkflowUI(id = "nlw-import")

-  )

-  #includeHTML("www/footer.html")

+      ),

+     

+      style = "primary"

+    )

+  ),

+  nonLinearWorkflowUI(id = "nlw-import")

 )