inst/shinyApp/ui.r

In epurdom/clusterExperimentShiny: A Shiny App to accompany clusterExperiment

shinyUI(navbarPage("Cluster Experiment",
                   tabPanel("Welcome Page",
                            startPageMessage("startMessage", "")),
                   tabPanel("Getting Started",
                            tabsetPanel(
                                tabPanel("Setup",
                                          h4("Set working directory"),            
                                          p("Enter a working directory for this Cluster Experiment session and click on 'Choose Working Directory' to set it"),
                                          fluidRow(
                                              column(6,
                                                     textInput("workingDirectory", label = "eg: 'homeDirectory/subdirectory/filename.r", 
                                                    value = path.expand("~"), width = '100%')
                                              )
                                          ),
                                          actionButton("createWD", "Choose Working Directory"),
                                          tags$hr(),
                                          checkboxInput("makeScript", label = "Would you like to create a reproducible R script from this work session?", value = FALSE),
                                          conditionalPanel(condition = "input.makeScript",
                                                           fluidRow(
                                                               column(6, 
                                                                      p("Enter file path and name of file to store script"),
                                                                      uiOutput("createScriptInputs")
                                                               ),
                                                               column(6, 
                                                                      p("Enter any descriptive comments for the beginning of the R file:"),
                                                                      textInput("fileComments", label = "eg: Name, date, experiment", value = "")
                                                               )
                                                           ),
                                                           p("Click below on 'Create File' to create the R script. If file already exists, any code will be appended to the end of existing file"),
                                                           actionButton("createReproducibleFile", label = "Create File")
                                          ),
                                          tags$hr(),
                                          checkboxInput("autoCreateObject", label = "Would you like to automatically save the internal cluster experiment object every time it is updated?", value = FALSE),
                                          conditionalPanel(condition = "input.autoCreateObject",
                                                           p("Enter file path and name (with extension .rds, see 'saveRDS') in order to create a continuously updated R object:"),
                                                           uiOutput("createObjectInputs")
                                          )
                                ),
                                
                                tabPanel("Upload Data",
                                         fluidRow(
                                             column(12,p("The following choices regarding transformation of the data (will take effect only when run clusterMany/RSEC)"))
                                         ),
                                         fluidRow(
                                             column(12,countInfo("trans"))
                                         ),
                                         tabsetPanel(
                                             tabPanel("RDS file input",
                                                      rdaFileInput("fileInput", "User rds file"),
                                                      h4("Summary of object uploaded:"),
                                                      uiOutput("isRda")),
                                             tabPanel("CSV format input",
                                                      fluidRow(
                                                          column(8, csvAssay("fileInput", "")),
                                                          column(4, 
                                                                 h5(" First 4 rows and columns of uploaded table:"),
                                                                 tableOutput("csvAssayContents")
                                                          )
                                                      ),
                                                      fluidRow(
                                                          column(8, csvColData("fileInput", "")),
                                                          column(4, 
                                                                 h5(" First 4 rows and columns of uploaded table:"),
                                                                 tableOutput("csvColContents")
                                                          )
                                                      ),
                                                      fluidRow(
                                                          column(8, csvRowData("fileInput", "")),
                                                          column(4, 
                                                                 h5(" First 4 rows and columns of uploaded table:"),
                                                                 tableOutput("csvRowContents")
                                                          )
                                                      ),
                                                      actionButton("makeObject", 
                                                                   "Create Summarized Experiment object from selected data"),
                                                      h5("Summary of summarized experiment created from uploaded data:"),
                                                      #h3(paste(capture.output(show(sE)),collapse="\n")),
                                                      uiOutput("isAssay")
                                             )
                                             
                                         )
                                )
                            )
                   ),
                   tabPanel("RSEC",
#                                                          h3("Core imputs for RSEC")
#                                                 ),
                            fluidRow(
                                column(6,
                                       #Displays basic help text for Shiny App and clusterMany
                                       RSECHelpText()
                                ),
                                column(6,
                                       #textual output of code that is to be run
                                       h3("Code to be run internally:"),
                                       textOutput("RSECCode"),
                                       #Action button that allows one to run above code
                                       actionButton("runRSEC", "Run This Code"),
                                       textOutput("numRSECIterations")
                                )
                            ),
                            navlistPanel(
                                tabPanel("Main Options",
                                         RSECInputs("rsec")
                                ),
                                tabPanel("Dimensionality Reduction",
                                         #Allows user to enter all inputs
                                         h3("Choose Dimensionality Reduction Options"),
                                         dimReduceInput("rsec", "dim inputs",isRSEC=TRUE,sidelabel="Set dimensionality reduction for clustering?"),
                                         dimReduceInput("rsec", isRSEC=TRUE,singleChoice=TRUE,sidelabel="Set dimensionality reduction for making dendrogram?",dimVal="dendroReduce",ndimVal="dendroNDims")
                                         
                                ),
                                tabPanel("Specialized control",
                                         specializedInputs("rsec", "specialized inputs",isRSEC=TRUE)
                                ),
                                tabPanel("Plot Clusters",
                                         tabsetPanel(
                                             tabPanel("Default Plot",
                                                      downloadButton("downloadDefaultPlotPCRSEC", label = "DownLoad this Plot"),
                                                      plotOutput("imgRSEC")                                                     
                                             )
                                         )
                                )
                        )
                   ),
                   tabPanel("Cluster Many",
                            conditionalPanel(condition = paste0("!input['showCMDir']"),
                                             column(12,clusterManyHelpText())
                                             ),
                            fluidRow(
                                column(6, checkboxInput("showCMDir", value = FALSE, label = "Hide Directions?")),
                                
                                column(6,
                                       #textual output of code that is to be run
                                       h3("Code to be run internally:"),
                                       textOutput("clusterManyCode"),
                                       #Action button that allows one to run above code
                                       actionButton("runCM", "Run This Code"),
                                       textOutput("numClusterIterations")
                                )
                            ),
                            navlistPanel(
                                tabPanel("Main Options",
                                         h3("Core imputs for clusterMany"),
                                         sSBInputs("parameters", "SSB inputs")
                                ),
                                tabPanel("Dimensionality Reduction",
                                         #Allows user to enter all inputs
                                         h3("Choose Dimensionality Reduction Options"),
                                         dimReduceInput("parameters", "dim inputs")
                                ),
                                tabPanel("Further clustering options",
                                         h3("Warning!"),
                                         h4("If you change options on the 'Main Options' tab, you should return to this tab to see what options have changed. It is best to complete the 'Main Options' before starting this page"),
                                         clusterFunctionInputs("parameters", "cluster function inputs")
                                ),
                                tabPanel("Specialized control",
                                         specializedInputs("parameters", "specialized inputs")
                                ),
                                tabPanel("Plot Clusters",
                                         tabsetPanel(
                                             tabPanel("Default Plot",
                                                      downloadButton("downloadDefaultPlotPCCM", label = "DownLoad this Plot"),
                                                      plotOutput("imgCE")                                                     
                                             )
                                         )
                                )
                            )
                   ),
                   tabPanel("Combine Many",
#                             conditionalPanel(condition = paste0("!input['showCombManyDir']"),
#                                              column(12,combineManyHelpText())
#                             ),
                            fluidRow(
                                column(6, combineManyHelpText()),
                                column(6,
                                       #textual output of code that is to be run
                                       h3("Code to be run internally:"),
                                       textOutput("combineManyCode"),
                                       #Action button that allows one to run above code
                                       actionButton("runCombineMany", "Run This Code")
                                )
                            ),
                            navlistPanel(
                                tabPanel("Combine Many Inputs",
                                         h2("Inputs for Combine Many"),
                                         #uiOutput("combineManyWhichClusters"),
                                         combineManyInput("cMInputs", "")
                                ),
                                tabPanel("Plot Clusters",
                                         downloadButton("downloadDefaultPlotPCCombineMany", label = "DownLoad this Plot"),
                                         plotOutput("imgCombineManyPC")
                                ),
                                tabPanel("Plot CoClusters",
                                         downloadButton("downloadDefaultPlotCoClustersCombineMany", label = "DownLoad this Plot"),
                                         plotOutput("imgCombineManyPCC")
                                )
                            )
                   ),
                   tabPanel("Make Dendrogram",
                            fluidRow(
                                column(6,
                                       #Displays basic help text for Shiny App and clusterMany
                                       makeDendrogramHelpText()
                                ),
                                column(6,
                                       #textual output of code that is to be run
                                       h3("Code to be run internally:"),
                                       textOutput("makeDendrogramCode"),
                                       #Action button that allows one to run above code
                                       actionButton("runMakeDendrogram", "Run This Code")
                                )
                            ),
                            navlistPanel(
                                tabPanel("Make Dendrogram",
                                         h2("Inputs for Make Dendrogram"),
                                         makeDendrogramInput("mDInputs", "")#,
                                         #uiOutput("makeDendrogramWhichClusters")
                                ),
                                tabPanel("Plot Dendrogram",
                                         downloadButton("downloadDefaultPlotPDMD", label = "DownLoad this Plot"),
                                         plotOutput("imgPlotDendrogram")
                                ),
                                tabPanel("Plot HeatMap",
                                         downloadButton("downloadDefaultPlotPHMD", label = "DownLoad this Plot"),
                                         plotOutput("imgPlotHeatmapMD")
                                )
                            )
                   ),
                   tabPanel("Merge Clusters",
                            fluidRow(
                                column(6,
                                       mergeClustersHelpText()
                                ),
                                column(6,
                                       #textual output of code that is to be run
                                       h3("Code to be run internally:"),
                                       #Action button that allows one to run above code
                                       textOutput("mergeClustersCode")
                                       
                                ),
                                fluidRow(
                                    column(3,actionButton("runMergeClusters", "Run This Code")),
                                    column(3,actionButton("updateDendrogram", "Update dendrogram"))
                                )
                            ),
                            navlistPanel(
                                tabPanel("Dendrogram used for merging",
                                         p("Informative Dendrogram for choosing how to merge cluster inputs:"),
                                         downloadButton("downloadPlotPDMC", label = "DownLoad this Plot"),
                                         plotOutput("imgInitalMergeClusters")
                                ),
                                tabPanel("Set Parameters",
                                         mergeClustersInput("mergeCInputs", "")
                                ),
                                tabPanel("Plot Clusters",
                                         downloadButton("downloadDefaultPlotClustersMergeClusters", label = "DownLoad this Plot"),
                                         plotOutput("imgPlotClustersMergeClusters")
                                ),
                                tabPanel("Plot Heatmap",
                                         downloadButton("downloadDefaultPlotHeatmapMergeClusters", label = "DownLoad this Plot"),
                                         plotOutput("imgPlotHeatmapMergeClusters")
                                ),
                                tabPanel("PCA Plot",
                                         h3("PCA plot feature in development")
                                )
                            )
                   ),
                   navbarMenu("Personalized Plots",
                              tabPanel("plotClusters",
                                       fluidRow(
                                           column(6,
                                                  plotClustersHelpText()
                                           ),
                                           column(6,
                                                  h3("Code to be Run:"),
                                                  textOutput("plotClustersCode"),
                                                  actionButton("runPCCM", "Run Plot Cluster Code")
                                           )
                                       ),
                                       navlistPanel("Plot Clusters",
                                                    tabPanel("Specialized Inputs",
                                                             h3("Specialized Plot Cluster Inputs"),
                                                             uiOutput("plotClustersWhichClusters"),
                                                             plotClustersInput("pCInputs", 
                                                                               "inputs for plot Clusters, cM")
                                                    ),
                                                    tabPanel("Output Plot",
                                                             downloadButton("downloadSpecializedPlotPCCM", label = "DownLoad this Plot"),
                                                             plotOutput("imgPC")
                                                    )
                                       )
                              ),
                              tabPanel("plotCoClustering",
                                       fluidRow(
                                           column(6,
                                                  plotCoClusteringHelpText()
                                           ),
                                           column(6,
                                                  h3("Code to be Run:"),
                                                  textOutput("plotCoClusteringCode"),
                                                  actionButton("runPlotCoClustering", "Run Plot CoClustering Code")
                                           )
                                       ),
                                       navlistPanel(tabPanel("Specialized Inputs",
                                                             plotCoClusteringInput("plotCoClustering", 
                                                                                 "inputs for plotCoClustering")
                                                    ),
                                                    tabPanel("Output Plot",
                                                             downloadButton("downloadSpecializedPlotCoClustering",
                                                                            label = "DownLoad this Plot"),
                                                             plotOutput("imgSpecializedPlotCoClustering")
                                                    )
                                       )
                              ),
                              tabPanel("Plot Dendrogram",
                                       fluidRow(
                                           column(6,
                                                  plotDendrogramHelpText()
                                           ),
                                           column(6,
                                                  h3("Code to be Run:"),
                                                  textOutput("plotDendrogramCode"),
                                                  actionButton("runPlotDendrogram", "Run Plot Dendrogram Code")
                                           )
                                       ),
                                       navlistPanel("Plot Dendrogram",
                                                    tabPanel("Specialized Inputs",
                                                             plotDendrogramInput("plotDendrogram", 
                                                                                 "inputs for plotDendrogram")
                                                    ),
                                                    tabPanel("Output Plot",
                                                             downloadButton("downloadSpecializedPlotDendrogram",
                                                                            label = "DownLoad this Plot"),
                                                             plotOutput("imgSpecializedPlotDendrogram")
                                                    )
                                       )
                              ),
                              tabPanel("Plot Heatmap",
                                       fluidRow(
                                           column(6,
                                                  plotHeatmapHelpText()
                                           ),
                                           column(6,
                                                  h3("Code to be Run:"),
                                                  textOutput("plotHeatmapCode"),
                                                  actionButton("runPlotHeatmap", "Run Plot Heatmap Code")
                                           )
                                       ),
                                       navlistPanel(
                                           tabPanel("Specialized Inputs",
                                                    plotHeatmapInput("plotHeatmap", 
                                                                        "inputs for plotHeatmap")
                                           ),
                                           tabPanel("Output Plot",
                                                    downloadButton("downloadSpecializedPlotHeatmap",
                                                                   label = "DownLoad this Plot"),
                                                    plotOutput("imgSpecializedPlotHeatmap")
                                           )
                                       )
                              ),
                              tabPanel("PCA Plot",
                                       navlistPanel(
                                           tabPanel("Specialized Inputs"),
                                           tabPanel("Output Plot")
                                       )
                              )
                             
                   ),
                   tabPanel("Save Object",
                            saveObjectMessage("saveObject", ""),
                            textOutput("saveObjectMessage")
                   ),
                   tabPanel("What clusters",
                            whatClusters("whatClusters", ""),
                            actionButton("showSummmary", "Show Summary"),
                            tableOutput("cESummary")
                   )
)
)