inst/shiny/ui_09_3_celdaWorkflow.R

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

# User Interface for Celda Workflow ---
shinyPanelCelda <- fluidPage(
    h1("Celda"),
    h5(tags$a(href = paste0(docs.artPath, "ui_celda_curated_workflow.html"),
              "(help)", target = "_blank")),
    inlineCSS(list(".panel-danger>.panel-heading" = "background-color:#dcdcdc; color:#000000", ".panel-primary>.panel-heading" = "background-color:#f5f5f5; color:#000000; border-color:#dddddd", ".panel-primary" = "border-color:#dddddd;", ".panel-primary>.panel-heading+.panel-collapse>.panel-body" = "border-color:#dddddd;")),
    bsCollapse(
        id = "CeldaUI", 
        open = "Data Input",
        bsCollapsePanel(
            "Identify Number of Feature Modules",
            fluidRow(
                column(
                    4,
                    panel(
                        selectInput("celdaassayselect", "Choose an Assay:",
                                    choices = c()),
                        selectInput("celdafeatureselect", "Choose Feature Selection Method:",
                                    choices = c("None", "SeuratFindHVG", "Scran_modelGeneVar")),
                        conditionalPanel("input.celdafeatureselect == 'SeuratFindHVG'",
                                         selectInput("celdaseurathvgmethod", "Select HVG method:",
                                                     choices = c("vst", "dispersion", "mean.var.plot"))),
                        conditionalPanel("input.celdafeatureselect != 'None'",
                                         numericInput("celdafeaturenum",
                                                      "Select number of variable features:", min = 1, max = 5000, value = 2500)),
                        numericInput("celdarowcountsmin",
                                     "Keep features with this many counts:", value = 3),
                        numericInput("celdacolcountsmin",
                                     "In at least this many cells:", value = 3),
                        numericInput("celdaLinit", "Select Number of Initial Feature Modules:", min = 1, max = 25, value = 10),
                        numericInput("celdaLmax", "Select Number of Maximum Feature Modules:", min = 15, max = 200, value = 100),
                        actionButton("celdamodsplit", "Recursive Module Split"),
                        hidden(
                            numericInput("celdaLselect", "Select Number of Feature Modules:", min = 1, max = 100, value = 25),
                            actionButton("celdaLbtn", "Select Number of Modules")
                        )
                    )
                ),
                column(
                    8,
                    fluidRow(
                        column(
                            12,
                            hidden(
                                tags$div(class = "celda_modsplit_plots", tabsetPanel(id = "celdaModsplitTabset", type = "tabs")
                                )
                            )
                        )
                    )
                )
            ),
            style = "primary"
        ),
        
        bsCollapsePanel(
            "Identify Number of Cell Clusters",
            fluidRow(
                column(
                    4,
                    panel(
                        numericInput("celdaKinit", "Select Number of Initial Cell Modules:", min = 1, max = 10, value = 5),
                        numericInput("celdaKmax", "Select Number of Maximum Cell Modules:", min = 15, max = 40, value = 25),
                        actionButton("celdacellsplit", "Recursive Cell Split"),
                        hidden(
                            numericInput("celdaKselect", "Select Number of Cell Clusters:", min = 2, max = 20, value = 10),
                            actionButton("celdaKbtn", "Select Number of Clusters")
                        )
                    )
                ),
                column(
                    8,
                    fluidRow(
                        column(
                            12,
                            hidden(
                                tags$div(
                                    class = "celda_cellsplit_plots",
                                    fluidRow(
                                        tabsetPanel(
                                            tabPanel("Rate of perplexity change",
                                                     panel(
                                                         plotlyOutput(outputId = "plot_cellsplit_perpdiff", height = "auto")
                                                     )),
                                            tabPanel("Perplexity Plot",
                                                     panel(
                                                         plotlyOutput(outputId = "plot_cellsplit_perp", height = "auto")
                                                     )),
                                            tabPanel("Preliminary UMAP Plots",
                                                     uiOutput("celdaKplots"))
                                        )
                                    )
                                )
                            )
                         )
                       )
                      )
                    ),
                    style = "primary"
                ),
                
                bsCollapsePanel(
                    "Visualization",
                    tabsetPanel(
                        tabPanel(
                            "Embeddings",
                            fluidRow(
                                column(
                                    4,
                                    panel(
                                        radioButtons("celdaPlot", "Plot Type:", c("UMAP", "TSNE")),
                                        conditionalPanel(
                                            condition = "input.celdaPlot == 'UMAP'",
                                            
                                            numericInput("celdaUMAPmaxCells",
                                                         label =
                                                             "Max.cells: Maximum number of cells to plot",
                                                         value = 25000,
                                                         min = 1,
                                                         step = 1),
                                            numericInput("celdaUMAPminClusterSize",
                                                         label =
                                                             "Min.cluster.size: Do not subsample cell
                              clusters below this threshold",
                                                         value = 100,
                                                         min = 1,
                                                         step = 1),
                                            numericInput("celdaUMAPSeed",
                                                         label =
                                                             "Seed: ",
                                                         value = 12345),
                                            numericInput("celdaUMAPmindist",
                                                         label =
                                                             "Min.dist: Effective minimum distance
                                between embedded points",
                                                         value = 0.75),
                                            numericInput("celdaUMAPspread",
                                                         label =
                                                             "Spread: ",
                                                         value = 1),
                                            numericInput("celdaUMAPnn",
                                                         label =
                                                             "nNeighbors: ",
                                                         value = 30),
                                            
                                            actionButton("CeldaUmap", "Run UMAP")
                                            
                                            
                                        ),
                                        
                                        conditionalPanel(
                                            condition = "input.celdaPlot == 'TSNE'",
                                            numericInput("celdatSNEmaxCells",
                                                         label =
                                                             "Max.cells: Maximum number of cells to
                                plot",
                                                         value = 25000,
                                                         min = 1,
                                                         step = 1),
                                            numericInput("celdatSNEminClusterSize",
                                                         label =
                                                             "Min.cluster.size: Do not subsample cell
                              clusters below this threshold",
                                                         value = 100,
                                                         min = 1,
                                                         step = 1),
                                            numericInput("celdatSNEPerplexity",
                                                         label =
                                                             "Perplexity: ",
                                                         value = 20),
                                            numericInput("celdatSNEmaxIter",
                                                         label =
                                                             "Max.iter: Maximum number of iterations in
                              tSNE generation",
                                                         value = 2500),
                                            numericInput("celdatSNESeed",
                                                         label =
                                                             "Seed: ",
                                                         value = 12345),
                                            actionButton("CeldaTsne", "Run tSNE")
                                        )
                                    )
                                ),
                                column(
                                    8,
                                    panel(
                                        conditionalPanel(
                                            condition = "input.celdaPlot == 'UMAP'",
                                            plotlyOutput("celdaumapplot", height = "auto")
                                            
                                        ),
                                        conditionalPanel(
                                            condition = "input.celdaPlot == 'TSNE'",
                                            plotlyOutput("celdatsneplot", height = "auto")
                                        )
                                    )
                                )
                            )
                        ),
                        
                        #tabPanel("Heatmap",
                        #        fluidRow(
                        #           panel(
                        #              plotOutput("celdaheatmapplt")
                        #         )
                        #     )
                        #),
                        tabPanel(
                            "Module Analysis",
                            fluidRow(
                                column(
                                    4,
                                    panel(
                                        numericInput(inputId = "celdamodheatmapnum",
                                                     label = "Select module to display on heatmap:", value = 10, step = 1),
                                        numericInput(inputId = "celdamodheatmaptopcells",
                                                     label = "Select number of cells to display on heatmap:", value = 100),
                                        
                                        actionButton("celdamodheatmapbtn", "Plot Module Heatmap")
                                    )
                                ),
                                column(
                                    8,
                                    panel(
                                        plotOutput(outputId = "celdamodheatmapplt") %>% withSpinner(size = 3, color = "#0dc5c1", type = 8),
                                        plotOutput(outputId = "celdamodprobplt") %>% withSpinner(size = 3, color = "#0dc5c1", type = 8)
                                        
                                    )
                                )
                            )
                        ),
                        tabPanel("Probablity Map",
                                 fluidRow(
                                     panel(
                                         plotOutput("celdaprobmapplt")
                                     )
                                 )
                        )
                    ),
                    style = "primary"
                )
            ),
            nonLinearWorkflowUI(id = "nlw-celda")
        )