inst/app/contributions/DE_DataExploration/ui.R

In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

# DE DataExporation ui.R

suppressMessages(library(magrittr))

# list of menu Items
menuList <- list(
  shinydashboard::menuItem("Data Exploration",
                           # id="dataExplorationID",
                           tabName = "expore", icon = icon("wpexplorer"), startExpanded = FALSE,
                           shinydashboard::menuSubItem("Expression", tabName = "DE_expression"),
                           shinydashboard::menuSubItem("Panel plot", tabName = "DE_panelPlot"),
                           shinydashboard::menuSubItem("Panel plot factorials", tabName = "DE_panelPlotFact")
                           # shinydashboard::menuSubItem("Sorted plot", tabName = "DE_sortedPl")
  )
)

source(paste0(packagePath, .Platform$file.sep, "modulesUI.R"), local = TRUE)
# list of tab Items
tabList <- list(
  # DE_expression ----
  expressionTab = shinydashboard::tabItem(
    "DE_expression",
    shinydashboardPlus::box(
      title = "Expression overview", solidHeader = TRUE, width = 12, status = "primary",
      fluidRow(div(tags$h3("Expression based on subset of cells"), align = "center")),
      tags$p("Similar to Co-expression - selection, but with a focus on subsets of cells and genes."),
      tags$p("Limit the cells to visualize by cluster or any other factorial."),
      tags$p("Visualize specific genes in 3D and over the current clustering (not changeable)."),
      tags$p("Projections will be not be effected by this sub selection."),
      br(),
      fluidRow(
        column( offset = 3,
                width = 12, 
                cellSelectionUI("DE_Exp_dataInput")
        )
      ),
      br(),
      fluidRow(
        column(
          width = 12,
          clusterUI("DE_expclusters")
        )
      ),
      br(),
      fluidRow(
        column( offset = 1,
                width = 10, 
                sc_textInput("DE_gene_id", "Enter gene(s) of interest", value = defaultValue("DE_gene_id", defaultValueSingleGene))
        )
      ),
      br(),
      fluidRow(
        column(
          width = 3,
          sc_selectInput("DE_expclusters_x",
                         label = "X",
                         choices = c(defaultValue("DE_expclusters_x", "tsne1"), "tsne2", "tsne3"),
                         selected = defaultValue("DE_expclusters_x", "tsne1")
          )
        ),
        column(
          width = 3,
          sc_selectInput("DE_expclusters_y",
                         label = "Y",
                         choices = c(defaultValue("DE_expclusters_y", "tsne1"), "tsne2", "tsne3"),
                         selected = defaultValue("DE_expclusters_y", "tsne2")
          )
        ),
        column(
          width = 3,
          sc_selectInput("DE_expclusters_z",
                         label = "Z",
                         choices = c(defaultValue("DE_expclusters_z", "tsne1"), "tsne2", "tsne3"),
                         selected = defaultValue("DE_expclusters_z", "tsne3")
          )
        )
      ),
      fluidRow(
        column(
          width = 12,
          plotly::plotlyOutput("DE_tsne_plt") %>% jqui_resizable()
        )
      ),
      br(),
      fluidRow(column(
        width = 3,
        sc_selectInput("DE_gene_vio_x",
                       label = "X",
                       choices = defaultValue("DE_gene_vio_x", "sampleNames"),
                       selected = defaultValue("DE_gene_vio_x", "sampleNames")
        )
      )),
      br(),
      fluidRow(
        column(
          width = 12,
          plotOutput("DE_gene_vio_plot") %>% jqui_resizable()
        )
      )
    )
  ),
  # DE_panelPlot ----
  DE_panelPlotTab = shinydashboard::tabItem(
    "DE_panelPlot",
    shinydashboardPlus::box(
      title = "Panel Plot", solidHeader = TRUE, width = 12, status = "primary",
      fluidRow(
        column(
          width = 12,
          
          footer = tags$ul(
            tags$li(
              strong("Panel plot"),
              ":Select a cluster. Enter",
              strong("ONE"),
              "or",
              strong("MULTIPLE"),
              "gene ids to visualize expression in all clusters"
            ),
            tags$li("If the x-axis is a categorical value and the y-axis is UMI.counts the y-axis related to the count for that gene. Otherwise, all genes are used. Only in this case the check box 'same scale' is used.")
          )
        )
      ),
      fluidRow(
        column(
          width = 12, offset = 1,
          actionButton("updatePanelPlot", "apply changes", width = "80%")
        )
      ),
      br(),
      cellSelectionUI("DE_PanelPlotCellSelection"),
      shinydashboardPlus::box(
        width = 6, 
        fluidRow(
          column(
            width = 6,
            sc_selectInput("DE_dim_x",
                           label = "X",
                           choices = c(defaultValue("DE_dim_x", "tsne1"), "tsne2", "tsne3"),
                           selected = defaultValue("DE_dim_x", "tsne1")
            )
          ),
          column(
            width = 6,
            sc_selectInput("DE_dim_y",
                           label = "Y",
                           choices = c("tsne1", defaultValue("DE_dim_y", "tsne2"), "tsne3"),
                           selected = defaultValue("DE_dim_y", "tsne2")
            )
          )
        ),
        fluidRow(
          align = 'right',
          column(
            width = 3,
            sc_checkboxInput("DE_panelplotSameScale", "same scale", value = defaultValue("DE_panelplotSameScale", TRUE))
          ), 
          column(
            width = 3,
            sc_checkboxInput("DE_panelplotPvalue", "apply t-test", value = defaultValue("DE_panelplotPvalue", FALSE))
          ), checkbsTT("DE_panelplotPvalue"),
          column(
            width = 6,
            sc_selectInput("DE_nCol",
                           label = "number of columns for plot",
                           choices = c(1:10),
                           selected = defaultValue("DE_nCol", 4)
            )
          )
        )
      ),
      fluidRow(
        column(
          width = 12,
          sc_textInput("DE_panelplotids", "Comma separated gene names", value = defaultValue("DE_panelplotids", defaultValueMultiGenes))
        )
      ),
      fluidRow(column(
        12,
        plotOutput("DE_panelPlot") %>% jqui_resizable()
      )),
      br(),
      actionButton("save2HistPanel", "save to history")
    )
  ),
  # DE_panelPlot ----
  DE_panelPlotTabFact = shinydashboard::tabItem(
    "DE_panelPlotFact",
    shinydashboardPlus::box(
      title = "Panel Plot Factorial", solidHeader = TRUE, width = 12, status = "primary",
      fluidRow(
        column(
          width = 12,
          
          footer = tags$ul(
            tags$li(
              strong("Panel plot for factorials"),
              ":Select a cluster. Enter",
              strong("ONE"),
              "or",
              strong("MULTIPLE"),
              "gene ids to visualize expression in all clusters"
            ),
            tags$li("If the x-axis is a categorical value and the y-axis is UMI.counts the y-axis related to the count for that gene. Otherwise, all genes are used. Only in this case the check box 'same scale' is used.")
          )
        )
      ),
      fluidRow(
        column(
          width = 12, offset = 1,
          actionButton("updatePanelPlotFact", "apply changes", width = "80%")
        )
      ),
      br(),
      cellSelectionUI("DE_PanelPlotFactCellSelection"),
      shinydashboardPlus::box(
        width = 6, 
        fluidRow(
          column(
            width = 4,
            sc_selectInput("DE_pFact_dim_x",
                           label = "X",
                           choices = c(defaultValue("DE_pFact_dim_x", "tsne1"), "tsne2", "tsne3"),
                           selected = defaultValue("DE_pFact_dim_x", "tsne1")
            )
          ),
          column(
            width = 4,
            sc_selectInput("DE_pFact_dim_y",
                           label = "Y",
                           choices = c("tsne1", defaultValue("DE_pFact_dim_y", "tsne2"), "tsne3"),
                           selected = defaultValue("DE_pFact_dim_y", "tsne2")
            )
          ),
          column(
            width = 4,
            sc_selectInput("DE_pFact_dim_col",
                           label = "color",
                           choices = c("tsne1", defaultValue("DE_pFact_dim_col", "tsne2"), "tsne3"),
                           selected = defaultValue("DE_pFact_dim_col", "tsne2")
            )
          )
        ),
        fluidRow(
          align = 'right',
          column(
            width = 3,
            sc_checkboxInput("DE_panelplotFactSameScale", "same scale", value = defaultValue("DE_panelplotFactSameScale", TRUE))
          ), 
          column(
            width = 3,
            sc_checkboxInput("DE_panelplotFactPvalue", "apply t-test", value = defaultValue("DE_panelplotFactPvalue", FALSE))
          ), checkbsTT("DE_panelplotPvalue"),
          column(
            width = 6,
            sc_selectInput("DE_pFactnCol",
                           label = "number of columns for plot",
                           choices = c(1:10),
                           selected = defaultValue("DE_nCol", 4)
            )
          )
        )
      ),
      fluidRow(
        column(
          width = 12,
          sc_selectInput("DE_pFactIds",
                         label = "Factorials to plot individually",
                         choices = defaultValue("DE_pFactIds", "dbCluster"),
                         selected = defaultValue("DE_pFactIds", "dbCluster"), 
                         multiple = F
                         )
        )
      ),
      fluidRow(column(
        12,
        plotOutput("DE_panelPlotFact") %>% jqui_resizable()
      )),
      br(),
      actionButton("save2HistPanelFact", "save to history")
    )
  ),
  # DE_scaterQC ----
  DE_scaterQCTab = shinydashboard::tabItem(
    "DE_scaterQC",
    shinydashboardPlus::box(
      title = "Quality control plot from the scater package", solidHeader = TRUE, 
      width = 12, status = "primary", height = "1627px",
      fluidRow(
        column(10, offset = 0,
               actionButton("runScater", "apply changes", width = "40%"),
               actionButton("stopScater", "stop calculations", width = "40%", class = "btn-danger")
        ),
        column(width = 2,
               sc_numericInput("maxMemory", "max memory to be used in GB",
                               min = 1, max = 2000, step = 1, value = 2))
      ),
      br(),
      fluidRow(
        column(
          12,
          offset = 0,
          div(style = "height:672px;",
              imageOutput("DE_scaterQC")
          ) # PNG output with temp file
        )
      ),
      br(),
      actionButton("save2HistScater", "save to history")
    )
  )
)