inst/shiny/ui_08_3_heatmap.R

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

shinyPanelHeatmap <- fluidPage(
  tags$div(
    class = "container",
    h1("Heatmap"),
    p("Generic heatmap plotting panel for customized figure.",
      style = "color:grey;"),
    tags$a(href = "https://www.sctk.science/articles/tab08_heatmap",
           "(help)", target = "_blank"),
    panel(
      fluidRow(
        div(style="display:inline-block;vertical-align:top;width:120px;margin-left:20px;",
            h4("Assay to Plot")),
        div(style="display:inline-block;vertical-align:bottom;width:120px;margin-top:5px;",
            selectInput("hmAssay", NULL, currassays))
      ),
      fluidRow(
        div(style="display:inline-block;vertical-align:top;width:180px;margin-left:20px;",
            h4("Import from analysis")),
        div(style="display:inline-block;vertical-align:bottom;width:150px;margin-top:5px;",
            selectInput("hmImport", NULL,
                        c("None",
                          "Differential Expression",
                          "Find Marker"),
                        selected = "None")),
        div(style="display:inline-block;vertical-align:bottom;width:50px;margin-left:8px;margin-bottom:15px;",
            actionButton("hmImportRun", "Import"))
      ),
      conditionalPanel(
        condition = "input.hmImport == 'Differential Expression'",
        uiOutput("hmImpDEGUI")
      ),
      hr(),
      # Subset ####
      h3("Cell/Feature Subsetting"),
      p("Only to plot cells/features of interests", style = "color:grey;"),
      tabsetPanel(
        id = 'hmSubsetTSP',
        tabPanel(
          title = "Cell", value = 'hmSubsetCellTP',
          tagList(
            uiOutput('hmCellColUI'),
            DT::dataTableOutput("hmCellColTable"),
            actionButton('hmCellColTable_addAll', "Add all filtered"),
            actionButton('hmCellColTable_clear', "Clear selection"),
          )
        ),
        tabPanel(
          title = "Feature", value = 'hmSubsetGeneTP',
          tagList(
            uiOutput('hmGeneColUI'),
            DT::dataTableOutput("hmGeneColTable"),
            actionButton('hmGeneColTable_addAll', "Add all filtered"),
            actionButton('hmGeneColTable_clear', "Clear selection"),
          )
        ),
        tabPanel(
          title = "Manual Enter", value = 'hmSubsetManualTP',
          fluidRow(
            column(
              width = 6,
              selectInput("hmCellTextBy", "Match input cell identifiers by:",
                          c("Row Names", clusterChoice), selected = "Row Names"),
              checkboxInput('hmCellTextEM', "Exact Match", value = TRUE),
              checkboxInput('hmCellTextFM', "First Match", value = TRUE),
              textAreaInput(
                inputId = 'hmCellText',
                label = "Enter Cell Identifiers",
                placeholder = "One cell per line, with no symbol separator."
              ),
              uiOutput('hmCellNEnteredUI'),
              actionButton("hmCellAddFromText", "Add")
            ),
            column(
              width = 6,
              selectInput("hmGeneTextBy", "Match input feature identifiers by:",
                          c("Row Names", featureChoice), selected = "Row Names"),
              checkboxInput('hmGeneTextEM', "Exact Match", value = TRUE),
              checkboxInput('hmGeneTextFM', "First Match", value = TRUE),
              textAreaInput(
                inputId = 'hmGeneText',
                label = "Enter Feature Identifiers",
                placeholder = "One Feature per line, with no symbol separator."
              ),
              uiOutput('hmGeneNEnteredUI'),
              actionButton("hmGeneAddFromText", "Add")
            )
          )
        )
      ),
      uiOutput("hmCellSumUI"),
      uiOutput("hmGeneSumUI"),
      hr(),
      # Annotation ####
      h3("Annotation Setting"),
      p("Stick additional information at sides of the plot",
        style = "color:grey;"),
      tabsetPanel(
        id = 'hmAnnTSP',
        tabPanel(
          title = "Cell", value = 'hmAnnCellTP',
          uiOutput('hmCellAnnUI'),
          uiOutput('hmCellAnnAssUI')
        ),
        tabPanel(
          title = "Feature", value = 'hmAnnGeneTP',
          uiOutput('hmGeneAnnUI'),
          uiOutput('hmGeneAnnAssUI')
        )
      ),
      hr(),
      # Others ####
      h3("Heatmap Setting"),
      p("Settings for split, label, dendrogram, color scheme and etc.",
        style = "color:grey;"),
      panel(
        fluidRow(
          column(
            width = 6,
            uiOutput('hmColSplitUI'),
            checkboxGroupInput('hmAddLabel', "Add cell/feature labels",
                               choiceNames = c('cells', 'features'),
                               inline = TRUE, choiceValues = c(1, 2)),
            conditionalPanel(
              condition = "input.hmAddLabel.includes('1')",
              selectInput('hmAddCellLabel', "Add cell labels from",
                          c("Default cell IDs", clusterChoice),
                          selected = "Default cell IDs")
            ),
            conditionalPanel(
              condition = "input.hmAddLabel.includes('2')",
              selectInput('hmAddGeneLabel', "Add feature labels from",
                          c("Default feature IDs", featureChoice),
                          selected = "Default feature IDs")
            ),
            uiOutput('hmTrimUI')
          ),
          column(
            width = 6,
            uiOutput('hmRowSplitUI'),
            checkboxGroupInput('hmShowDendro', "Show dendrograms for",
                               choiceNames = c('cells', 'features'),
                               inline = TRUE, choiceValues = c(1, 2),
                               selected = c(1, 2)),
            checkboxInput("hmScale", "Z-Score Scale", value = TRUE)
          )
        ),
        h4("Color Scheme"),
        selectizeInput(
          inputId = 'hmCSPalette',
          label = "Choose from preset:",
          choices = NULL,
        ),
        fluidRow(
          column(
            width = 4,
            colourpicker::colourInput('hmCSLow', 'Low color',value = 'blue')
          ),
          column(
            width = 4,
            colourpicker::colourInput('hmCSMedium', 'Medium color',value = 'white')
          ),
          column(
            width = 4,
            colourpicker::colourInput('hmCSHigh', 'High color',value = 'red')
          )
        )
      ),
      hr(),
      withBusyIndicatorUI(actionButton("plotHeatmap", "Plot Heatmap")),
      div(
        style = 'height:800px;',
        plotOutput("Heatmap")
      )
    )
  )
)