inst/shiny/ui_01_columnAnnotation.R

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

shinyPanelColumnAnnotation <- fluidPage(
  includeCSS('styles.CSS'),
  h5(tags$a(href = paste0(docs.artPath, "import_annotation.html"),
            "(help)", target = "_blank")),
  panel(
    heading = "Options for editing and importing Cell Annotation data",
    tabsetPanel(
      tabPanel(
        "Bins",
        panel(
          uiOutput("inputSelectAttribute_colData"),
          uiOutput("inputSelectAttributeValue_colData"),
          textInput("inputCriteria_colData", "criteria parameter"),
          selectInput("inputOperator_colData", "select comparison",
                      choices = c("=",">","<",">=","<=")),
          textInput("inputBinName_colData", "bin name"),
          actionButton("buttonConfirmBin_colData", "Confirm Bin")
        )
      ),
      tabPanel(
        "Merge Columns",
        panel(
          uiOutput("inputSelectAttributeMerge1_colData"),
          uiOutput("inputSelectAttributeMerge2_colData"),
          textInput("inputSelectSeparatorMerge_colData",
                    "add separator between merged values", value = "_"),
          actionButton("buttonConfirmMerge_colData","Confirm Merge")
        )
      ),
      tabPanel(
        "Magic Fill",
        panel(
          uiOutput("inputSelectAttributeFill1_colData"),
          uiOutput("inputSelectAttributeFill2_colData"),
          uiOutput("inputSelectAttributeFillvalue_colData"),
          textInput("inputReplaceText_colData", "new value"),
          actionButton("buttonConfirmFill_colData","Confirm Fill")
        )
      ),
      tabPanel(
        "Clean",
        panel(
          uiOutput("inputSelectAttributeClean_colData"),
          selectInput("inputRemovalOperation_colData",
                      "select removal criteria",
                      choices = c("remove alphabets", "remove digits",
                                  "remove spaces","remove symbols")),
          actionButton("buttonConfirmClean_colData","Confirm Clean")
        )
      ),
      tabPanel(
        "Add Column",
        panel(
          textInput("inputEmptyColumnName_colData", "enter new empty column name"),
          textInput("inputDefaultValueAddColumn_colData", "default value to fill"),
          actionButton("buttonConfirmEmptyColumnName_colData","Create Column")
        )
      ),
      tabPanel(
        "Delete Column",
        panel(
          uiOutput("inputSelectAttributeDelete_colData"),
          actionButton("buttonConfirmDeleteColumn_colData", "Delete")
        )
      ),
      tabPanel(
        "Import Cell Annotation from File",
        panel(
          radioButtons(
            inputId = "editorChoiceRadio_colData",
            label = "Select source for column annotation:",
            choices = c("Replace Cell Annotations" = "replace",
                        "Add to existing Cell Annotations" = "concatenate"),
            selected = "concatenate"
          ),
          h6("You can either replace the existing colData or you can add/merge the new colData with the existing one."),
          conditionalPanel(
            condition = "input.editorChoiceRadio_colData == 'concatenate'",
            HTML("<h6><span style='color:red'> Warning:</span> Adding to existing colData will override the columns with same names! </h6>")
          ),
          fileInput('uploadFile_colData', 'Choose file to upload',
                    accept = c(
                      'text/csv',
                      'text/comma-separated-values',
                      '.csv'
                    )),
          actionButton(inputId = "importDataButton_colData",
                       label = "Import")
        )
      )
    ),
    br(),
    uiOutput("changesWarning_colData"),
    fluidRow(
      column(
        6,
        panel(
          "Save",
          h6("Changes made to the annotation must be saved before they can be used in other modules of the toolkit:"),
          actionButton("buttonSave_colData","Save",icon = icon("save"))
        )
      ),
      column(
        6,
        panel(
          "Reset",
          h6("Reset annotation to point after changes were last saved:"),
          actionButton("buttonRestore_colData",
                       "Reset", icon = icon("sync"))
        )
      )
    )
  ),
  panel(heading = "Table of Cell Annotations",
        uiOutput("outputColumnAnnotationTable_colData")
  )
)