inst/shinyapp/ui/baseline.R

In gongyh/RamanD2O: RamanD2O: an R/Shiny app designed for the analysis of cellular Ramanome data

# Baseline tab
tabItem(
  tabName = "bl",
  h2("Baseline"),
  br(),
  fluidRow(
    box(
      title = "Settings", status = "info",
      solidHeader = TRUE, collapsible = FALSE,
      column(
        12,
        fluidRow(
          column(6, uiOutput("hs_select_for_baseline")),
          column(6,
                 withBusyIndicatorUI(actionButton("baseline",
                                                  "Baseline",
                                                  class = "btn-success")),
                 class = "top25")
        ),
        fluidRow(
          column(6, selectInput("select_baseline", "Baseline method",
            choices = c("polyfit", "als"), selected = "als"
          )),
          # two baseline method
          conditionalPanel(
            condition = "input.select_baseline == 'polyfit'",
            conditionalPanel(
              condition = "input.polyfit_custom == false",
              column(3, numericInput("polyfit_order", "Order",
                                     1, min = 0, max = 15, step = 1))
            ),
            conditionalPanel(
              condition = "input.polyfit_custom == true",
              column(1, actionButton("polyfit_custom_plus", "",
                                     icon = icon("plus")), class = "top25"),
              column(1, actionButton("polyfit_custom_minus", "",
                                     icon = icon("minus")), class = "top25"),
              column(1)
            ),
            column(3, checkboxInput("polyfit_custom", "Custom range",
                                    value = FALSE), class = "top25")
          ),
          conditionalPanel(
            condition = "input.select_baseline == 'als'"
          )
        ),
        conditionalPanel(
          condition = paste0("input.polyfit_custom ==",
                             " true & input.select_baseline == 'polyfit'"),
          uiOutput("polyfit_custom_multi")
        ),
        radioButtons("select_negative", "How to handle negative values",
          choices = c(
            "Set to zero" = "zero",
            "Pull up" = "up",
            "Keep intact" = "keep"
          ),
          selected = "up", inline = TRUE
        )
      )
    ),
    box(
      title = "Notes", status = "info", solidHeader = TRUE, collapsible = FALSE,
      column(
        12,
        p("1. Choose the target spectra collection
          from the dropdown selector."),
        p("2. Choose baseline method, currently support polyfit and ALS."),
        p("3. Negative values can be set to zero, or pull the
          whole spectrum up, or leave as it is."),
        p("4. Row of the spectra table (bottom left) can be selected
          to visual the spectrum (bottom right).")
      )
    )
  ),
  fluidRow(
    box(
      title = "Spectra Table", status = "warning",
      solidHeader = TRUE, collapsible = TRUE,
      column(12,
             DTOutput("baselined_table", height = "400px") %>% withSpinner())
    ),
    box(
      title = "Spectra Figure", status = "warning",
      solidHeader = TRUE, collapsible = TRUE,
      column(12, plotlyOutput("after_baseline_plot") %>% withSpinner())
    )
  )
)