R/maintabs.R

In LCMSQA: Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment

maintabs_ui <- function(fdata, standard_skip = FALSE) {
  tabsetPanel(
    id = "tabs",
    tabPanel(
      "Total Ion Current",
      br(),
      pickerInput(
        "tic_files", "Files",
        choices = unique(as.character(fdata$file)),
        selected = unique(as.character(fdata$file)),
        multiple = TRUE, options = list(`actions-box` = TRUE)
      ),
      splitLayout(
        checkboxInput("collapse", "Collapse"),
        checkboxInput("bpc", "Show Base Peak Chromatogram"),
        cellWidths = 300,
        cellArgs = list(style = "padding-left: 10px")
      ),
      withSpinner(plotlyOutput("tic"))
    ),
    tabPanel(
      "Mass Spectrum",
      br(),
      h4("Please click a data point in the chromatogram"),
      br(),
      fluidRow(
        selectizeInput(
          "massspec_file", "File", choices = unique(as.character(fdata$file)),
          selected = unique(as.character(fdata$file))[1]
        ),
        selectizeInput(
          "yaxis", "Spectrum Y-axis",
          choices = c("Relative Abundance", "Absolute Intensity"),
          selected = "Relative Abundance"
        )
      ),
      h5("Chromatogram", style = "color:skyblue"),
      uiOutput("masschrom_slider"),
      withSpinner(plotlyOutput("masschrom")),
      h5("Mass spectrum", style = "color:lightcoral"),
      br(),
      withSpinner(plotlyOutput("massspec"))
    ),
    tabPanel(
      "Extracted Ion Chromatogram",
      br(),
      pickerInput(
        "xic_files", "Files",
        choices = unique(as.character(fdata$file)),
        selected = unique(as.character(fdata$file)),
        multiple = TRUE, options = list(`actions-box` = TRUE)
      ),
      withSpinner(plotlyOutput("xic"))
    ),
    tabPanel(
      "Feature Detection",
      br(),
      h4("Feature Definitions"),
      br(),
      splitLayout(
        DTOutput("feature_tbl"),
        uiOutput("feature_fig"),
        cellArgs = list(style = "padding: 10px")
      ),
      uiOutput("peak_tbl"),
      uiOutput("peak_fig")
    ),
    if (!standard_skip) {
      tabPanel(
        "Standard Information",
        br(),
        DTOutput("standard_tbl")
      )
    }
  )
}