R/component_levels_addin.R

In akoyabio/phenoptrReports: Create reports using Phenoptics data

# This is an RStudio Addin that provides a GUI frontend
# to component_levels_report.

#' Generate a component levels report for a selected export folder.
#'
#' `addin_50_component_levels` opens a GUI that allows you to select
#' an export folder containing component data files for multiplex samples.
#' A component levels report is created for the samples and saved in
#' the export directory.
#' @export
addin_50_component_levels = function() {
  intro <- shiny::tagList(shiny::p(
    'This app reads component data files for multiplex samples',
    'and creates a component levels report showing signal levels',
    'for bright and dark pixels in each sample.'
  ))

  default_quantiles = 0.999

  ui <- miniUI::miniPage(
    shiny::tags$head(
      shiny::tags$style(shiny::HTML("
      .well {
        padding-top: 10px;
        padding-bottom: 5px;
      }
      h3 { margin-top: 10px; }
    "))),
    miniUI::gadgetTitleBar("Component levels report",
      right=miniUI::miniTitleBarButton('done', 'Create Report', primary=TRUE)),

    miniUI::miniContentPanel(
      intro,

      shiny::wellPanel(
        shiny::h3('Select Export directory'),
        'Click the "Browse" button to select a directory',
        'containing component data files for multiplex samples.',
        shiny::br(), shiny::br(),

        shiny::actionButton('browse', 'Browse...'),
        shiny::br(), shiny::br(),
        shiny::textOutput('export_dir')
      ),

      shiny::wellPanel(
        shiny::h3('Report options'),
        'Enter the quantiles to show, separated by comma or space.',
        shiny::textInput('quantiles', '', value=default_quantiles),
        shiny::checkboxInput('export_data', 'Export data from pairs plots')
      ),

      shiny::h4(shiny::textOutput('error'), style='color: maroon')
    )
  )

  server <- function(input, output, session) {
    export_dir = shiny::reactiveVal()
    quantiles = shiny::reactiveVal(default_quantiles)

    # Handle the browse button by selecting a folder
    shiny::observeEvent(input$browse, {
      shiny::req(input$browse)
      export_dir(phenoptrReports::choose_directory(
        caption='Select an export folder'
      ))

      output$export_dir = shiny::renderText(export_dir())
      set_error_text()
    })

    # Handle the quantiles text box
    shiny::observeEvent(input$quantiles, {
      shiny::req(input$quantiles)

      # Parse out comma/space delimited numbers
      quants = phenoptrReports:::parse_comma_space_values(input$quantiles)
      if (length(quants) > 0 && !anyNA(quants)) {
        quantiles(quants)
      } else {
        quantiles(NULL)
      }
    })

    # Handle the done button by processing files or showing an error
    shiny::observeEvent(input$done, {
      error_text = get_error_text()

      if (error_text == '') {
        shiny::showNotification('Processing, please wait!', duration=NULL,
                                closeButton=FALSE, type='message')

        # Log the command to the console for convenient debugging
        cmd = stringr::str_glue(
          'phenoptrReports::component_levels_report(\n',
          '  export_path="{export_dir()}",\n',
          '  quantiles={deparse(quantiles())},\n',
          '  export_data={input$export_data})')
        message('Running command\n', cmd)
        phenoptrReports::component_levels_report(export_dir(), quantiles(),
                                                 input$export_data)
        shiny::stopApp()
      } else {
        shiny::showNotification(error_text, type='message')
      }
    })

    # Handle the cancel button by quitting
    shiny::observeEvent(input$cancel, {
      shiny::stopApp()
    })

    # Set error message in response to user input
    # For some reason this doesn't work as a reactive so just make
    # it a function and call as needed
    set_error_text = function() {
      output$error = shiny::renderText(get_error_text())
    }

    get_error_text = function() {
      if (is.null(export_dir())) {
        'Please select an output directory.'
      } else if (length(list.files(export_dir(), pattern='component_data.tif'))==0) {
        'Please select an export directory containing component data files.'
      } else if (!shiny::isTruthy(quantiles())) {
        'Quantiles must be numeric and separated by space or comma.'
      } else ''
    }

    # Initialize
    output$error = shiny::renderText('Please select an output directory.')
  }

  # Run the gadget in a dialog
  viewer <- shiny::dialogViewer('Create component levels report')
  shiny::runGadget(ui, server, viewer = viewer)
}