FreesearchR/inst/apps/data_analysis_modules/ui.R

library(shiny)
library(bslib)
library(datamods)
library(shinyWidgets)
library(DT)
requireNamespace("gt")

# ns <- NS(id)

ui_elements <- list(
  ##############################################################################
  #########
  #########  Import panel
  #########
  ##############################################################################
  "import" = bslib::nav_panel(
    title = "Import",
    shiny::fluidRow(
      column(
        width = 6,
        shiny::h4("Choose your data source"),
        # shiny::conditionalPanel(
        #   condition = "output.has_input=='yes'",
        #   # Input: Select a file ----
        #   shiny::helpText("Analyses are performed on provided data")
        # ),
        # shiny::conditionalPanel(
        #   condition = "output.has_input=='no'",
        # Input: Select a file ----
        shinyWidgets::radioGroupButtons(
          inputId = "source",
          # label = "Choice: ",
          choices = c("File upload" = "file", "REDCap server" = "redcap","Sample data"="env"),
          checkIcon = list(
            yes = icon("square-check"),
            no = icon("square")
          )
        ),
        shiny::conditionalPanel(
          condition = "input.source=='file'",
          datamods::import_file_ui("file_import",
                                   title = "Choose a datafile to upload",
                                   file_extensions = c(".csv", ".txt", ".xls", ".xlsx", ".rds", ".fst", ".sas7bdat", ".sav", ".ods", ".dta")
          )
        ),
        shiny::conditionalPanel(
          condition = "input.source=='redcap'",
          m_redcap_readUI("redcap_import")
        ),
        shiny::conditionalPanel(
          condition = "input.source=='env'",
          import_globalenv_ui(id = "env", title = NULL)
        )


        # )
      ),
      column(
        width = 6,
        shiny::markdown("
                           # Welcome

                           This is the ***freesearchR*** web data analysis tool. An opiniotaed tool for easy data analysis at the hands of the clinician.

                           By intention, this is a focused app, with only few data modification tools included to keep the workflow streamlined.
                           ")
      )
    ),
    shiny::conditionalPanel(
      condition = "input.source=='redcap'",
      DT::DTOutput(outputId = "redcap_prev")
    ),
    shiny::br(),
    shiny::actionButton(inputId = "act_start", label = "Start")
  ),
  ##############################################################################
  #########
  #########  Data overview panel
  #########
  ##############################################################################
  "overview" =
    # bslib::nav_panel_hidden(
    bslib::nav_panel(
      # value = "overview",
      title = "Overview and modifications",
      bslib::navset_bar(
        fillable = TRUE,
        # bslib::nav_panel(
        #   title = "Edit",
        #   datamods::edit_data_ui(id = "edit_data")
        # ),
        # bslib::nav_panel(
        #   title = "Overview",
        #   DT::DTOutput(outputId = "table")
        # ),
        bslib::nav_panel(
          title = "Rename and select",
          tags$h3("Select, rename and convert variables"),
          fluidRow(
            column(
              width = 6,
              # radioButtons(),
              shiny::actionButton("data_reset", "Restore original data"),
              shiny::tags$br(),
              shiny::helpText("Reset to original imported dataset"),
              shiny::tags$br(),
              datamods::update_variables_ui("vars_update")
            ),
            column(
              width = 6,
              tags$b("Original data:"),
              # verbatimTextOutput("original"),
              verbatimTextOutput("original_str"),
              tags$b("Modified data:"),
              # verbatimTextOutput("modified"),
              verbatimTextOutput("modified_str")
            )
          )
        ),
        bslib::nav_panel(
          title = "Filter and modify",
          shinyWidgets::html_dependency_winbox(),
          fluidRow(
            # column(
            #   width = 3,
            #   shiny::uiOutput("filter_vars"),
            #   shiny::conditionalPanel(
            #     condition = "(typeof input.filter_vars !== 'undefined' && input.filter_vars.length > 0)",
            #     datamods::filter_data_ui("filtering", max_height = "500px")
            #   )
            # ),
            # column(
            #   width = 9,
            #   DT::DTOutput(outputId = "filtered_table"),
            #   tags$b("Code dplyr:"),
            #   verbatimTextOutput(outputId = "filtered_code")
            # ),
            shiny::column(
              width = 8,
              toastui::datagridOutput(outputId = "table_mod"),
              shiny::tags$b("Reproducible code:"),
              shiny::verbatimTextOutput(outputId = "filtered_code")
            ),
            shiny::column(
              width = 4,
              shiny::actionButton("modal_cut", "Create factor from a variable"),
              shiny::tags$br(),
              shiny::tags$br(),
              shiny::actionButton("modal_update", "Reorder factor levels"),
              shiny::tags$br(),
              shiny::tags$br(),
              IDEAFilter::IDEAFilter_ui("data_filter") # ,
              # shiny::actionButton("save_filter", "Apply the filter")
            )
          )
        )


        # column(
        #   8,
        #   shiny::verbatimTextOutput("filtered_code"),
        #   DT::DTOutput("filtered_table")
        # ),
        # column(4, IDEAFilter::IDEAFilter_ui("data_filter"))
      )
    ),
  ##############################################################################
  #########
  #########  Data analyses panel
  #########
  ##############################################################################
  "analyze" =
    # bslib::nav_panel_hidden(
    bslib::nav_panel(
      # value = "analyze",
      title = "Analyses",
      bslib::navset_bar(
        title = "",
        # bslib::layout_sidebar(
        #   fillable = TRUE,
        sidebar = bslib::sidebar(
          shiny::helpText(em("Please specify relevant settings for your data, and press 'Analyse'")),
          shiny::uiOutput("outcome_var"),
          shiny::uiOutput("strat_var"),
          shiny::conditionalPanel(
            condition = "input.strat_var!='none'",
            shiny::radioButtons(
              inputId = "add_p",
              label = "Compare strata?",
              selected = "no",
              inline = TRUE,
              choices = list(
                "No" = "no",
                "Yes" = "yes"
              )
            ),
            shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
          ),
          shiny::radioButtons(
            inputId = "all",
            label = "Specify covariables",
            inline = TRUE, selected = 2,
            choiceNames = c(
              "Yes",
              "No"
            ),
            choiceValues = c(1, 2)
          ),
          shiny::conditionalPanel(
            condition = "input.all==1",
            shiny::uiOutput("include_vars")
          ),
          shiny::radioButtons(
            inputId = "specify_factors",
            label = "Specify categorical variables?",
            selected = "no",
            inline = TRUE,
            choices = list(
              "Yes" = "yes",
              "No" = "no"
            )
          ),
          shiny::conditionalPanel(
            condition = "input.specify_factors=='yes'",
            shiny::uiOutput("factor_vars")
          ),
          bslib::input_task_button(
            id = "load",
            label = "Analyse",
            icon = shiny::icon("pencil", lib = "glyphicon"),
            label_busy = "Working...",
            icon_busy = fontawesome::fa_i("arrows-rotate",
                                          class = "fa-spin",
                                          "aria-hidden" = "true"
            ),
            type = "primary",
            auto_reset = TRUE
          ),
          shiny::helpText("If you change the parameters, press 'Analyse' again to update the tables")
          # )
        ),
        bslib::nav_panel(
          title = "Baseline characteristics",
          gt::gt_output(outputId = "table1")
        ),
        bslib::nav_panel(
          title = "Regression table",
          gt::gt_output(outputId = "table2")
        ),
        bslib::nav_panel(
          title = "Regression checks",
          shiny::plotOutput(outputId = "check")
        )
      )
    ),
  ##############################################################################
  #########
  #########  Documentation panel
  #########
  ##############################################################################
  "docs" = bslib::nav_panel(
    title = "Documentation",
    shiny::markdown(readLines(here::here("inst/apps/data_analysis_modules/www/intro.md"))),
    shiny::br()
  )
)

ui <- bslib::page(
  title = "freesearcheR",
  theme = bslib::bs_theme(
    primary = "#1E4A8F",
    secondary = "#FF6F61",
    bootswatch = "minty",
    base_font = bslib::font_google("Montserrat"),
    code_font = bslib::font_google("Open Sans")
  ),
  bslib::page_navbar(
    id = "main_panel",
    ui_elements$import,
    ui_elements$overview,
    ui_elements$analyze,
    ui_elements$docs
  )
)