ui.R

library(shinyFiles)
library(plotly)
library(shinybusy)
library(shinythemes)
library(shinyWidgets)
library(shinyhelper)
library(shinyjs)
library(colourpicker)
library(cicerone)

#####################################################################################
# Introduction and Features panel (Landing page of the Shiny-calorie web application)
#####################################################################################
intro_panel <- tabPanel(
  "Home",
  div(class="tile_upper_landing_page",
  div(img(src = "shiny_logo.png", height="400px"), style = "text-align: center; display: flex; justify-content: center; align-items: center;"),
  br(),
  p("A Shiny/R web application for general indirect calorimetry analysis", style="text-align: center; display: flex; justify-content: center; align-items: center;"),
  div(actionButton("btn_to_analysis", "Go to analysis", class="custom-button"), style = "text-align: center; display: flex; justify-content: center; align-items: center;"),
  ),
  div(class="tile_lower_landing_page",
  h2("Visualization and statistical data analysis", style="text-align:center;"),
  div(class="image-container", tags$a(href="https://calorimetry.readthedocs.io/en/latest/introduction.html", target="_blank", img(src = "app_landing_page.png", class="zoom-image")), style = "text-align: center; display: flex; justify-content: center; align-items: center;"),
  ),
  br(),
  div(class="tile_bottom_landing_page",
  h2("Metadata analysis", style="text-align:center;"),
  div(class="image_container", tags$a(href="https://calorimetry.readthedocs.io/en/latest/metadata.html", target="_blank", tags$img(src = "app_landing_page_bottom.png", class="zoom-image")), style = "text-align: center; display: flex; justify-content: center; align-items: center;"),
  ),
  div(class="flex-container",
  div(class="flex-div-right",
    span("Shiny-Calorie: A context-aware application for indirect calorimetry data analysis and visualization using R", style = "font-size: 12px; visibility: visible;"),
    tags$a(id = "contact_me", href = "", icon("fa-solid fa-square-envelope", "fa-1x"), style = "display:inline; "),
    tags$a(href = "http://github.com/stephanmg/calorimetry", icon("fa-brands fa-square-github", "fa-1x")),
    tags$a(href = "http://twitter.com/smgrein", icon("fa-brands fa-square-x-twitter", "fa-1x")),
    tags$a(href = "http://youtube.com/@Shiny-Calorie", icon("fa-brands fa-square-youtube", "fa-1x"))
   ))
)

################################################################################
# validation sidebar panel
################################################################################
validation_panel <- sidebarPanel(
   fileInput("rerself", "RER self (means)"),
   fileInput("rercalr", "RER CalR (means)"),
   h1("Plotting control"),
   textInput("plotTitle", "Plot title", paste0("Average of RER value")),
   actionButton("plottingvalidation", "Show plots"),
   actionButton("reset", "Reset session"),
)

################################################################################
# file loading sidebar panel
################################################################################
sidebar_file_panel <- sidebarPanel(
   numericInput("nFiles", "Number of files", value = 1, min = 1, step = 1),
   uiOutput("fileInputs"),
)

################################################################################
# main content panel
################################################################################
main_content <- mainPanel(
   width=8,
   tags$head(tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/jspdf/2.3.1/jspdf.umd.min.js")),
   tags$style(HTML("
   .shiny-output-error {
   color: #ff6347;
   font-weight: bold;
   }
   "
   )),
   tabsetPanel(
      id = "additional_content",
      tabPanel("Main plot", 
         tagList(
            conditionalPanel("input.plot_type != 'Metadata'", h3("Overview")),
            conditionalPanel("input.plot_type != 'Metadata'", checkboxInput("windowed_plot", "Add windowed time-trace plot", value=FALSE)),
            plotlyOutput("plot"),
            conditionalPanel("output.plotRendered && input.plot_type != 'Metadata'", checkboxInput("stylize_plot", "Stylize plot")),
            conditionalPanel("input.stylize_plot == true", uiOutput("stylize_plot_plotting_control")),
            conditionalPanel("output.plotRendered && input.plot_type != 'Metadata'", checkboxInput("add_average_with_se", "Add trend line")),
            conditionalPanel("output.plotRendered && input.plot_type != 'Metadata' && input.add_average_with_se == true", checkboxInput("add_average_with_se_one_plot", "One plot", value=FALSE)),
            conditionalPanel("input.add_average_with_se == true", selectInput("averaging_method_with_facets", "Method for smoothing", choices=c("gam", "sawitzky-golay"), selected="gam")),
            conditionalPanel("input.add_average_with_se == true", numericInput("averaging_method_with_facets_confidence_levels", "SE", min=1, max=10, value=2)),
            conditionalPanel("input.add_average_with_se == true", numericInput("averaging_method_with_facets_basis_functions", "Number of Basis functions", min = 10, max=40, value=20)),
            conditionalPanel("input.add_average_with_se == true", selectInput("averaging_method_with_facets_basis_function", "Basis function", choices=c("cs", "tp", "cr", "ps", "gp", "ts"), selected="cr")),
            conditionalPanel("input.add_average_with_se == true", numericInput("averaging_method_with_facets_alpha_level", "Transparency level", min=0.0, max=1.0, value=0.2, step=0.05)),
            conditionalPanel("input.add_average_with_se == true && input.with_facets != true", colourInput("averaging_method_with_facets_color", "Color", "blue")),
            conditionalPanel("output.plotRendered && input.plot_type == 'TotalHeatProduction'", checkboxInput("add_time_trace_below", "Add time trace(s)")),
            conditionalPanel("output.plotRendered && input.plot_type == 'TotalHeatProduction' && input.add_time_trace_below == true", plotlyOutput("timeTrace")),
            conditionalPanel("input.windowed_plot == true", hr()),
            conditionalPanel("input.windowed_plot == true && input.plot_type != 'Metadata'", h3("Windowed time-trace plot")),
            conditionalPanel("(output.plotRendered && (input.plot_type == 'RawMeasurement' || input.plot_type == 'HeatProduction' || input.plot_type == 'FuelOxidation' || input.plot_type == 'TotalHeatProduction' || input.plot_type == 'RestingMetabolicRate')) && input.windowed_plot == true", plotlyOutput("windowPlot")),
            conditionalPanel("input.windowed_plot == true", sliderInput("interval_length_for_window", "Interval length [min]", min=5, max=240, value=30)),
            conditionalPanel("input.windowed_plot == true", sliderInput("interval_steps_for_window", "Steps [#]", min=1, max=10, value=2)),
            conditionalPanel("input.windowed_plot == true", checkboxInput("boxplots_or_sem_plots", "Time boxplot", value=FALSE)),
            conditionalPanel("input.windowed_plot == true && input.connect_medians_of_boxplots != true && input.with_facets == true", checkboxInput("facet_medians", "Display only facet medians", value=FALSE)),
            conditionalPanel("input.windowed_plot == true && input.connect_medians_of_boxplots != true && input.with_facets == true", checkboxInput("facet_medians_statistics", "Display test statistics", value=FALSE)),
            conditionalPanel("input.facet_medians == true", checkboxInput("facet_medians_in_one_plot", "One plot", value=TRUE)),
            conditionalPanel("input.windowed_plot == true && input.boxplots_or_sem_plots == true", checkboxInput("connect_medians_of_boxplots", "Connect individual medians", value=FALSE))
         )
      ),
      tabPanel("Statistical testing", uiOutput("test")),
      tabPanel("Summary statistics", plotlyOutput("summary")),
      tabPanel("Details", uiOutput("details")),
      tabPanel("Statistical model", uiOutput("modelling")),
      tabPanel("Explanation", htmlOutput("explanation"))
   )
)

################################################################################
# Plotting validation
################################################################################
plotting_validation_panel <- mainPanel(
   plotOutput("plotvalidation")
)


################################################################################
# Data export
################################################################################

page_for_study_details <- fluidPage(
   h4("Study details"),
   tags$style(HTML(
      "
   .study-desc-table {
    width: 100%;
    border-collapse: collapse;
    margin: 12px 0;
    font-size: 10px;
    font-family: Arial, sans-serif;
}

.study-desc-table th, .study-desc-table td {
    padding: 6px 12px;
    text-align: left;
    border-bottom: 1px solid #ddd;
}

.study-desc-table th {
    background-color: #f4f4f4;
    color: #333;
    font-weight: bold;
}

.study-desc-table tr:hover {
    background-color: #555;
}

.study-desc-table tr:nth-child(even) {
    background-color: #fafafa;
}

.study-desc-table td {
    color: #fafafa;
}
      "
   )),
   tags$table(
      class = "study-desc-table",
      tags$thead(
         tags$tr(
            tags$th("File type"),
            tags$td(textOutput("file_type_detected"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Name"),
            tags$td(textOutput("study_name"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Lab"),
            tags$td(textOutput("lab"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Mouse strain"),
            tags$td(textOutput("mouse_strain"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Date"),
            tags$td(textOutput("date"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Author"),
            tags$td(textOutput("author"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Number of samples"),
            tags$td(textOutput("number_of_samples"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Number of genotypes"),
            tags$td(textOutput("number_of_genotypes"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Number of diets"),
            tags$td(textOutput("number_of_diets"))
         )
      ),
      tags$tbody(
         tags$tr(
            tags$th("Number of sexes"),
            tags$td(textOutput("number_of_sexes"))
         )
      )
   )
)

################################################################################
# Data export
################################################################################
page_for_data_export <-  fluidPage(
   tabsetPanel(id = "tabsDE", type = "hidden",
      tabPanelBody("DE",
   h4("Selected and calculated quantities", title = "This will export the currently selected quantity (see plotting above) and all quantities calculated during calculations"),
   selectInput("export_format", "Format", choices = c("CalR", "Excel")),
   textInput("export_file_name", "File name (Leave empty for auto-generation of a file name)"),
   downloadButton("downloadData", "Download"),
   h4("All data (Input and data frames for plotting)", title = "This will export all calculated data, the selected quantity for plotting, as well as all data frames so far for plotting. Note that in order to export TEE or RMR, you need to calculate both TEE and RMR first."),
   downloadButton("downloadAllData", "Download as zip file", icon=icon("file-archive")),
   h4("Data tables for plotting", title = "This will download only the data tables for plotting"),
   textInput("export_file_name2", "File name (Leave empty for auto-generation of a file name)"),
   downloadButton("downloadPlottingData", "Download"),
   )),
    fluidPage(
      fluidRow(
         column(8, style = "padding: 0px;",
         span(textOutput("message"), style = "color:red")
))))

################################################################################
# Data curation
################################################################################
page_for_data_curation <- fluidPage(
   h4("Time trimming"),
   tabsetPanel(id = "tabsDC", type = "hidden",
      tabPanelBody("DC",
   p("Selection of experimental times"),
   conditionalPanel(condition = "input.do_select_date_range == true", uiOutput("daterange")),
   checkboxInput(inputId = "curate", label = "Trim data (start and end of measurement times)"),
   conditionalPanel(condition = "input.curate == true", sliderInput("exclusion_start", "Exclude hours from start of measurements", 0, 24, 2, step = 1)),
   conditionalPanel(condition = "input.curate == true", sliderInput("exclusion_end", "Exclude hours from end of measurements", 0, 24, 2, step = 1)),
   # FIXME: Calendrical day selection needs fix for zeitgeber time, needs changes to utility function for zeitgeber time, thus the do_select_date_range checkbox is disabled now
   conditionalPanel(condition = "input.use_zeitgeber_time == false", checkboxInput("do_select_date_range", label = "Select dates", value=FALSE)),
   tags$script(HTML("$('#do_select_date_range').prop('disabled', true);")),
   tags$script(HTML("$('#use_default_plot_style').prop('disabled', true);"))
)))


################################################################################
# Data curation selection
################################################################################
page_for_data_curation_selection <- fluidPage(
   h4("Select days and samples"),
   tabsetPanel(id = "tabsDC", type = "hidden",
      tabPanelBody("DC",
   uiOutput("select_day"),
   uiOutput("select_animal"),
   div(actionButton("apply_selection", "Apply selection"), style="text-align: center; margin-left: 50px;"),
   br()
)))

################################################################################
# Data import example data
################################################################################
page_for_data_import_example_data <- fluidPage(
   h4("Examples"),
   div(actionButton("example_data_single", "UCP1 KO study", style = "margin: 5px; width: 200px; border: 1px solid white; background-color: rgba(42,82,190,0.5)"), style="text-align: center"), br(),
   div(actionButton("example_data_single_alternative", "DAKO study", style = "margin: 5px; width: 200px; border: 1px solid white; background-color: rgba(213,173,65,0.5)"), style="text-align: center"),
   hr(),
   h4("User guide"),
   div(actionButton("guide", "Getting help", style = "margin: 5px; width: 200px; border: 1px solid white; background-color: rgba(255,69,0,0.5)"), style="text-align: center"),
   br()
)

################################################################################
# Data import select equation
################################################################################
page_for_data_import_select_equation <- fluidPage(
   withMathJax(),
   h4("Heat production"),
   conditionalPanel("input.plot_type != 'CompareHeatProductionFormulas'", selectInput("variable1", "Select equation", choices = c("Heldmaier1", "Heldmaier2", "Weir", "Ferrannini"), selected="Heldmaier2")),
   conditionalPanel("input.plot_type == 'CompareHeatProductionFormulas'", selectInput("variable2", "Select second equation", choices = c("Heldmaier1", "Heldmaier2", "Lusk", "Weir", "Elia", "Brouwer", "Ferrannini"))),
   selectInput("kj_or_kcal", "Unit of energy", choices = c("kJ", "kcal", "mW")),
   withMathJax(),
   tags$head(
      tags$script(type = "text/x-mathjax-config", HTML(
         'MathJax.Hub.Config({
         TeX: {
            equationNumbers: {
               autoNumber: "AMS",
               formatNumber: function (n) { return "[" + n + "]"; }
               }
            }
            });'
         )
      )
   ),
   uiOutput("heat_production_equations"),
   hr(),
   h4("Miscellaneous"),
   checkboxInput("regularize_time", "Regularize time", value=TRUE),
   conditionalPanel("input.regularize_time == true", checkboxInput("override_interval_length", "Specify manually", value=TRUE)),
   conditionalPanel("input.regularize_time == true", sliderInput("override_interval_length_minutes", "dt", min=1, max=30, value=15)),
   checkboxInput("common_columns_only", "Common columns", value=FALSE),
   tags$script(HTML("
   $(document).ready(function() {
   // $('#regularize_time').prop('disabled', true);
   $('#common_columns_only').hover(function() {
      $(this).attr('title', 'Use only common columns across cohorts');
   })
   $('#regularize_time').hover(function() {
      $(this).attr('title', 'Interpolate to a regular time-grid');
   })
   })
   "))
)

################################################################################
# Data import custom data
################################################################################
page_for_data_import <- fluidPage(
   tabsetPanel(id = "tabsHP", type = "hidden",
      tabPanelBody("HP",
   add_busy_bar(color = "#0FFF50"),
   h3("Metadata"),
   div("Provided through standardized Excel metadata sheets [7]"),
   checkboxInput(inputId = "havemetadata", label = "Have additional metadata?"),
   conditionalPanel(condition = "input.havemetadata == true", uiOutput("metadatafile")),
   hr(),
   h3("Datasets"),
   p("Specify number of file(s)"),
   numericInput("nFiles", "Number of cohorts", value = 1, min = 1, step = 1),
   uiOutput("fileInputs"),
   hr(),
   div(actionButton("load_data", "Load data"), style="text-align: center; margin-left: 50px"),
   br(),
   tags$style(HTML("
       #reset {
          background-color: #637DFF; /* Pastel Blue */
          color: white;
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #reset:hover {
          background-color: #A3B8FF;
          border-color: white;
        }
        #plotting {
          background-color: #77DD77; /* Pastel Green */
          color: white;
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #plotting:hover {
          background-color: #5CB85C; 
          border-color: white;
        }
        #refresh {
          background-color: #8DBBD0; /* Pastel Light Blue */
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #refresh:hover {
          background-color: #6E98AA;
          border-color: white;
        }
        #load_data { /* Pastel Red */
          background-color: #FF6961;
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #load_data:hover {
          background-color: #FFB3AB;
          border-color: white;
        }
   ")),
)))

################################################################################
# Data import preprocessing
################################################################################
page_for_data_import_preprocessing <- fluidPage(
   h4("Data preprocessing"),
   checkboxInput(inputId="coarsen_data_sets", "Coarsen datasets"),
   conditionalPanel(condition = "input.coarsen_data_sets == true", numericInput("coarsening_factor", "Factor", value = 1, min = 1, max = 10, step=1)),
   checkboxInput(inputId="use_zeitgeber_time", "Use zeitgeber time", value = TRUE),
   checkboxInput(inputId="correct_clock_change", "Correct clock change", value = FALSE),
   checkboxInput(inputId="recalculate_RER", "Re-calculate RER", value = TRUE),
   tags$script(HTML("
      $(document).ready(function() {
      $('#correct_clock_change').attr('title', 'Correct for daylight saving time');
      })
   ")),
   checkboxInput(inputId="drop_nan_rows", "Drop NaN rows", value = TRUE),
   checkboxInput(inputId="use_raw_data_curation", "Amend raw data", value = FALSE),
   conditionalPanel(condition  ="input.use_raw_data_curation == true", 
      h4("Raw data curation"),
      checkboxInput(inputId = "z_score_removal_of_outliers", label = "Remove outliers automatically by z-score"),
      conditionalPanel(condition = "input.z_score_removal_of_outliers == true", numericInput("sds", "Number of SDs", value = 2, step=1, min = 0, max = 3)),
      conditionalPanel(condition = "input.z_score_removal_of_outliers == true", selectInput("target_columns", "Measurements", c("VO2", "VCO2"), multiple=TRUE, selected=c("VO2", "VCO2"))),
      checkboxInput(inputId = "remove_zero_values", label = "Remove zero values automatically"),
      conditionalPanel(condition = "input.remove_zero_values == true", numericInput("eps", "Epsilon", value=1e-6, min=1e-9, max=1e-3, step=1e-3)),
      checkboxInput(inputId = "toggle_outliers", "Manually mark outliers above threshold", value = FALSE),
      conditionalPanel("input.toggle_outliers == true", numericInput(inputId = "threshold_toggle_outliers", "Threshold", value=20.67, min = 0, max = 100, step = 0.01)),
      checkboxInput(inputId = "toggle_lasso_outliers", "Select and remove outliers by box selection"), 
      conditionalPanel("input.toggle_lasso_outliers == true", actionButton("remove_lasso_points", "Remove lasso selection")),
      h4("Consistency checks"),
      checkboxInput(inputId = "negative_values", label = "Detect negative values", value = FALSE),
      checkboxInput(inputId = "detect_nonconstant_measurement_intervals", label = "Detect non-constant measurement intervals", value = FALSE),
      checkboxInput(inputId = "highly_varying_measurements", label = "Detect highly varying measurements", value = FALSE),
      conditionalPanel("input.highly_varying_measurements == true", sliderInput("threshold_for_highly_varying_measurements", "Threshold [%]", min = 0, max = 200, step = 10, value = 200)),
   ),
   hr()
)


################################################################################
# Visualization
################################################################################
page_for_visualization <- fluidPage(
   useShinyjs(),
   fluidRow(
      column(8, style = "padding: 0px;",
      h4("Variable selection")),
   tabsetPanel(id = "tabsPC", type = "hidden",
      tabPanelBody("PC",
   selectInput(inputId = "ic_system", "Select indirect calorimetry platform", factor(c("General", "COSMED", "Sable"))),
   conditionalPanel(condition = "input.ic_system == 'General'", selectInput("plot_type", "Select quantity to plot", factor(c("Metadata", "RawMeasurement", "TotalHeatProduction", "RestingMetabolicRate", "HeatProduction", "FuelOxidation")))),
   conditionalPanel(condition = "input.ic_system == 'COSMED'", selectInput("plot_type", "Select quantity to plot", factor(c("Metadata", "RawMeasurement", "TotalHeatProduction", "RestingMetabolicRate", "HeatProduction", "FuelOxidation", "EstimateRMRforCOSMED", "CompareHeatProductionFormulas")))),
   conditionalPanel(condition = "input.ic_system == 'Sable'", selectInput("plot_type", "Select quantity to plot", factor(c("Metadata", "RawMeasurement", "TotalHeatProduction", "RestingMetabolicRate", "HeatProduction", "FuelOxidation", "Locomotion", "LocomotionBudget", "CompareHeatProductionFormulas")))),
   conditionalPanel(condition = "input.plot_type == 'RawMeasurement'", uiOutput("myr")),
   conditionalPanel(condition = "input.plot_type == 'FuelOxidation'", selectInput("goxlox", "FuelOxidation", choices = c("Glucose oxidation", "Lipid oxidation", "Protein oxidation", "Nitrogen oxidation"))),
   conditionalPanel(condition = "input.plot_type == 'TotalHeatProduction' || input.plot_type == 'DayNightActivity'", selectInput("box_violin_or_other", "Type of visualization", c("Boxplot", "Violinplot", "Dotplot"), selected="Violinplot")),
   conditionalPanel(condition = "input.plot_type == 'DayNightActivity'", selectInput("box_violin_or_other", "Type of visualization", c("Boxplot", "Violinplot", "Dotplot"), selected="Boxplot")),
   conditionalPanel(condition = "input.plot_type == 'HeatProduction'", uiOutput("myp")),
   conditionalPanel(condition = "input.plot_type == 'HeatProduction'", uiOutput("wmeans")),
   conditionalPanel(condition = "input.plot_type == 'HeatProduction'", uiOutput("wmeans_choice")),
   conditionalPanel(condition = "input.plot_type == 'HeatProduction'", uiOutput("wstats")),
   conditionalPanel(condition = "input.plot_type == 'HeatProduction'", uiOutput("wmethod")),
))),
column(width=8, style="padding: 0px",
   div(style="text-align: center; margin-left: 50px;", actionButton("plotting", "Show plot")),
   br()
))



################################################################################
# Grouping and filtering
################################################################################
page_for_visualization_grouping <- fluidPage(
   h4("Grouping and filtering"),
   checkboxInput(inputId = "with_grouping", label = "Select group and filter by condition"),
   conditionalPanel(condition = "input.with_grouping == true", uiOutput("condition_type")),
   conditionalPanel(condition = "input.with_grouping == true", uiOutput("select_data_by")),
   checkboxInput(inputId = "with_facets", label = "Select a group as facet"),
   conditionalPanel(condition = "input.with_facets == true", uiOutput("facets_by_data_one")),
   conditionalPanel(condition = "input.with_facets == true", selectInput("orientation", "Orientation", choices = c("Horizontal", "Vertical"))),
   checkboxInput(inputId = "select_temperature", label = "Select temperature"),
   conditionalPanel(condition = "input.select_temperature == true", uiOutput("temperature_type")),
   conditionalPanel(condition = "input.select_temperature == true", sliderInput(inputId = "temperature_mean", label = "Temperature [°C]", min=0, max=30, value=4, step=1)),
   conditionalPanel(condition = "input.select_temperature == true", sliderInput(inputId = "temperature_deviation", label = "Deviation from temperature [°C]", min=0, max=1, value=0.05, step=0.05)),
   uiOutput("checkboxgroup_gender")
)

################################################################################
# Experimental times
################################################################################
page_for_visualization_experimental_times <- fluidPage(
   h4("Experimental times"),
   checkboxInput(inputId = "timeline", label = "Annotate day/night light cycle"),
   conditionalPanel(condition = "input.use_zeitgeber_time != false",
   checkboxInput(inputId = "only_full_days_zeitgeber", label = "Select full days based on zeitgeber time", value = FALSE)),
   conditionalPanel(condition = "input.use_zeitgeber_time == false",
   checkboxInput(inputId = "only_full_days", label = "Select full consecutive calendrical days", value = FALSE)),
   conditionalPanel(condition = "input.only_full_days == true", sliderInput(inputId = "full_days_threshold", label = "Fraction of day missing [%]", min = 0, max = 100, value = 0, step = 1)),
   conditionalPanel(condition = "input.plot_type == 'Locomotion'", checkboxInput(inputId = "have_box_coordinates", label = "Custom cage coordinates", value = FALSE)),
   conditionalPanel(condition = "input.plot_type == 'Locomotion'", colourInput(inputId = "cage_color", label = "Cage Color", "white")),
   conditionalPanel(condition = "input.have_box_coordinates == true", h2("Cage configuration")),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "food_x_min", label = "Food hamper (x_min)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "food_x_max", label = "Food hamper (x_max)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "food_y_min", label = "Food hamper (y_min)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "food_y_max", label = "Food hamper (y_max)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", hr()),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "water_x_min", label = "Water bottle (x_min)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "water_x_max", label = "Water bottle (x_max)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "water_y_min", label = "Water bottle (y_min)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "water_y_max", label = "Water bottle (y_max)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", hr()),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "scale_x_min", label = "Scale (x_min)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "scale_x_max", label = "Scale (x_max)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "scale_y_min", label = "Scale (y_min)", min = 0, max = 100, value = 0)),
   conditionalPanel(condition = "input.have_box_coordinates == true", sliderInput(inputId = "scale_y_max", label = "Scale (y_max)", min = 0, max = 100, value = 0)),
   selectInput("light_cycle", "Light phase selection", c("Day", "Night"), multiple = TRUE, selected = c("Day", "Night")),
)

################################################################################
# Advanced options
################################################################################
page_for_visualization_advanced_options <- fluidPage(
   h4("Advanced options"),
   conditionalPanel(condition = "input.plot_type == 'EstimateRMRforCOSMED'", h3("Time Interval or Steady-State method to estimate RMR")),
   conditionalPanel(condition = "input.plot_type == 'EstimateRMRforCOSMED'", selectInput("rmr_method", "Method", choices = c("SS", "TI"))),
   conditionalPanel(condition = "input.plot_type == 'EstimateRMRforCOSMED'", sliderInput("rmr_method_frequency", "Frequency", min = 0, max = 30, value = 10)),
   conditionalPanel(condition = "input.plot_type == 'EstimateRMRforCOSMED'", sliderInput("rmr_method_begin", "Duration", min = 3, max = 10, value = 3)),
   conditionalPanel(condition = "input.rmr_method == 'SS' && input.plot_type == 'EstimateRMRforCOSMED'", h4("CVs")),
   conditionalPanel(condition = "input.rmr_method == 'SS' && input.plot_type == 'EstimateRMRforCOSMED'", sliderInput("SS_method_VO2", "VO2", min = 0, max = 100, value = 10)),
   conditionalPanel(condition = "input.rmr_method == 'SS' && input.plot_type == 'EstimateRMRforCOSMED'", sliderInput("SS_method_VCO2", "VCO2", min = 0, max = 100, value = 10)),
   conditionalPanel(condition = "input.rmr_method == 'SS' && input.plot_type == 'EstimateRMRforCOSMED'", sliderInput("SS_method_RER", "RER", min = 0, max = 100, value = 5)),
   conditionalPanel(condition = "input.rmr_method == 'SS' && input.plot_type == 'EstimateRMRforCOSMED'", sliderInput("SS_method_VE", "VE*", min = 0, max = 100, value = 10)),
   conditionalPanel(condition = "input.plot_type == 'RestingMetabolicRate'", sliderInput("window", "Window size", min = 1, max = 30, value = 5, step = 1)),
   conditionalPanel(condition = "input.plot_type == 'RestingMetabolicRate'", sliderInput("rmr_averaging", "Averaging width", min = 1, max = 30, value = 1, step = 1)),
   conditionalPanel(condition = "input.plot_type == 'RestingMetabolicRate'", sliderInput("percentage_best", "Fraction best", min = 1, max = 100, value = 1, step = 1)),
   conditionalPanel(condition = "input.plot_type == 'RestingMetabolicRate'", selectInput("cvs", "Component:", choices = c("CO2", "O2"), multiple = FALSE, selected = "O2")),
   h5("Time averaging of measurements"),
   checkboxInput(inputId = "override_averaging", label = "Override averaging method (mean)"),
   conditionalPanel(condition = "input.override_averaging == true", selectInput("avg_method_for_statistics", "Method", choices = c("mean", "median"))),
   h5("Light cycle configuration"),
   checkboxInput(inputId = "override_metadata_light_cycle", label = "Override"),
   conditionalPanel(condition = "input.plot_type == 'RestingMetabolicRate'", sliderInput("threshold_light_day", "Light threshold (Day)", min = 0, max = 100, value = 10)),
   conditionalPanel(condition = "input.plot_type == 'TotalHeatProduction'", sliderInput("threshold_light_day", "Light threshold (Day)", min = 0, max = 100, value = 10)),
   sliderInput(inputId = "light_cycle_start", label = "Light cycle start", min = 0, max = 24, value = 6),
   sliderInput(inputId = "light_cycle_stop", label = "Light cycle stop", min = 0, max = 24, value = 18),
   colourInput(inputId = "light_cycle_day_color", label = "Color day", "#FFBF00"),
   colourInput(inputId = "light_cycle_night_color", label = "Color night", "#B2BEB5"),
   conditionalPanel(condition = "input.plot_type != 'RestingMetabolicRate'", h5("Time averaging of raw data")),
   conditionalPanel(condition = "input.plot_type != 'RestingMetabolicRate'", sliderInput("averaging", "Time averaging [min]", 0, 30, 10, step = 1)),
   conditionalPanel(condition = "input.plot_type != 'RestingMetabolicRate'", sliderInput("running_average", "Moving average (k)", 0, 10, 1, step = 1)),
   conditionalPanel(condition = "input.plot_type != 'RestingMetabolicRate'", selectInput("running_average_method", "Method", choices = c("Mean", "Max", "Median", "Sum")))
)

################################################################################
# Visualization control
################################################################################
page_for_visualization_control <- fluidPage(
   h4("Actions"),
   tags$style(HTML("
        #reset {
          background-color: #637DFF; /* Pastel Blue */
          color: white;
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #reset:hover {
          background-color: #A3B8FF;
          border-color: white;
        }
        #plotting {
          background-color: #77DD77; /* Pastel Green */
          color: white;
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #plotting:hover {
          background-color: #5CB85C; 
          border-color: white;
        }
        #refresh {
          background-color: #8DBBD0; /* Pastel Light Blue */
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #refresh:hover {
          background-color: #6E98AA;
          border-color: white;
        }
        #load_data { /* Pastel Red */
          background-color: #FF6961;
          border-color: white;
          display: block;
          text-align: center;
          width: 150px;
        }
        #load_data:hover {
          background-color: #FFB3AB;
          border-color: white;
        }
        #apply_selection {
         background-color: #77DD77; /* Pastel Green */
          color: white;
          border-color: white;
          display: block;
          text-align: center;
        }
        #apply_selection:hover {
          background-color: #5CB85C; 
          border-color: white;
        }
   ")),
   actionButton("refresh", "Refresh plot"), br(),
   actionButton("reset", "Reset session"), br(),
   h4("Defaults"),
   checkboxInput("use_default_plot_style", "Use default plot style", value=TRUE),
   checkboxInput("use_default_plot_style", "Use default color palette", value=TRUE),
)


################################################################################
# Sidebar content
################################################################################
sidebar_content <- fluidPage(
   useShinyjs(),
   tags$head(
    tags$style(HTML("
     .menu-button {
        display: block;
        width: 100%;
        text-align: center;
        color: white;
        background-color: #283e4f;
        border-radius: 2px;
        border: none;
        cursor: pointer;
        transition: background 0.3s ease;
        text-decoration: none;
      }
      .menu-button:hover {
        background-color: #0056b3;
      }
      .active-button {
        background-color: #0056b3 !important;
        font-weight: bold;
      }
      .section-content {
        display: none;  /* Hide all sections initially */
      }
    "))
  ),
   sidebarPanel(
      width=2,
      h3("Dataset import"),
      actionLink("toggleA_example", "Example data", class = "menu-button"),
      br(),
      actionLink("toggleA_custom", "Custom data", class = "menu-button"),
      br(),
      actionLink("toggleA_preprocessing", "Import options", class = "menu-button"),
      hr(),
      h3("Statistics and visualization"),
      actionLink("toggleB_variable_selection", "Variable selection", class = "menu-button"),
      br(),
      actionLink("toggleB_groups", "Grouping and filtering", class = "menu-button"),
      br(),
      actionLink("toggleB_experimental_times", "Experimental times", class = "menu-button"),
      br(),
      actionLink("toggleB_advanced_options", "Advanced options", class = "menu-button"),
      br(),
      actionLink("toggleB_control", "Plotting control", class = "menu-button"),
      hr(),
      h3("Data curation"),
      actionLink("toggleC_data_curation", "Trimming", class = "menu-button"),
      br(),
      actionLink("toggleC_data_curation_selection", "Select days and samples", class = "menu-button"),
      hr(),
      h3("Result summary"),
      actionLink("toggleD", "Download data", class = "menu-button"),
      br(),
      actionLink("toggleE", "Study details", class = "menu-button")
   ),
   column(2, id ="middle_panel", style="border: 1px solid #ddd;",
      div(id = "sectionA_example", class = "section-content",
         page_for_data_import_example_data,
      ),
      div(id = "sectionA_custom", class = "section-content",
         page_for_data_import
      ),
      div(id = "sectionA_preprocessing", class = "section-content",
         page_for_data_import_preprocessing,
         page_for_data_import_select_equation
      ),
      div(id = "sectionB_control", class = "section-content", 
         page_for_visualization_control
      ),
      div(id = "sectionB_variable_selection", class = "section-content",
         page_for_visualization
      ),
      div(id = "sectionB_groups", class = "section-content",
         page_for_visualization_grouping
      ),
      div(id = "sectionB_experimental_times", class = "section-content",
         page_for_visualization_experimental_times
      ),
      div(id = "sectionB_advanced_options", class = "section-content",
         page_for_visualization_advanced_options,
      ),
      div(id = "sectionC_data_curation", class = "section-content",
         page_for_data_curation
      ),
      div(id = "sectionC_data_curation_selection", class = "section-content",
         page_for_data_curation_selection
      ),
      div(id = "sectionD", class = "section-content",
         page_for_data_export
      ),
      div(id = "sectionE", class = "section-content",
         page_for_study_details
      ),
   ),
   main_content
)

################################################################################
# Visualization panel
################################################################################
visualization <- tabPanel(
  "Analysis",
  sidebar_content,
   div(class="footer_version", 
    span(textOutput("session_id"), style = "font-size: 10px; visibility: visible;"),
   )
)

################################################################################
# Validation panel
################################################################################
validation <- tabPanel(
   "Validation of calorimetry data",
   titlePanel("Validation of results by comparing RER values (CalR and our method)"),
   p("Use the file choser dialog below to select files for RER Calr and our method"),
   sidebarLayout(
      validation_panel, plotting_validation_panel
   )
)

################################################################################
# Documentation
################################################################################
documentation <- tabPanel(
      "Help",
      style = "text-align: center",
      titlePanel("Getting general help for Shiny-Calorie:"),
      div(style = "width: 50%",
      helpText("", style = "text-align: right; padding-right: 20px") %>% helper(
         type = "markdown",
         align = "right",
         content = "general_help",
         size = "l",
         colour = "red",
         style = "zoom: 300%; text-align: right"
      )),
  br(),
  br(),
  h3("Supported input file formats"),
  div(style="display: flex; justify-content: center",
  tags$table(class = "fileformat-types",
   tags$tr(
      tags$td(icon("file-excel")),
      tags$td(icon("minus")),
      tags$td("Promethion/Sable")
   ),
   tags$tr(
      tags$td(icon("file-excel")),
      tags$td(icon("minus")),
      tags$td("COSMED")
   ),
   tags$tr(
      tags$td(icon("file-csv")),
      tags$td(icon("minus")),
      tags$td("TSE PhenoMaster v7")
   ),
   tags$tr(
      tags$td(icon("file-csv")),
      tags$td(icon("minus")),
      tags$td("TSE PhenoMaster v8")
   ),
   tags$tr(
      tags$td(icon("file-csv")),
      tags$td(icon("minus")),
      tags$td("TSE LabMaster v6")
   ),
   tags$tr(
      tags$td(icon("file-csv")),
      tags$td(icon("minus")),
      tags$td("TSE LabMaster v5")
   )
   )),
   br(),
    span(textOutput("git_info"), style = "font-size: 10px; visibility: visible;")
)

################################################################################
# Contact
################################################################################
contact <- tabPanel(
   "Contact",
   style = "text-align: center",
   titlePanel("Contact the developer of the application"),
   tags$address(
      p("Stephan Grein", style = "display:inline; "),
      tags$a(id = "contact_me", href = "", icon("fa-solid fa-square-envelope", "fa-1x"), style = "display:inline; "),
      br(),
      p("IRU Mathematics and Life Sciences", style = "display:inline; "),
      br(),
      p("LIMES/HCM, University of Bonn"),
      tags$script(HTML(
         "var encMail = 'c21nLmlydUBnbWFpbC5jb20K'; const form = document.getElementById('contact_me'); form.setAttribute('href', 'mailto:'.concat(atob(encMail)).concat('?subject=Shiny-Calorie'));"
      ))
   ),
   h2("Follow updates on our socials"),
   tags$table(class = "contact", style = "margin-left: auto; margin-right: auto",
      tags$tr(
         tags$td(tags$a(href = "http://github.com/stephanmg/calorimetry", icon("fa-brands fa-square-github", "fa-3x"))),
         tags$td(tags$a(href = "http://twitter.com/smgrein", icon("fa-brands fa-square-twitter", "fa-3x"))),
      )
   ),
   h2("Documentation and tutorial videos"),
   tags$table(class = "contact", style = "margin-left: auto; margin-right: auto",
      tags$tr(
         tags$td(tags$a(href = "http://youtube.com/@Shiny-Calorie", icon("fa-brands fa-square-youtube", "fa-3x")))
      )
   )
)

################################################################################
# main navigation bar (top)
################################################################################
ui <- tagList(
  tags$head(tags$title("Shiny-Calorie: A context-aware application for indirect calorimetry data analysis and visualization using R")),
  useShinyjs(),
  tags$head(tags$script(type = "text/javascript", src = "code.js")),
  tags$head(tags$link(rel = "stylesheet", type = "text/css", href = "style.css")),
  tags$head(tags$link(rel = "shrotcut icon", href="favicon.ico")),
  navbarPage(
    id="navbar",
    header = list(use_cicerone()),
    theme = shinytheme("superhero"),
    title=NULL,
    intro_panel,
    visualization,
    tabPanel("Metadata converter"),
    tabPanel("Documentation"),
    documentation,
    contact
  ),
  # tags$div(style="display: none;", textOutput("keepAlive"))
)