ui.R

# #### UI -----

# ui shiny ----
ui <- dashboardPage(
  dashboardHeader(
    title = div("Cancer Survival", style = "text-align: left;"),  # Align title to the left
    titleWidth = 250  # Adjust the width as needed
  ),
  ## menu ----
  dashboardSidebar(
    sidebarMenu(
      menuItem(
        text = "Background",
        tabName = "background",
        icon = shiny::icon("book")
      ),
      
      menuItem(
        text = "Database Snapshot",
        tabName = "dbs",
        icon = shiny::icon("database"),
        menuSubItem(
          text = "Snapshot",
          tabName = "snapshotcdm"
        )
      ),
      
      menuItem(
        text = "Cohorts",
        tabName = "cohorts",
        icon = shiny::icon("person"),
        menuSubItem(
          text = "Cohort concepts",
          tabName = "cohort_concepts"
        ),
        menuSubItem(
          text = "Cohort Attrition Table",
          tabName = "cohort_attrition"
        ),
        menuSubItem(
          text = "Cohort Attrition Figures",
          tabName = "cohort_attr_fig"
        )
      ),
      
      menuItem(
        text = "Characteristics",
        tabName = "char",
        icon = shiny::icon("hospital-user"),
        menuSubItem(
          text = "Demographics",
          tabName = "demographics"
        )
      ),

      menuItem(
        text = "Overall Survival",
        tabName = "os",
        icon = shiny::icon("line-chart")
        ,
        menuSubItem(
          text = "Survival Plots",
          tabName = "survival_results"
        ),
        menuSubItem(
          text = "Summary Survival Plots",
          tabName = "summary_plots"
        ),
        menuSubItem(
          text = "Risk Table",
          tabName = "risk_results"
        ),
        menuSubItem(
          text = "Survival Estimates",
          tabName = "stats_results"
        ) 
      ),
      
      menuItem(
        text = "Data Partners",
        tabName = "dp",
        icon = shiny::icon("users-viewfinder"),
        menuSubItem(
          text = "Data Partners",
          tabName = "test"
        )
      ),
      
      # Logo HDS
      tags$div(
        style = "position: relative; margin-top: 20px; text-align: center; margin-bottom: 0;",
        a(img(
          src = "EHDEN_Logo_JPG.jpg",  # Replace with the correct file name and extension
          height = "60px",  # Adjust the height as needed
          width = "auto"     # Let the width adjust proportionally
        ),
        href = "https://www.ehden.eu/",
        target = "_blank"
        )
      ) ,
      
      # Logo HDS
      tags$div(
        style = "position: relative; margin-top: 20px; text-align: center; margin-bottom: 0;",
        a(img(
          src = "Logo_HDS.png",  # Replace with the correct file name and extension
          height = "80px",  # Adjust the height as needed
          width = "auto"     # Let the width adjust proportionally
        ),
        href = "https://www.ndorms.ox.ac.uk/research/research-groups/Musculoskeletal-Pharmacoepidemiology",
        target = "_blank"
        )
      ) ,
      
      # Logo UOXD
      tags$div(
        style = "position: relative; margin-top: -20px; text-align: center; margin-bottom: 0;",
        a(img(
          src = "logoOxford.png",  # Replace with the correct file name and extension
          height = "100px",  # Adjust the height as needed
          width = "auto"     # Let the width adjust proportionally
        ),
        href = "https://www.ndorms.ox.ac.uk/research/research-groups/Musculoskeletal-Pharmacoepidemiology",
        target = "_blank"
        )
      )
      
      
    )
  ),
  
  ## body ----
  dashboardBody(
    use_theme(mytheme),
    tabItems(
      # background  ------
      tabItem(
        tabName = "background",
        h3("Characterising Comorbidities, Medication Use, and Survival in Eight Incident Cancers Across Europe: A Multinational Network Cohort Study of 1.7 Million Patients"),
        tags$h4(tags$strong("Please note, the results presented here should be considered as
                                                preliminary and subject to change.")),
        
        tags$h5(
          "This app is a companion to the study focussing trends in comorbidities, concomitant treatments, and overall survival for eight cancers (Breast, Colorectal, Lung, Liver, Stomach, Head & Neck, Prostate, and Pancreas) for a variety of different electronic health records and cancer registries across Europe (Spain, Netherlands, Norway, Finland, Portugal, Estonia, Switzerland, and the United Kingdom)."
        ),
        
        
        tags$h5(
          tags$span("Background:", style = "font-weight: bold;"),
          "Real-world evidence provides valuable insights into cancer burden, presentation, and variations in care. This study examines patient characteristics and overall survival for breast, pancreatic, prostate, colorectal, lung, stomach, liver, and head and neck cancers using data from 11 electronic health records and cancer registries from eight European countries, mapped to the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM)."
        ),
        
        tags$h5(
          tags$span("Methods:", style = "font-weight: bold;"),
          "Patients aged 18 years or older with a primary cancer diagnosis between January 1st, 2000, and December 31st, 2019, were included. Patients were followed from cancer diagnosis until death, database exit, or study end. Mortality data was sourced from linked national death registries for most databases. Patient characteristics, including sex, age, comorbidities, and medication use, were summarised. Age-standardised overall survival at one, five, and ten years were calculated using the Kaplan-Meier method and stratified by cancer type, age group and sex."
          
        ),
        
        tags$h5(
          tags$span("Findings:", style = "font-weight: bold;"),
          "There were 1,796,278 eligible cancer patients included with most diagnoses in individuals aged 60-79 years. Top comorbidities and medications were relatively consistent across databases, with certain variations observed by cancer type, possibly indicative of early cancer signs. For instance, anaemia was frequent in colorectal (9%-23%) and stomach cancers (10%-34%), while chronic obstructive pulmonary disease (18%-34%) and pneumonia (15%-33%) were common in lung cancer patients. Breast and prostate cancers had the highest one, five and ten-year overall survival, and pancreatic cancer showed the lowest survival in all databases. Slight variations in cancer survival estimates were observed across data sources and countries."
          
        ),
        
        
        tags$h5(
          tags$span("Interpretation:", style = "font-weight: bold;"),
          "Integrating varied real-world data sources, utilizing the standardized OMOP-CDM structure, facilitates federated analyses and may offer promising avenues to enhance our understanding of cancer outcomes, including prodromes, which are often recorded in routinely collected healthcare data before cancer onset."
          
        ),

        
        tags$h5(
          tags$span("Funding:" , style = "font-weight: bold;"),
          "This research was funded by the European Health Data and Evidence Network (EHDEN) (grant number 806968), and the Oxford NIHR Biomedical Research Centre."
        ),
        
        tags$h5("The results of this study are published in the following preprint and journal:"
        ),
        tags$ol(
          tags$li(strong("Preprint"),"(",tags$a(href="https://www.ndorms.ox.ac.uk/research/research-groups/Musculoskeletal-Pharmacoepidemiology","Paper Link"),")" )),
        
        tags$ol(
          tags$li(strong("Journal Article"),"(",tags$a(href="https://www.ndorms.ox.ac.uk/research/research-groups/Musculoskeletal-Pharmacoepidemiology","Paper Link"),")" )),
        
        
        tags$h5("The analysis code used to generate these results can be found",
                tags$a(href="https://github.com/oxford-pharmacoepi/CancerSurvivalWp2Analysis", "here"),
                ".The cohort diagnostics including the clinical codelists for each cancer can be found",
                tags$a(href="https://dpa-pde-oxford.shinyapps.io/CancerExtrapolationDiagnostics/", "here")
                
        ),
        
        tags$h5("Any questions regarding this shiny app or the study please contact",
                tags$a(href="mailto:danielle.newby@ndorms.ox.ac.uk", "Danielle Newby"), "or the corresponding author",
                tags$a(href="mailto:tduarte@idiapjgol.org", "Talita Duarte Salles")
                
        ),
        
        tags$hr()
        
      ),
      
      # cdm snapshot ------
      tabItem(
        tags$h5("Snapshot of the cdm from database"),
        tabName = "snapshotcdm",
        htmlOutput('tbl_cdm_snaphot'),
        tags$hr(),
        div(
          style = "display:inline-block",
          downloadButton(
            outputId = "gt_cdm_snaphot_word",
            label = "Download table as word"
          ),
          style = "display:inline-block; float:right"
        )
      ) ,
      
      
      tabItem(
        tabName = "test",
        h4("Thanks go to all the Data Partners and collaborators who participated in this study"),
        fluidRow(
          column(width = 3, div(class = "logo-container", img(src = "logoOxford.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "idiap.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "nice.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "CPRD.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "sidiap.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "iknl.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "crnorway.svg", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "hus.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "huvm.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "gcr.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "eci.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "uoe.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "imasis.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "imasis1.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "ulsm.jpeg", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "ulsra.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "ulsedv.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "ulsge.jpeg", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "ipci.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "erasmus.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "odysseus.png", height = "100px"))),
          column(width = 3, div(class = "logo-container", img(src = "utartu.png", height = "100px")))
        ),
        tags$style(HTML("
    .logo-container {
      display: flex;
      justify-content: center;
      align-items: center;
      height: 120px; /* Adjusted height to include margin space */
      margin: 10px 0; /* Adds space above and below each logo */
    }
    .logo-container img {
      max-height: 100px;
      max-width: 90%;
    }
  "))
      ),

      tabItem(
        tabName = "demographics",
        tags$h5("The patient characteristics for the study populations are presented below:"),
        

        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "demographics_database_selector",
            label = "Database",
            choices = unique(tableone_whole$cdm_name),
            selected = unique(tableone_whole$cdm_name),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "demographics_cohort_selector",
            label = "Cancer",
            choices = unique(tableone_whole$group_level),
            selected = "cohort_name",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "demographics_selector",
            label = "Demographics",
            choices = unique(tableone_whole$strata_level),
            selected = "Overall",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "width: 80vh; height: 5vh;",  # Set width to 100% for responsive design
          checkboxInput("show_cond_meds", "Include Comorbidities & Medications", value = FALSE)
        ),

        
        # tags$hr(),
        gt_output("gt_patient_characteristics") %>% 
          withSpinner() ,
        
        
        div(style="display:inline-block",
            downloadButton(
              outputId = "gt_patient_characteristics_word",
              label = "Download table as word"
            ),
            style="display:inline-block; float:right") ,
        
     # ) ,
      
      div(style="display:inline-block",
          downloadButton(
            outputId = "gt_patient_characteristics_csv",
            label = "Download table as csv"
          ),
          style="display:inline-block; float:right")

    ) ,
      
      
      
      tabItem(
        tabName = "stats_results",
        tags$h5("Survival results containing one, five and ten year survival, restricted mean survival and median survival for each database are presented below:"),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "surv_est_database_name_selector",
            label = "Database",
            choices = unique(med_surv_km_sex_age$Database),
            selected = unique(med_surv_km_sex_age$Database),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "surv_est_cohort_name_selector",
            label = "Cancer",
            choices = unique(survival_km$Cancer),
            selected = "Breast",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "surv_est_sex_selector",
            label = "Sex",
            choices = unique(survival_km$Sex),
            selected = "Both",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "surv_est_age_selector",
            label = "Age",
            choices = unique(med_surv_km_sex_age$Age),
            selected = "All",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        DTOutput("dt_surv_est"),
        
        div(style="display:inline-block",
            downloadButton(
              outputId = "gt_surv_est_word",
              label = "Download table as word"
            ), 
            style="display:inline-block; float:right")
        
      ),

      tabItem(
        tabName = "risk_results",
        tags$h5("The risk table showing the numbers at risk are presented below:"),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "risk_table_database_name_selector",
            label = "Database",
            choices = unique(survival_risk_table$Database),
            selected = unique(survival_risk_table$Database),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "risk_table_cohort_name_selector",
            label = "Cancer",
            choices = unique(survival_risk_table$Cancer),
            selected = "Breast",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "risk_table_sex_selector",
            label = "Sex",
            choices = unique(survival_risk_table$Sex),
            selected = "Both",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "risk_table_age_selector",
            label = "Age",
            choices = unique(survival_risk_table$Age),
            selected = "All",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        htmlOutput('dt_risk_table'),
        
        div(style="display:inline-block",
            downloadButton(
              outputId = "gt_risk_table_word",
              label = "Download table as word"
            ), 
            style="display:inline-block; float:right")
        
      ),
      
      
      tabItem(
        tabName = "cohort_attr_fig",
        tags$h5("Attrition Diagrams for study populations:"),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "attrition_database_name_selector1",
            label = "Database",
            choices = unique(attritioncdm$Database),
            selected = unique(attritioncdm$Database)[1],
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = FALSE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "attrition_cohort_name_selector1",
            label = "Cancer",
            choices = unique(attritioncdm$Cancer),
            selected = "Breast",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = FALSE
          )
        ),
        
        
        div(
          style = "width: 80%; height: 90%;",  # Set width to 100% for responsive design
          grVizOutput("attrition_diagram", width = "400px", height = "100%") %>%
            withSpinner(),
          h4("Download Figure"),
          div("Width:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block;",
            textInput("attrition_download_width", "", 600, width = "50px")
          ),
          div("pixels", style = "display: inline-block; margin-right: 25px;"),
          downloadButton("cohort_attrition_download_figure", "Download plot")
        )
        
      ),
      
      
      # cohort definition ------
      tabItem(
        tabName = "cohort_concepts",
        
        pickerInput(
          inputId = "cohort_set_input",
          label = "Cohort Set",
          choices = unique(cohort_set$cohort_name),
          selected = unique(cohort_set$cohort_name)[1],
          options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
          multiple = FALSE
        ),
        tabsetPanel(
          type = "tabs",
          tabPanel(
            "Cohort definition",
            uiOutput("markdown")
          ),
          tabPanel(
            "JSON",
            h4(),
            rclipboardSetup(),
            uiOutput("clip"),
            verbatimTextOutput("verb"),
          ) ,
          tabPanel(
            "Concept sets",
            
            
            htmlOutput('tbl_concept_sets'),
            
            div(style="display:inline-block",
                downloadButton(
                  outputId = "dt_concept_sets_word",
                  label = "Download table as word"
                ), 
                style="display:inline-block; float:right")
            
          ),
          
        )

      ),
      
      tabItem(
        tags$h5("The cohort attrition showing how the final study populations were obtained are presented below:"),
        tabName = "cohort_attrition",
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "attrition_database_name_selector",
            label = "Database",
            choices = unique(attritioncdm$Database),
            selected = unique(attritioncdm$Database)[1],
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "attrition_cohort_name_selector",
            label = "Study cohort",
            choices = unique(attritioncdm$Cancer),
            selected = "Breast",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        htmlOutput('dt_attrition'),
        
        div(style="display:inline-block",
            downloadButton(
              outputId = "gt_attrition_word",
              label = "Download table as word"
            ), 
            style="display:inline-block; float:right")
        
      ),
      
      tabItem(
        tabName = "summary_plots",
        tags$h5("Plots of summary survival statistics for the study are presented below:"),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survivalsum_database_selector",
            label = "Database",
            choices = unique(med_surv_km_sex_age$Database),
            selected = unique(med_surv_km_sex_age$Database),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survivalsum_cohort_name_selector",
            label = "Cancer",
            choices = unique(med_surv_km_sex_age$Cancer),
            selected = unique(med_surv_km_sex_age$Cancer),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survivalsum_sex_selector",
            label = "Sex",
            choices = unique(med_surv_km_sex_age$Sex),
            selected = "Both",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survivalsum_age_selector",
            label = "Age",
            choices = unique(med_surv_km_sex_age$Age),
            selected = "All",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survivalsum_variable_selector",
            label = "Summary Statistic",
            choices = unique(med_surv_km_sex_age$Variable),
            selected = "One Year Survival",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = FALSE
          )
        ),
        
        div(style="display: inline-block;vertical-align:top; width: 150px;",
            pickerInput(inputId = "survsum_plot_facet",
                        label = "Facet by",
                        choices = c("Cancer",
                                    "Database",
                                    "Sex",
                                    "Age"
                        ),
                        selected = c("Cancer" ),
                        options = list(
                          `actions-box` = TRUE,
                          size = 10,
                          `selected-text-format` = "count > 3"),
                        multiple = TRUE)
        ),
        div(style="display: inline-block;vertical-align:top; width: 150px;",
            pickerInput(inputId = "survsum_plot_group",
                        label = "Colour by",
                        choices = c("Sex",
                                    "Age",
                                    "Cancer",
                                    "Database"),
                        selected = c("Cancer"),
                        options = list(
                          `actions-box` = TRUE,
                          size = 10,
                          `selected-text-format` = "count > 3"),
                        multiple = TRUE)
        ),
        
        div(
          style = "width: 80%; height: 90%;",  # Set width to 100% for responsive design
          plotOutput("survivalPlotSum",
                     height = "800px"
          ) %>%
            withSpinner(),
          h4("Download Figure"),
          div("Height:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block;",
            textInput("survivalsum_download_height", "", 30, width = "50px")
          ),
          div("cm", style = "display: inline-block; margin-right: 25px;"),
          div("Width:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block;",
            textInput("survivalsum_download_width", "", 35, width = "50px")
          ),
          div("cm", style = "display: inline-block; margin-right: 25px;"),
          div("dpi:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block; margin-right:",
            textInput("survivalsum_download_dpi", "", 600, width = "50px")
          ),
          downloadButton("survivalsum_download_plot", "Download plot")
        )
        ) ,
      
      tabItem(
        tabName = "survival_results",
        
        tags$h5("The Kaplan-Meier survival plots are presented below. We present the crude and age standardized KM curves. We calculated age-standardised survival estimates for all ages combined for both sexes and for  using the direct method using",
                tags$a(href = "https://www.sciencedirect.com/science/article/pii/S0959804904005283", "ICSS weightings"),
                
                "We were unable to estimate age survival for some countries due to the small number of cases in some age and cancer-specific strata, so they are not presented as results."),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survival_database_selector",
            label = "Database",
            choices = unique(survival_km$Database),
            selected = unique(survival_km$Database),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survival_cohort_name_selector",
            label = "Cancer",
            choices = unique(survival_km$Cancer),
            selected = "Breast",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survival_sex_selector",
            label = "Sex",
            choices = unique(survival_km$Sex),
            selected = "Both",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survival_age_selector",
            label = "Age",
            choices = unique(survival_km$Age),
            selected = "All",
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        div(
          style = "display: inline-block;vertical-align:top; width: 150px;",
          pickerInput(
            inputId = "survival_type_selector",
            label = "Database Type",
            choices = unique(survival_km$database_type),
            selected = unique(survival_km$database_type),
            options = list(`actions-box` = TRUE, size = 10, `selected-text-format` = "count > 3"),
            multiple = TRUE
          )
        ),
        
        
        div(style="display: inline-block;vertical-align:top; width: 150px;",
            pickerInput(inputId = "surv_plot_facet",
                        label = "Facet by",
                        choices = c("Cancer",
                                    "Database",
                                    "Sex",
                                    "Age",
                                    "database_type"
                        ),
                        selected = c("Cancer" ),
                        options = list(
                          `actions-box` = TRUE,
                          size = 10,
                          `selected-text-format` = "count > 3"),
                        multiple = TRUE,)
        ),
        div(style="display: inline-block;vertical-align:top; width: 150px;",
            pickerInput(inputId = "surv_plot_group",
                        label = "Colour by",
                        choices = c("Sex",
                                    "Age",
                                    "Cancer",
                                    "Database"),
                        selected = c("Database"),
                        options = list(
                          `actions-box` = TRUE,
                          size = 10,
                          `selected-text-format` = "count > 3"),
                        multiple = TRUE,)
        ),
        div(
          style = "width: 80vh; height: 5vh;",  # Set width to 100% for responsive design
          checkboxInput("show_ci", "Show Confidence Intervals", value = FALSE)
        ),
        
        
          div(
            style = "width: 100%;",  # Use percentage to make it responsive within the column
            numericInput("facet_ncol", "Number of Facets Columns:", value = 2, min = 1, max = 10, step = 1)
        ),
  
        
        div(
          style = "width: 80%; height: 90%;",  # Set width to 100% for responsive design
          plotOutput("survivalPlot",
                     height = "800px"
          ) %>%
            withSpinner(),
          h4("Download Figure"),
          div("Height:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block;",
            textInput("survival_download_height", "", 30, width = "50px")
          ),
          div("cm", style = "display: inline-block; margin-right: 25px;"),
          div("Width:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block;",
            textInput("survival_download_width", "", 35, width = "50px")
          ),
          div("cm", style = "display: inline-block; margin-right: 25px;"),
          div("dpi:", style = "display: inline-block; font-weight: bold; margin-right: 5px;"),
          div(
            style = "display: inline-block; margin-right:",
            textInput("survival_download_dpi", "", 600, width = "50px")
          ),
          downloadButton("survival_download_plot", "Download plot")
        )
      )
    )
  )  
)