# app.R

# ---- Robust package setup ----

options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest"))

required_packages <- c(
  "shiny",
  "bslib",
  "shinyWidgets",
  "dplyr",
  "ggplot2",
  "plotly",
  "DT",
  "htmlwidgets",
  "pharmaverseadamjnj"
)

installed_packages <- rownames(installed.packages())
missing_packages <- setdiff(required_packages, installed_packages)

if (length(missing_packages) > 0) {
  install.packages(
    missing_packages,
    type = "binary",
    dependencies = TRUE
  )
}

# ---- Load packages only after all checks/installations are complete ----

library(shiny)
library(bslib)
library(shinyWidgets)
library(dplyr)
library(ggplot2)
library(plotly)
library(DT)
library(htmlwidgets)
library(pharmaverseadamjnj)

# ---- Data preparation ----

adsl <- pharmaverseadamjnj::adsl

adsl2 <- adsl %>%
  select(USUBJID, TRT01P, TRTDURD, WEIGHTBL, HEIGHTBL) %>%
  filter(
    !is.na(TRT01P),
    !is.na(TRTDURD),
    !is.na(WEIGHTBL),
    !is.na(HEIGHTBL)
  )

adsl3 <- adsl2 %>%
  mutate_if(is.character, as.factor)

tf_colors <- c(
  "Placebo" = "#0072B2",
  "Xanomeline High Dose" = "#D55E00",
  "Xanomeline Low Dose" = "#CC79A7"
)

duration_range <- range(adsl3$TRTDURD, na.rm = TRUE)
weight_range <- range(adsl3$WEIGHTBL, na.rm = TRUE)
height_range <- range(adsl3$HEIGHTBL, na.rm = TRUE)

# ---- Reusable plot functions ----

make_duration_plot <- function(data) {
  ggplot(
    data = data,
    aes(x = TRT01P, y = TRTDURD, fill = TRT01P)
  ) +
    geom_boxplot() +
    scale_x_discrete(name = "Treatment Group") +
    scale_y_continuous(
      limits = c(0, 250),
      breaks = seq(0, 250, 50),
      expand = c(0.05, 0.05),
      name = "Treatment Duration (Days)"
    ) +
    scale_fill_manual(
      values = tf_colors,
      name = "Treatment Group"
    ) +
    theme_bw() +
    theme(
      legend.position = "top",
      plot.title = element_text(face = "bold"),
      axis.title = element_text(face = "bold")
    )
}

make_height_weight_plot <- function(data) {
  ggplot(
    data = data,
    aes(
      x = HEIGHTBL,
      y = WEIGHTBL,
      shape = TRT01P,
      colour = TRT01P
    )
  ) +
    geom_point(size = 2.3, alpha = 0.85) +
    scale_x_continuous(
      limits = c(0, 150),
      breaks = seq(0, 150, 10),
      name = "Baseline Height (cm)"
    ) +
    scale_y_continuous(
      limits = c(0, 150),
      breaks = seq(0, 150, 10),
      name = "Baseline Weight (kg)"
    ) +
    scale_shape_manual(
      values = c(16, 17, 15),
      name = "Treatment Group"
    ) +
    scale_colour_manual(
      values = tf_colors,
      name = "Treatment Group"
    ) +
    theme_bw() +
    theme(
      legend.position = "top",
      plot.title = element_text(face = "bold"),
      axis.title = element_text(face = "bold")
    )
}

make_subject_table <- function(data) {
  data %>%
    rename(
      "Unique Subject Identifier" = USUBJID,
      "Treatment Group" = TRT01P,
      "Total Treatment Duration (Days)" = TRTDURD,
      "Baseline Weight (kg)" = WEIGHTBL,
      "Baseline Height (cm)" = HEIGHTBL
    )
}

# ---- UI ----

ui <- page_sidebar(
  title = "Clinical Subject-Level Explorer",

  theme = bs_theme(
    bootswatch = "cosmo",
    base_font = font_google("Source Sans 3"),
    heading_font = font_google("Source Sans 3")
  ),

  sidebar = sidebar(
    title = "Dashboard Controls",
    width = 340,

    div(
      class = "text-muted",
      "Filter the subject-level dataset and download the current filtered outputs."
    ),

    hr(),

    h5("Subject Selection"),

    pickerInput(
      inputId = "treatment_filter",
      label = "Treatment Group",
      choices = levels(adsl3$TRT01P),
      selected = levels(adsl3$TRT01P),
      multiple = TRUE,
      options = pickerOptions(
        actionsBox = TRUE,
        liveSearch = TRUE,
        selectedTextFormat = "values",
        noneSelectedText = "No treatment groups selected",
        selectAllText = "Select All",
        deselectAllText = "Deselect All",
        iconBase = "glyphicon",
        tickIcon = "glyphicon-ok"
      )
    ),

    pickerInput(
      inputId = "subject_filter",
      label = "Subject",
      choices = levels(adsl3$USUBJID),
      selected = levels(adsl3$USUBJID),
      multiple = TRUE,
      options = pickerOptions(
        actionsBox = TRUE,
        liveSearch = TRUE,
        selectedTextFormat = "values",
        noneSelectedText = "No subjects selected",
        selectAllText = "Select All",
        deselectAllText = "Deselect All",
        iconBase = "glyphicon",
        tickIcon = "glyphicon-ok"
      )
    ),

    hr(),

    h5("Clinical Measures"),

    sliderInput(
      inputId = "duration_filter",
      label = "Total Treatment Duration (Days)",
      min = floor(duration_range[1]),
      max = ceiling(duration_range[2]),
      value = c(floor(duration_range[1]), ceiling(duration_range[2])),
      step = 1
    ),

    sliderInput(
      inputId = "weight_filter",
      label = "Baseline Weight (kg)",
      min = floor(weight_range[1]),
      max = ceiling(weight_range[2]),
      value = c(floor(weight_range[1]), ceiling(weight_range[2])),
      step = 1
    ),

    sliderInput(
      inputId = "height_filter",
      label = "Baseline Height (cm)",
      min = floor(height_range[1]),
      max = ceiling(height_range[2]),
      value = c(floor(height_range[1]), ceiling(height_range[2])),
      step = 1
    ),

    hr(),

    h5("Downloads"),

    downloadButton(
      outputId = "download_duration_plot",
      label = "Treatment Duration PNG",
      class = "btn-primary btn-sm w-100"
    ),

    br(),
    br(),

    downloadButton(
      outputId = "download_height_weight_plot",
      label = "Height vs Weight PNG",
      class = "btn-primary btn-sm w-100"
    ),

    br(),
    br(),

    downloadButton(
      outputId = "download_subject_table",
      label = "Filtered Table CSV",
      class = "btn-secondary btn-sm w-100"
    )
  ),

  div(
    class = "mb-4",
    h2("Clinical Subject-Level Explorer"),
    p(
      class = "text-muted",
      "Interactive review of treatment duration and baseline subject characteristics by treatment group."
    )
  ),

  layout_columns(
    col_widths = c(6, 6),
    card(
      full_screen = TRUE,
      card_header("Treatment Duration by Treatment Group"),
      plotlyOutput("duration_plot", height = "420px")
    ),
    card(
      full_screen = TRUE,
      card_header("Baseline Weight vs Baseline Height"),
      plotlyOutput("height_weight_plot", height = "420px")
    )
  ),

  br(),

  card(
    full_screen = TRUE,
    card_header("Filtered Subject-Level Data"),
    DTOutput("subject_table")
  )
)

# ---- Server ----

server <- function(input, output, session) {

  filtered_data <- reactive({
    req(input$treatment_filter)
    req(input$subject_filter)

    adsl3 %>%
      filter(
        TRT01P %in% input$treatment_filter,
        USUBJID %in% input$subject_filter,
        TRTDURD >= input$duration_filter[1],
        TRTDURD <= input$duration_filter[2],
        WEIGHTBL >= input$weight_filter[1],
        WEIGHTBL <= input$weight_filter[2],
        HEIGHTBL >= input$height_filter[1],
        HEIGHTBL <= input$height_filter[2]
      )
  })

  output$duration_plot <- renderPlotly({
    f1 <- make_duration_plot(filtered_data())

    ggplotly(f1) %>%
      layout(
        legend = list(
          orientation = "h",
          x = 0.5,
          xanchor = "center",
          y = 1.02,
          yanchor = "bottom"
        ),
        margin = list(t = 45)
      )
  })

  output$height_weight_plot <- renderPlotly({
    f2 <- make_height_weight_plot(filtered_data())

    ggplotly(f2) %>%
      layout(
        legend = list(
          orientation = "h",
          x = 0.5,
          xanchor = "center",
          y = 1.02,
          yanchor = "bottom"
        ),
        margin = list(t = 45)
      )
  })

  output$subject_table <- renderDT({
    datatable(
      make_subject_table(filtered_data()),
      extensions = c("ColReorder"),
      rownames = FALSE,
      filter = "top",
      class = "stripe hover compact",
      fillContainer = FALSE,
      autoHideNavigation = FALSE,
      options = list(
        colReorder = TRUE,
        bPaginate = TRUE,
        paging = TRUE,
        lengthChange = TRUE,
        searching = TRUE,
        info = TRUE,
        pageLength = 5,
        lengthMenu = c(5, 10, 12, 20, 50, 100),
        dom = '<"top"lf>rt<"bottom"ip>',
        language = list(
          info = "Showing _START_ to _END_ of _TOTAL_ entries"
        )
      )
    )
  })

  output$download_duration_plot <- downloadHandler(
    filename = function() {
      paste0("treatment_duration_plot_", Sys.Date(), ".png")
    },
    content = function(file) {
      ggsave(
        filename = file,
        plot = make_duration_plot(filtered_data()),
        device = "png",
        width = 8,
        height = 6,
        dpi = 300
      )
    }
  )

  output$download_height_weight_plot <- downloadHandler(
    filename = function() {
      paste0("height_weight_plot_", Sys.Date(), ".png")
    },
    content = function(file) {
      ggsave(
        filename = file,
        plot = make_height_weight_plot(filtered_data()),
        device = "png",
        width = 8,
        height = 6,
        dpi = 300
      )
    }
  )

  output$download_subject_table <- downloadHandler(
    filename = function() {
      paste0("filtered_subject_level_data_", Sys.Date(), ".csv")
    },
    content = function(file) {
      write.csv(
        make_subject_table(filtered_data()),
        file,
        row.names = FALSE
      )
    }
  )
}

# ---- Run app ----

shinyApp(ui = ui, server = server)