app.R

library(shiny)
library(ggplot2)
library(dplyr)
library(plotly)
library(readxl)

# Read the data
amr_data = read_excel("amr_data.xlsx", sheet = "individual CTAs")
View(amr_data)
data_plot2 = read_excel("amr_data.xlsx", sheet = "Time Series")
View(data_plot2)

# Convert Year to date
amr_data$Year = as.Date(paste0(amr_data$Year, "-01-01"))
data_plot2$Year = as.Date(paste0(data_plot2$Year, "-01-01"))


# UI
ui = fluidPage(
  titlePanel("University of Calgary (AMR Visualization)"),
  
  sidebarLayout(
    sidebarPanel(
      selectInput("region", "Select Region:",
                  choices = c("All", unique(amr_data$Region))),
      uiOutput("syndrome"),
      uiOutput("pathogen"),
      uiOutput("antibiotic"),
      actionButton("submit", "Submit"),
      uiOutput("warning_text"),
      br(),
      br(),
      downloadButton("downloadData", "Download Data", class = "btn-success")
    ),
    
    mainPanel(
      plotlyOutput("amr_plot"),
      plotlyOutput("amr_plot2")
    )
  )
)


# Server logic
server = function(input, output, session) {
  output$syndrome = renderUI({
    if (input$region == "All") {
      choices = unique(amr_data$Infectious_Syndrome)
    } else {
      choices = unique(amr_data$Infectious_Syndrome[amr_data$Region == input$region])
    }
    selectInput("syndrome", "Select Infectious Syndrome:", choices = choices)
  })
  output$pathogen = renderUI({
    if (input$region == "All") {
      if (!is.null(input$syndrome)) {
        choices = unique(amr_data$Bacterial_Pathogen[amr_data$Infectious_Syndrome == input$syndrome])
      } else {
        choices = unique(amr_data$Bacterial_Pathogen)
      }
    } else {
      if (!is.null(input$syndrome)) {
        choices = unique(amr_data$Bacterial_Pathogen[amr_data$Region == input$region & amr_data$Infectious_Syndrome == input$syndrome])
      } else {
        choices = unique(amr_data$Bacterial_Pathogen[amr_data$Region == input$region])
      }
    }
    selectInput("pathogen", "Select Bacterial Pathogen:", choices = choices)
  })
  output$antibiotic = renderUI({
    if (input$region == "All") {
      if (!is.null(input$syndrome) & !is.null(input$pathogen)) {
        choices = unique(amr_data$Antibiotic_Type[amr_data$Bacterial_Pathogen == input$pathogen & amr_data$Infectious_Syndrome == input$syndrome])
      } else {
        choices = unique(amr_data$Antibiotic_Type)
      }
    } else {
      if (!is.null(input$syndrome) & !is.null(input$pathogen)) {
        choices = unique(amr_data$Antibiotic_Type[amr_data$Region == input$region & amr_data$Bacterial_Pathogen == input$pathogen & amr_data$Infectious_Syndrome == input$syndrome])
      } else {
        choices = unique(amr_data$Antibiotic_Type[amr_data$Region == input$region])
      }
    }
    selectInput("antibiotic", "Select Antibiotic Type:", choices = choices)
  })
  output$warning_text = renderUI({
    req(input$submit)
    if (input$region == "All" || is.null(input$syndrome) || is.null(input$pathogen) || is.null(input$antibiotic)) {
      tagList(
        p("Please select all filters.", style = "color:red;")
      )
    }
  })
  filtered_data = reactive({
    data = amr_data
    if (input$region != "All") {
      data = filter(data, Region == input$region)
    }
    if (!is.null(input$syndrome)) {
      data = filter(data, Infectious_Syndrome == input$syndrome)
    }
    if (!is.null(input$pathogen)) {
      data = filter(data, Bacterial_Pathogen == input$pathogen)
    }
    if (!is.null(input$antibiotic)) {
      data = filter(data, Antibiotic_Type == input$antibiotic)
    }
    data
  })
  filtered_data_plot2 = reactive({
    data_plot2 %>%
      filter(Infectious_Syndrome == input$syndrome,
             Bacterial_Pathogen == input$pathogen,
             Antibiotic_Type == input$antibiotic)
  })
  observeEvent(input$submit, {
    output$amr_plot = renderPlotly({
      p = ggplot(filtered_data(), aes(x = Year, y = Percent_AMR, group = Region, color = Region, text = paste(Region, ": ", round(Percent_AMR, 2), "%", sep = ""))) +
        geom_line(size = 1) +
        labs(x = "Year", y = "Percentage (%)", title = "Countries, territories and areas (CTAs)") +
        theme_minimal() +
        theme(legend.position = "none") +
        ylim(0, 100)
      
      ggplotly(p, tooltip = "text")
    })
    
    output$amr_plot2 = renderPlotly({
      p = ggplot(filtered_data_plot2(), aes(x = Year, y = Median, group = 1, text = paste("Median: ", round(Median, 2), "%\nQ1: ", round(Q1, 2), "%\nQ3: ", round(Q3, 2), "%", sep = ""))) +
        geom_line(size = 1) +
        geom_ribbon(aes(ymin = Q1, ymax = Q3), alpha = 0.3) +
        labs(x = "Year", y = "Percentage (%)", title = "Median") +
        theme_minimal() +
        theme(legend.position = "none") +
        ylim(0, 100)
      
      ggplotly(p, tooltip = "text")
    })
  })
  observeEvent(input$region, {
    if (input$region == "All") {
      updateSelectInput(session, "syndrome", selected = NULL, choices = unique(amr_data$Infectious_Syndrome))
      updateSelectInput(session, "pathogen", selected = NULL, choices = unique(amr_data$Bacterial_Pathogen))
      updateSelectInput(session, "antibiotic", selected = NULL, choices = unique(amr_data$Antibiotic_Type))
    } else {
      updateSelectInput(session, "syndrome", selected = NULL, choices = unique(amr_data$Infectious_Syndrome[amr_data$Region == input$region]))
      updateSelectInput(session, "pathogen", selected = NULL, choices = unique(amr_data$Bacterial_Pathogen[amr_data$Region == input$region]))
      updateSelectInput(session, "antibiotic", selected = NULL, choices = unique(amr_data$Antibiotic_Type[amr_data$Region == input$region]))
    }
    output$amr_plot = renderPlotly(NULL)
    output$amr_plot2 = renderPlotly(NULL)
  })
  observeEvent(c(input$syndrome, input$pathogen, input$antibiotic), {
    output$amr_plot = renderPlotly(NULL)
    output$amr_plot2 = renderPlotly(NULL)
    output$warning_text = renderUI(NULL)
  })
  output$downloadData = downloadHandler(
    filename = function() {
      paste("filtered_data", Sys.Date(), ".csv", sep = "")
    },
    content = function(file) {
      write.csv(filtered_data(), file, row.names = FALSE)
    }
  )
}


# Run 
shinyApp(ui = ui, server = server)