app.R

library(shiny)
library(sf)
library(stringr)
library(dplyr)
library(leaflet)

options(sf_use_s2 = FALSE)

# Load the shapefiles and data
cas <- readRDS("cas.rds")

inland <- readRDS("inland.rds")
marine <- readRDS("marine.rds")


# Example species list
species_list <- sort(unique(cas$valid_name))


ui <- fluidPage(
  titlePanel("Global fish distribution across biogeographic realm"),
  tags$head(tags$style(HTML("
    body { background-color: #f2f2f2; color: #333333; }
    .well { background-color: #ffffff; border: none; }
    #map { height: 100vh; }  /* Set the map to take the full viewport height */
    #controls {
      background-color: rgba(255, 255, 255, 0.3);
      padding: 15px;
      border-radius: 8px;
    }
  "))),
  fluidRow(
    column(2,  # Left side navigation panel (20% of the width)
           div(id = "controls", class = "panel panel-default",
               fixed = FALSE, draggable = TRUE,
               width = "100%", height = "100vh",
               #img(src = "path_to_logo.png", height = "100px"), # Replace with actual logo path
               selectizeInput("species",
                              HTML(paste0("Choose/Input a species (<span style='color:red;'>", scales::comma(nrow(cas)), "</span>):")),
                              choices = NULL,
                              selected = NULL),
               actionButton("run", "Run", class = "btn-primary")
           ),
           div(
             tags$h5(HTML("<strong>Acknowledgements</strong>:")),
             tags$p(HTML("<small>Heartfelt thanks to the hundreds of taxonomists for their selfless dedication. Data source (updated June 2024): <a href='http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp' target='_blank'> Eschmeyer's Catalog of Fishes</a>.</small>"))
           ),
           div(
               tags$h5(HTML("<strong>References</strong>:")),
               tags$p(HTML("<small>[1]Fricke R, Eschmeyer WN, Van der Laan R.(2024). <a href='http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp' ",
                           "target='_blank'>Catalog of fishes: genera, species, references </a>. California Academy of Sciences, San Francisco, CA, USA.</small>")),
               tags$p(HTML("<small>[2]Costello MJ, Tsai P, Wong PS, Cheung AKL, Basher Z, Chaudhary C.(2017). Marine biogeographic realms and species endemicity. <em>Nature Communications</em>, 8(1), 1057. </small>")),
               tags$p(HTML("<small>[3]Tedesco PA, Beauchard O, Bigorne R, Blanchet S, Buisson L, Conti L, Cornu J,Dias MS, Grenouillet G, Hugueny B, Jézéquel C, Leprieur F, Brosse S, Oberdorff T.(2017). A global database on freshwater fish species occurrence in drainage basins. <em>Scientific Data</em>, 4(1), 1-6.</small>"))
               ),
           tags$map(HTML(paste0(
             '<script type="text/javascript" id="clstr_globe" src="//clustrmaps.com/globe.js?d=fcrVhJisR3nagD85u6uUHpeDl2frZFCBy5i5BhDcpss"></script>'
           ))),
    ),
    column(10,  # Right side map panel (80% of the width)
           leafletOutput("map", width = "100%", height = "100vh")
    )
  )
)


# Server logic
server <- function(input, output, session) {

  # Update selectize input with species list (server-side)
  updateSelectizeInput(session, "species",
                       choices = species_list,
                       server = TRUE)

  observeEvent(input$run, {
    sp <- input$species

    realm <- cas %>%
      dplyr::filter(valid_name %in% sp) %>%
      dplyr::select(biogeographic_realm) %>%
      str_split(";") %>%
      unlist()


    # Create map with Leaflet
    output$map <- renderLeaflet({
      leaflet() %>%
        addProviderTiles("OpenStreetMap.Mapnik") %>%
        addPolygons(data = marine[which(marine$name %in% realm),],
                    fillColor = "#00A8E6", fillOpacity = 0.5, color = NA, group = "Marine") %>%
        addPolygons(data = inland[which(inland$BasinName %in% realm),],
                    fillColor = "#EEB134", fillOpacity = 0.5, color = NA, group = "Inland") %>%
        #setView(lng = 0, lat = 20, zoom = 2) %>%
        addControl(
          html = paste(
            "<strong>Data Source (Updated 2024-06): ",
            "<a href='http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp' ",
            "target='_blank'>Eschmeyer's Catalog of Fishes</a></strong><br>",
            "<small>Feel free to contact: <a href='mailto:ly_ding@126.com'>ly_ding@126.com</a></small>"
          ),
          position = "bottomright",
          className = "leaflet-control-custom"
        )
    })
  })

  # Add a popup showing species name and biogeographic realm on map click
  observeEvent(input$map_click, {
    click <- input$map_click
    if (is.null(click))
      return()

    # Extract the species Latin name and realm for popup
    sp <- input$species
    habitat <- cas %>%
      dplyr::filter(valid_name %in% sp) %>%
      dplyr::select(habitat)

    leafletProxy("map") %>%
      clearPopups() %>%
      addPopups(
        lng = click$lng, lat = click$lat,
        popup = paste0(
          "<strong>Species: </strong>", "<em>", sp, "</em>",
          "<br><strong>Habitat: </strong>", habitat
        )
      )
  })

}

# Run the app
shinyApp(ui, server)