R/mod_spatial.R

In rahulchauhan049/bdvisDashboard: Dashboard For biodiversity data visualization

# Module UI

#' @title   mod_spatial_ui and mod_spatial_server
#' @description  A shiny Module.
#'
#' @param id shiny id
#' @param input internal
#' @param output internal
#' @param session internal
#'
#' @rdname mod_spatial
#'
#' @keywords internal
#' @export
#' @importFrom shiny NS tagList
mod_spatial_ui <- function(id) {
  ns <- NS(id)
  
  fluidPage(
    fluidRow(
      column(
        4,
        style = "padding: 0 0 0 0;",
        plotlyOutput(
          ns("countryBar"),
          height = "360px")
        ),
      column(
        4,
        style = "padding: 0 0 0 0;",
        plotlyOutput(
          ns("pie"),
          height = "360px"
        ),
      absolutePanel(
        top = 10,
        left = 20,
        selectInput(
          ns("pieselect"),
          "Select Column to be displayed",
          c(
            "basisOfRecord",
            "kingdom",
            "phylum",
            "order",
            "family",
            "genus",
            "species"
          ),
          selected = "basisOfRecord"
        )
      )
    ),
    column(
      4,
      style = "padding: 0 0 0 0;",
      plotlyOutput(
        ns("records"),
        height = "360px")
      )
    ),
    fluidRow(
      column(
        12,
        leafletOutput(
          ns("mymap"),
          height = "240px"
        ),
        absolutePanel(
          top = 60,
          right = 20,
          selectInput(
            ns("mapTexture"),
            "Map Texture",
            choices = list(
              "OpenStreetMap.Mapnik" = "OpenStreetMap.Mapnik",
              "OpenStreetMap.BlackAndWhite" = "OpenStreetMap.BlackAndWhite",
              "Stamen.Toner" = "Stamen.Toner",
              "CartoDB.Positron" = "CartoDB.Positron",
              "Esri.NatGeoWorldMap" = "Esri.NatGeoWorldMap",
              "Stamen.Watercolor" = "Stamen.Watercolor",
              "Stamen.Terrain" = "Stamen.Terrain",
              "Esri.WorldImagery" = "Esri.WorldImagery",
              "Esri.WorldTerrain" = "Esri.WorldTerrain"
            ),
            selected = "Stamen.Toner"
          ),
          selectInput(
            ns("mapColor"),
            "Points Color",
            choices = list(
              "Red" = 'red',
              "Green" = "green",
              "Blue" = "blue",
              "Black" = "black"
            )
          )
        )
      )
    )
  )
}

# Module Server

#' @rdname mod_spatial
#' @export
#' @keywords internal

mod_spatial_server <- function(input, output, session, data) {
  ns <- session$ns
  formattedData <- reactive({
    dataForBar <- format_bdvis(data(), source = 'rgbif')
    names(dataForBar) = gsub("\\.", "_", names(dataForBar))
    if ("Date_collected" %in% colnames(dataForBar)) {
      if (length(which(!is.na(dataForBar$Date_collected))) == 0) {
        stop("Date_collected has no data")
      }
      dayofYear <- as.numeric(
        strftime(
          as.Date(
            dataForBar$Date_collected,
            na.rm = T
          ),
          format = "%d"
        )
      )
      weekofYear <- as.numeric(
        strftime(
          as.Date(
            dataForBar$Date_collected,
            na.rm = T
          ),
          format = "%U"
        )
      )
      monthofYear <- as.numeric(
        strftime(
          as.Date(
            dataForBar$Date_collected,
            na.rm = T
          ),
          format = "%m"
        )
      )
      Year_ = as.numeric(
        strftime(
          as.Date(
            dataForBar$Date_collected,
            na.rm = T
          ),
          format = "%Y"
        )
      )
      dataForBar <-
        cbind(dataForBar[c("basisOfRecord",
                           "kingdom",
                           "phylum",
                           "order",
                           "family",
                           "genus",
                           "species")], dayofYear, weekofYear, monthofYear, Year_)
      
    } else {
      stop("Date_collected not found in data. Please use format_bdvis() to fix the problem")
    }
    return(dataForBar)
  })
  
  
  output$countryBar <- renderPlotly({
    country <-
      data.frame(table(na.omit(data()["countryCode"]))) %>%
      dplyr::rename(CountryName = Var1,
                    NumberOfRecords = Freq
                    )
    plot_ly(
      data = country,
      source = "barCountrt",
      x = ~ CountryName,
      y = ~ NumberOfRecords,
      name = "Countries",
      type = "bar"
    ) %>%
      layout(
      showlegend = FALSE,
      height = 320,
      paper_bgcolor = '#000000',
      plot_bgcolor = '#000000',
      xaxis = list(color = '#ffffff'),
      yaxis = list(color = '#ffffff'),
      leagend = list(color = '#ffffff')
    )
  })
  
  observe({
    click <- event_data("plotly_click", source = "barCountrt")
    if (is.null(click)) {
      output$mymap <- renderLeaflet({
        leaflet(data = data()) %>%
          addProviderTiles(input$mapTexture) %>%
          addCircles( ~ decimalLongitude, ~ decimalLatitude, color = input$mapColor)
      })
      output$temp <- renderText("as")
    } else {
      new <- data() %>% 
        filter(countryCode %in% click$x)
      leafletProxy("mymap", data = new) %>% 
        clearShapes() %>%
        addCircles( ~ decimalLongitude, ~ decimalLatitude, color = input$mapColor)
    }
  })
  
  observe({
    click <- event_data("plotly_selected", source = "barCountrt")
    if (is.null(click)) {
      output$mymap <- renderLeaflet({
        leaflet(data = data()) %>%
          addProviderTiles(input$mapTexture) %>%
          addCircles( ~ decimalLongitude, ~ decimalLatitude, color = input$mapColor)
      })
      output$temp <- renderText("as")
    } else {
      new <- data() %>% 
        filter(countryCode %in% click$x)
      leafletProxy("mymap", data = new) %>% 
        clearShapes() %>%
        addCircles( ~ decimalLongitude, ~ decimalLatitude, color = input$mapColor)
    }
  })
  
  observe({
    select <- event_data("plotly_click", source = "barCountrt")
    if (is.null(select)) {
      output$pie <- renderPlotly({
        if (input$pieselect == "kingdom") {
          label <- ~ kingdom
        } else if (input$pieselect == "phylum") {
          label <- ~ phylum
        } else if (input$pieselect == "family") {
          label <- ~ family
        } else if (input$pieselect == "genus") {
          label <- ~ genus
        } else if (input$pieselect == "species") {
          label <- ~ species
        } else if (input$pieselect == "order") {
          label <- ~ order
        } else {
          label <- ~ basisOfRecord
        }
        if (!nrow(data()[-which(data()[, input$pieselect] == ""),]) == 0) {
          dataa <- data()[-which(data()[, input$pieselect] == ""),]
        } else {
          dataa <- data()
        }
        
        plot_ly(
          data = na.omit(dataa[c("basisOfRecord",
                                 "kingdom",
                                 "phylum",
                                 "order",
                                 "family",
                                 "genus",
                                 "species")]),
          labels = label,
          type = 'pie',
          textposition = 'inside',
          textinfo = 'label+percent',
          insidetextfont = list(color = '#FFFFFF'),
          hoverinfo = 'text'
        ) %>% 
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
    } else {
      #create new dataset based on where user clicked on bar graph
      newData <- data() %>% 
        filter(countryCode %in% select$x)
      output$pie <- renderPlotly({
        if (input$pieselect == "kingdom") {
          label <- ~ kingdom
        } else if (input$pieselect == "phylum") {
          label <- ~ phylum
        } else if (input$pieselect == "family") {
          label <- ~ family
        } else if (input$pieselect == "genus") {
          label <- ~ genus
        } else if (input$pieselect == "species") {
          label <- ~ species
        } else if (input$pieselect == "order") {
          label <- ~ order
        } else {
          label <- ~ basisOfRecord
        }
        #Remove blank data from column(Blank! Not NA)
        if (!nrow(newData[-which(newData[, input$pieselect] == ""),]) == 0) {
          newData <- newData[-which(newData[, input$pieselect] == ""),]
        }
        
        plot_ly(
          data = na.omit(newData[c("basisOfRecord",
                                   "kingdom",
                                   "phylum",
                                   "order",
                                   "family",
                                   "genus",
                                   "species")]),
          labels = label,
          type = 'pie',
          textposition = 'inside',
          textinfo = 'label+percent',
          insidetextfont = list(color = '#FFFFFF'),
          hoverinfo = 'text'
        ) %>%
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
    }
  })
  
  observe({
    select <- event_data("plotly_selected", source = "barCountrt")
    if (is.null(select)) {
      output$pie <- renderPlotly({
        if (input$pieselect == "kingdom") {
          label <- ~ kingdom
        } else if (input$pieselect == "phylum") {
          label <- ~ phylum
        } else if (input$pieselect == "family") {
          label <- ~ family
        } else if (input$pieselect == "genus") {
          label <- ~ genus
        } else if (input$pieselect == "species") {
          label <- ~ species
        } else if (input$pieselect == "order") {
          label <- ~ order
        } else {
          label <- ~ basisOfRecord
        }
        if (!nrow(data()[-which(data()[, input$pieselect] == ""),]) == 0) {
          dataa <- data()[-which(data()[, input$pieselect] == ""),]
        } else {
          dataa <- data()
        }
        
        plot_ly(
          data = na.omit(dataa[c("basisOfRecord",
                                 "kingdom",
                                 "phylum",
                                 "order",
                                 "family",
                                 "genus",
                                 "species")]),
          labels = label,
          type = 'pie',
          textposition = 'inside',
          textinfo = 'label+percent',
          insidetextfont = list(color = '#FFFFFF'),
          hoverinfo = 'text'
        ) %>%
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
    } else {
      #create new dataset based on where user clicked on bar graph
      newData <- data() %>% 
        filter(countryCode %in% select$x)
      output$pie <- renderPlotly({
        if (input$pieselect == "kingdom") {
          label <- ~ kingdom
        } else if (input$pieselect == "phylum") {
          label <- ~ phylum
        } else if (input$pieselect == "family") {
          label <- ~ family
        } else if (input$pieselect == "genus") {
          label <- ~ genus
        } else if (input$pieselect == "species") {
          label <- ~ species
        } else if (input$pieselect == "order") {
          label <- ~ order
        } else {
          label <- ~ basisOfRecord
        }
        #Remove blank data from column(Blank! Not NA)
        if (!nrow(newData[-which(newData[, input$pieselect] == ""),]) == 0) {
          newData <- newData[-which(newData[, input$pieselect] == ""),]
        }
        
        plot_ly(
          data = na.omit(newData[c("basisOfRecord",
                                   "kingdom",
                                   "phylum",
                                   "order",
                                   "family",
                                   "genus",
                                   "species")]),
          labels = label,
          type = 'pie',
          textposition = 'inside',
          textinfo = 'label+percent',
          insidetextfont = list(color = '#FFFFFF'),
          hoverinfo = 'text'
        ) %>% 
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
    }
  })
  
  observe({
    select <- event_data("plotly_click", source = "barCountrt")
    if (is.null(select)) {
      output$records <- renderPlotly({
        dataload <- data()
        recordData1 <-
          (data.frame(
            names <-
              c(
                "kingdom",
                "phylum",
                "order",
                "family",
                "genus",
                "species"
              ),
            freq <-
              c(
                nrow(unique(na.omit(dataload["kingdom"]))),
                nrow(unique(na.omit(dataload["phylum"]))),
                nrow(unique(na.omit(dataload["order"]))),
                nrow(unique(na.omit(dataload["family"]))),
                nrow(unique(na.omit(dataload["genus"]))),
                nrow(unique(na.omit(dataload["species"])))
              )
          ))
        names(recordData1) <-
          c("NameOfField", "NumberOfUniqueNames")
        plot_ly(
          data = recordData1,
          x = ~ NameOfField,
          y = ~ NumberOfUniqueNames,
          name = "Frequency of records",
          type = "bar"
        ) %>%
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
    } else {
      output$records <- renderPlotly({
        newFilterData <- data() %>% 
          filter(countryCode %in% select$x)
        dataload <- newFilterData
        recordData1 <-
          (data.frame(
            names <-
              c(
                "kingdom",
                "phylum",
                "order",
                "family",
                "genus",
                "species"
              ),
            freq <-
              c(
                nrow(unique(na.omit(dataload["kingdom"]))),
                nrow(unique(na.omit(dataload["phylum"]))),
                nrow(unique(na.omit(dataload["order"]))),
                nrow(unique(na.omit(dataload["family"]))),
                nrow(unique(na.omit(dataload["genus"]))),
                nrow(unique(na.omit(dataload["species"])))
              )
          ))
        names(recordData1) <-
          c("NameOfField", "NumberOfUniqueNames")
        plot_ly(
          data = recordData1,
          x = ~ NameOfField,
          y = ~ NumberOfUniqueNames,
          name = "Frequency of records",
          type = "bar"
        ) %>% 
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
      
      
    }
  })
  
  observe({
    select <- event_data("plotly_selected", source = "barCountrt")
    if (is.null(select)) {
      output$records <- renderPlotly({
        dataload <- data()
        recordData1 <-
          (data.frame(
            names <-
              c(
                "kingdom",
                "phylum",
                "order",
                "family",
                "genus",
                "species"
              ),
            freq <-
              c(
                nrow(unique(na.omit(dataload["kingdom"]))),
                nrow(unique(na.omit(dataload["phylum"]))),
                nrow(unique(na.omit(dataload["order"]))),
                nrow(unique(na.omit(dataload["family"]))),
                nrow(unique(na.omit(dataload["genus"]))),
                nrow(unique(na.omit(dataload["species"])))
              )
          ))
        names(recordData1) <-
          c("NameOfField", "NumberOfUniqueNames")
        plot_ly(
          data = recordData1,
          x = ~ NameOfField,
          y = ~ NumberOfUniqueNames,
          name = "Frequency of records",
          type = "bar"
        ) %>%
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
    } else {
      output$records <- renderPlotly({
        newFilterData <- data() %>%
          filter(countryCode %in% select$x)
        dataload <- newFilterData
        recordData1 <-
          (data.frame(
            names <-
              c(
                "kingdom",
                "phylum",
                "order",
                "family",
                "genus",
                "species"
              ),
            freq <-
              c(
                nrow(unique(na.omit(dataload["kingdom"]))),
                nrow(unique(na.omit(dataload["phylum"]))),
                nrow(unique(na.omit(dataload["order"]))),
                nrow(unique(na.omit(dataload["family"]))),
                nrow(unique(na.omit(dataload["genus"]))),
                nrow(unique(na.omit(dataload["species"])))
              )
          ))
        names(recordData1) <-
          c("NameOfField", "NumberOfUniqueNames")
        plot_ly(
          data = recordData1,
          x = ~ NameOfField,
          y = ~ NumberOfUniqueNames,
          name = "Frequency of records",
          type = "bar"
        ) %>%
          layout(
          showlegend = FALSE,
          height = 320,
          paper_bgcolor = '#000000',
          plot_bgcolor = '#000000',
          xaxis = list(color = '#ffffff'),
          yaxis = list(color = '#ffffff'),
          leagend = list(color = '#ffffff')
        )
      })
      
      
    }
  })
}


## To be copied in the UI
# mod_spatial_ui("spatial_ui_1")

## To be copied in the server
# callModule(mod_spatial_server, "spatial_ui_1")