update with credits and debug

server.R

@@ -8,6 +8,15 @@ library(sp)
 library(rgdal)
 library(rgeos)
 
+library(htmlwidgets)
+library(htmltools)
+library(sf)
+library(tidyverse)
+library(shinythemes)
+library(DT)
+library(shinydashboard)
+
+
 
 source("prepare_data.R")
 
@@ -29,11 +38,12 @@ server <- function(input, output, session) {
   #selected_data= marineRect %>% dplyr::select(input$cell_datatype)
 
 
-
+  #############################################################################
+  ## LEAFLET
   output$mymap <- output$map <- renderLeaflet({
 
     selected_wt= cellsDat %>% filter(watertype == input$watertype)
-    selected_data=selected_wt %>% select(input$cell_datatype) %>% pull()
+    selected_data=selected_wt %>% dplyr::select(input$cell_datatype) %>% pull()
 
 
 
@@ -41,19 +51,25 @@ server <- function(input, output, session) {
       maFillColor=colorBin(bin_col_palette, selected_data, bins=c(2,4,5,10, max(selected_data)) )(selected_data)
       selected_interval_data=c(2,4,5,10, max(selected_data))
       conpal=colorBin(bin_col_palette, selected_data, bins=c(2,4,5,10, max(selected_data)) )
+      titre_legende="Number of species"
     } else if(input$cell_datatype =="mean_genetic_diversity") {
-      maFillColor= colorQuantile(gradiant_col_palette, selected_data,n=7 )(selected_data)
-      selected_interval_data=c(min(selected_data),max(selected_data))
-      conpal = colorQuantile(palette = gradiant_col_palette, domain = selected_interval_data,n=7)
+      bins_gd = c(0,0.001,0.002,0.003,0.005,0.01,0.025,max(selected_data))
+      maFillColor= colorBin(gradiant_col_palette, selected_data, bins=bins_gd)(selected_data)
+      selected_interval_data=bins_gd
+      conpal = colorBin(gradiant_col_palette, selected_data, bins=bins_gd)
+      titre_legende="Mean genetic diversity"
     } else if(input$cell_datatype =="temperature") {
       maFillColor= colorNumeric(gradiant_col_palette, selected_data )(selected_data)
       selected_interval_data=c(min(selected_data),max(selected_data))
       conpal = colorNumeric(palette = gradiant_col_palette, domain = selected_interval_data)
+      titre_legende="Mean surface temperature (°C)"
     } else {
       ## number of sequences by species
       maFillColor=colorBin(bin_col_palette, selected_data, bins=c(2,5,10,20,30, max(selected_data)) )(selected_data)
       selected_interval_data=c(2,5,10,20,30, max(selected_data))
       conpal=colorBin(bin_col_palette,selected_data, bins=c(2,5,10,20,30, max(selected_data)) )
+      titre_legende="Mean number of individual sequences per species"
+
     }
 
     leaflet() %>%
@@ -73,8 +89,24 @@ server <- function(input, output, session) {
        addLegend(conpal, 
                 selected_interval_data,
                 opacity = 1, 
-                title = input$cell_datatype,
+                title = titre_legende,
                 position = "bottomright")
   })
+
+  #############################################################################
+  ## TABLE
+  # Clickable object: create a null reactive value to store the ID of the layer
+  SelectedID <- reactiveVal(NULL)
+  # Observe statement
+  observe({
+    event <- input$map_shape_click
+    req(event)
+    SelectedID(event$id)
+    #print(event$id) # Verification
+  })
+
+
+
+
 }
 

ui.R

@@ -42,26 +42,31 @@ ui <- dashboardPage(
 
         # Select data type
         selectInput("cell_datatype", 
-                                          label = "Cell data you want to display",
+                                          label = "Cell values",
                                           choices = choices_datatype,
                                           selected = "mean_genetic_diversity"),
 
         hr(),
         # Link for source code
-        tags$a("Source code repository", href="https://github.com/Grelot/global_fish_genetic_diversity", target="_blank"),
+        tags$a("Developped by Pierre-Edouard GUERIN", href="https://github.com/Grelot/global_fish_genetic_diversity", target="_blank"),
         # Explanation
-        tags$footer(tags$p("Developped by Pierre-Edouard GUERIN")),
+        tags$footer(tags$p("")),
         # Link for paper
-        tags$a("Manel et al. 'Global patterns of fish genetic diversity' published in Nature Communication", href="", target="_blank"),
+        tags$a("Manel et al. 'Global determinants of freshwater and marine fish genetic diversity' Nature Communication", href="https://doi.org/10.1038/s41467-020-14409-7", target="_blank"),
         hr(), 
-        # Update info
-        tags$footer(tags$p("Last updated in February 2020", class = "credit"))
+        # Credits
+	    tags$a("Template inspired by the GAPeDNA app", href="https://github.com/virginiemarques/GAPeDNA", target="_blank"),
+		# Update info
+        tags$footer(tags$p("Last updated in February 2020 with kind help of Virginie Marques", class = "credit"))
       )
     )
   ),
+
   dashboardBody(
   	fluidRow(
+  		## the worldmap
   		leafletOutput("mymap",height=640,width=960)
+
   	)
   )
 )