first server working fine

server.R

@@ -9,47 +9,13 @@ library(rgdal)
 library(rgeos)
 
 
-###############################################################################
-# functions
-## from center of square coordinate (h,k) and length L return corner coordinates
-corners_of_square <- function(cells,L) {
-  corners=data.frame(
-    lng1=cells$x-L/2,
-    lat1=cells$y+L/2,
-    lng2=cells$x+L/2,
-    lat2=cells$y-L/2
-  )
-  return(corners)
-}
-## from (x,y) meters coordinates project to google map 
-change_projection_xy <- function(xy) {
-  colnames(xy) = c("x","y")
-  if(length(which(xy$y > 7300200 )) > 0) { xy$y[which(xy$y > 7300200)] = 7300100 }
-  if(length(which(xy$y < -7300200 )) > 0) { xy$y[which(xy$y < -7300200)] = -7300100 }  
-  if(length(which(xy$x > 17084470 )) > 0) { xy$x[which(xy$x > 17084470)] = 17074470 }
-  if(length(which(xy$x < -17084470 )) > 0) { xy$x[which(xy$x < -17084470)] = -17074470 }
-  coordinates(xy) = c("x", "y")
-  proj4string(xy) = CRS("+proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0")
-  xy = spTransform(xy,CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"))
-  xy_table=data.frame(x=as.double(xy@coords[,1]), y=as.double(xy@coords[,2]))
-  return(xy_table)
-}
-
-
-###############################################################################
-# LOAD DATA
-marine = read.table("donnees/figure_3a_underlying_data.tsv",header=T)
-marineCorners=corners_of_square(data.frame(x=marine$x,y=marine$y),194000)
-rect_1=change_projection_xy(data.frame(x=marineCorners$lng1,y=marineCorners$lat1))
-rect_2=change_projection_xy(data.frame(x=marineCorners$lng2,y=marineCorners$lat2))
-rect=cbind(rect_1,rect_2)
-colnames(rect)=c("lng1","lat1","lng2","lat2")
-marineRect=cbind(marine,rect)
-
+source("prepare_data.R")
 
 ###############################################################################
 # AESTETHICS
 gradiant_col_palette=c("#3333A2","#3333FF","#33CBFF","#33FFFF","#FFDF33","#FFA333","#FF3333")
+bin_col_palette=c("#FFCCCC","#FF6666","#FF0000","#990000")
+
 
 
 ###############################################################################
@@ -60,29 +26,55 @@ names(r_colors) <- colors()
 
 server <- function(input, output, session) {
 
-  points <- eventReactive(input$recalc, {
-    cbind(rnorm(40) * 2 + 13, rnorm(40) + 48)
-  }, ignoreNULL = FALSE)
+  #selected_data= marineRect %>% dplyr::select(input$cell_datatype)
+
+
 
   output$mymap <- output$map <- renderLeaflet({
+
+    selected_wt= cellsDat %>% filter(watertype == input$watertype)
+    selected_data=selected_wt %>% select(input$cell_datatype) %>% pull()
+
+
+
+    if(input$cell_datatype=="number_of_species") {
+      maFillColor=colorBin(bin_col_palette, selected_data, bins=c(2,4,5,10, max(selected_data)) )(selected_data)
+      selected_interval_data=c(2,4,5,10, max(selected_data))
+      conpal=colorBin(bin_col_palette, selected_data, bins=c(2,4,5,10, max(selected_data)) )
+    } else if(input$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)
+    } else if(input$cell_datatype =="temperature") {
+      maFillColor= colorNumeric(gradiant_col_palette, selected_data )(selected_data)
+      selected_interval_data=c(min(selected_data),max(selected_data))
+      conpal = colorNumeric(palette = gradiant_col_palette, domain = selected_interval_data)
+    } else {
+      ## number of sequences by species
+      maFillColor=colorBin(bin_col_palette, selected_data, bins=c(2,5,10,20,30, max(selected_data)) )(selected_data)
+      selected_interval_data=c(2,5,10,20,30, max(selected_data))
+      conpal=colorBin(bin_col_palette,selected_data, bins=c(2,5,10,20,30, max(selected_data)) )
+    }
+
     leaflet() %>%
       addProviderTiles(providers$Hydda.Base,
                        options = providerTileOptions(minZoom = 2, maxZoom = 400)) %>%
       clearBounds()  %>%
       setView(lng = 20, lat = 0, zoom = 2)  %>%
-
       addTiles() %>%
       addRectangles(
-        lng1=marineRect$lng1, lat1=marineRect$lat1,
-        lng2=marineRect$lng2, lat2=marineRect$lat2,
+        lng1=selected_wt$lng1, lat1=selected_wt$lat1,
+        lng2=selected_wt$lng2, lat2=selected_wt$lat2,
         color="#ffffff",
         weight = 1, smoothFactor = 0.55,
         opacity = 1.0, fillOpacity = 0.45,
-        fillColor = colorQuantile(gradiant_col_palette, marineRect$mean_genetic_diversity)(marineRect$mean_genetic_diversity)
-      )
+        fillColor = maFillColor
+      ) %>%
+       addLegend(conpal, 
+                selected_interval_data,
+                opacity = 1, 
+                title = input$cell_datatype,
+                position = "bottomright")
   })
 }
 
-
-
-

ui.R

@@ -2,15 +2,66 @@
 # load libraries
 library(shiny)
 library(leaflet)
+library(htmltools)
+library(htmlwidgets)
+library(sf)
+library(tidyverse)
+library(shinythemes)
+library(DT)
+library(shinydashboard)
+library(shinycssloaders)
 
+
+
+###############################################################################
+# DATA
+
+choices_datatype=list("Genetic diversity" = "mean_genetic_diversity",
+" Surface temperature" = "temperature",
+"Number of species" = "number_of_species",
+"Mean number of individual sequences per species" = "number_of_sequences")
+
+choices_watertype=c("marine","freshwater")
 ###############################################################################
 # UI
 
+ui <- dashboardPage(
+  dashboardHeader(title = "Worldmap of Fish Genetic Diversity",titleWidth=480),
+  dashboardSidebar(width=480,
+  	fluidRow(
+  	  column(width=12,
+  		align="center",
+		# Select freshwater or marine fishes
+        selectInput("watertype", 
+                                          label = "freshwater/marine species",
+                                          choices = choices_watertype,
+                                          selected = "marine"),
+
+                                   
 
 
+        # Select data type
+        selectInput("cell_datatype", 
+                                          label = "Cell data you want to display",
+                                          choices = choices_datatype,
+                                          selected = "mean_genetic_diversity"),
 
-ui <- fluidPage(
-  leafletOutput("mymap",height=640,width=960),
-  p(),
-  actionButton("recalc", "New points")
+        hr(),
+        # Link for source code
+        tags$a("Source code repository", href="https://github.com/Grelot/global_fish_genetic_diversity", target="_blank"),
+        # Explanation
+        tags$footer(tags$p("Developped by Pierre-Edouard GUERIN")),
+        # Link for paper
+        tags$a("Manel et al. 'Global patterns of fish genetic diversity' published in Nature Communication", href="", target="_blank"),
+        hr(), 
+        # Update info
+        tags$footer(tags$p("Last updated in February 2020", class = "credit"))
+      )
+    )
+  ),
+  dashboardBody(
+  	fluidRow(
+  		leafletOutput("mymap",height=640,width=960)
+  	)
+  )
 )