Commit 4d98a95e authored by peguerin's avatar peguerin
Browse files

update with credits and debug

parent 05df8063
...@@ -8,6 +8,15 @@ library(sp) ...@@ -8,6 +8,15 @@ library(sp)
library(rgdal) library(rgdal)
library(rgeos) library(rgeos)
library(htmlwidgets)
library(htmltools)
library(sf)
library(tidyverse)
library(shinythemes)
library(DT)
library(shinydashboard)
source("prepare_data.R") source("prepare_data.R")
...@@ -29,11 +38,12 @@ server <- function(input, output, session) { ...@@ -29,11 +38,12 @@ server <- function(input, output, session) {
#selected_data= marineRect %>% dplyr::select(input$cell_datatype) #selected_data= marineRect %>% dplyr::select(input$cell_datatype)
#############################################################################
## LEAFLET
output$mymap <- output$map <- renderLeaflet({ output$mymap <- output$map <- renderLeaflet({
selected_wt= cellsDat %>% filter(watertype == input$watertype) selected_wt= cellsDat %>% filter(watertype == input$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) { ...@@ -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) 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)) 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)) ) conpal=colorBin(bin_col_palette, selected_data, bins=c(2,4,5,10, max(selected_data)) )
titre_legende="Number of species"
} else if(input$cell_datatype =="mean_genetic_diversity") { } else if(input$cell_datatype =="mean_genetic_diversity") {
maFillColor= colorQuantile(gradiant_col_palette, selected_data,n=7 )(selected_data) bins_gd = c(0,0.001,0.002,0.003,0.005,0.01,0.025,max(selected_data))
selected_interval_data=c(min(selected_data),max(selected_data)) maFillColor= colorBin(gradiant_col_palette, selected_data, bins=bins_gd)(selected_data)
conpal = colorQuantile(palette = gradiant_col_palette, domain = selected_interval_data,n=7) selected_interval_data=bins_gd
conpal = colorBin(gradiant_col_palette, selected_data, bins=bins_gd)
titre_legende="Mean genetic diversity"
} else if(input$cell_datatype =="temperature") { } else if(input$cell_datatype =="temperature") {
maFillColor= colorNumeric(gradiant_col_palette, selected_data )(selected_data) maFillColor= colorNumeric(gradiant_col_palette, selected_data )(selected_data)
selected_interval_data=c(min(selected_data),max(selected_data)) selected_interval_data=c(min(selected_data),max(selected_data))
conpal = colorNumeric(palette = gradiant_col_palette, domain = selected_interval_data) conpal = colorNumeric(palette = gradiant_col_palette, domain = selected_interval_data)
titre_legende="Mean surface temperature (°C)"
} else { } else {
## number of sequences by species ## number of sequences by species
maFillColor=colorBin(bin_col_palette, selected_data, bins=c(2,5,10,20,30, max(selected_data)) )(selected_data) 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)) 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)) ) 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() %>% leaflet() %>%
...@@ -73,8 +89,24 @@ server <- function(input, output, session) { ...@@ -73,8 +89,24 @@ server <- function(input, output, session) {
addLegend(conpal, addLegend(conpal,
selected_interval_data, selected_interval_data,
opacity = 1, opacity = 1,
title = input$cell_datatype, title = titre_legende,
position = "bottomright") position = "bottomright")
}) })
#############################################################################
## TABLE
# Clickable object: create a null reactive value to store the ID of the layer
SelectedID <- reactiveVal(NULL)
# Observe statement
observe({
event <- input$map_shape_click
req(event)
SelectedID(event$id)
#print(event$id) # Verification
})
} }
...@@ -42,26 +42,31 @@ ui <- dashboardPage( ...@@ -42,26 +42,31 @@ ui <- dashboardPage(
# Select data type # Select data type
selectInput("cell_datatype", selectInput("cell_datatype",
label = "Cell data you want to display", label = "Cell values",
choices = choices_datatype, choices = choices_datatype,
selected = "mean_genetic_diversity"), selected = "mean_genetic_diversity"),
hr(), hr(),
# Link for source code # 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 # Explanation
tags$footer(tags$p("Developped by Pierre-Edouard GUERIN")), tags$footer(tags$p("")),
# Link for paper # 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(), hr(),
# Update info # Credits
tags$footer(tags$p("Last updated in February 2020", class = "credit")) 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( dashboardBody(
fluidRow( fluidRow(
## the worldmap
leafletOutput("mymap",height=640,width=960) leafletOutput("mymap",height=640,width=960)
) )
) )
) )
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