library(rgdal)
library(leaflet)
library(RColorBrewer)
library(raster)
library(maptools)
library(htmlwidgets)

# read in data
nc <- readShapeSpatial(system.file("shapes/sids.shp",
                                   package="maptools")[1], 
                       proj4string=CRS("+init=epsg:4326"))

# download leaflet basemap
map <- leaflet() %>% addTiles('http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png')

# plot map
map 

# add layers
map %>% addPolygons(data = nc)

# Generate a color code for administrative units
Colors<-brewer.pal(4,"OrRd")
SID74_Cat<-as.numeric(cut(nc$SID74,breaks=c(0,2,4,8,45),include.lowest=T))
SID_Cols<-Colors[SID74_Cat]

# Make popup
nc_leaflet<-leaflet() %>% addTiles('http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png',
                       attribution = paste(
                         '&copy; <a href="http://openstreetmap.org">OpenStreetMap</a> contributors',
                         '&copy; <a href="http://cartodb.com/attributions">CartoDB</a>'
                       )
) %>% addPolygons(data=nc, popup=paste(sep = "<br/>",
                              "<b>","SIDs deaths 1974","</b>",
                              nc$SID74), 
                              color = "gray",
                              fillColor=SID_Cols,
                              opacity=0.8,
                              fillOpacity = 0.6,
                              weight=2, group="Counties")

# plot
nc_leaflet

# Save html file to share
saveWidget(widget = nc_leaflet, file = "C:\\Users\\sturrockh\\Documents\\Work\\teaching\\Spatial Epi UCSF\\nc_leaflet.html")

# Add other types of data
elevation_USA <- getData('alt', country="USA")[[1]]
elevation_nc <- mask(elevation_USA[[1]], nc) 
nc_leaflet %>% addRasterImage(elevation_nc, group="Elevation") %>% addLayersControl(overlayGroups=c("Counties", "Elevation"))

# Check out http://leaflet-extras.github.io/leaflet-providers/preview/ for other basemap options
# for example
nc_leaflet<-leaflet() %>% addTiles('http://{s}.tile.thunderforest.com/spinal-map/{z}/{x}/{y}.png') %>%
 addPolygons(data=nc, popup=paste(sep = "<br/>",
                                       "<b>","SIDs deaths 1974","</b>",
                                       nc$SID74), 
                  color = "gray",
                  fillColor=SID_Cols,
                  opacity=0.8,
                  fillOpacity = 0.6,
                  weight=2, group="Counties")

nc_leaflet