How to "addTiles" on top of "addPolygons" in R's Leaflet?

Question

How do you set the layer order in R's leaflet package so that tiles show up on top of polygons filled with color?

Here's what I've got so far:

require(leaflet)
require(acs)
require(tigris)
require(rgdal)
census.income.end.year = 2015
county = 17
nd.counties=acs.fetch(geography=geo.make(state="ND", county=county), 
                      table.number="B01003", endyear = 2015)

tracts <- tigris::tracts(state = 'ND', county = county, cb=FALSE, year = 2015)

# create a geographic set to grab tabular data (acs)
geo<-geo.make(state=c("ND"),
              county = county,
              tract="*")

# add in median income
median.income <- acs.fetch(endyear = census.income.end.year, 
                           geography = geo, 
                           variable = c("B19013_001"))
income_df <- data.frame(paste0(as.character(median.income@geography$state), 
                               str_pad(as.character(median.income@geography$county), 3, 'left', '0'), 
                               str_pad(as.character(median.income@geography$tract), 5, 'left', '0')), 
                        median.income@estimate)

rownames(income_df)<-1:nrow(income_df)
names(income_df)<-c("GEOID", "hhincome")
income_merged <- geo_join(tracts, income_df, "GEOID", "GEOID")

income_merged <- spTransform(income_merged, CRS("+init=epsg:4326"))

qpal <- colorQuantile("plasma", income_df$hhincome, n = 4)

leaflet() %>% 
  setView( -96.7898, 46.8772, zoom=11) %>% 
  addPolygons(data = income_merged, 
              fillColor = qpal(income_merged$hhincome), 
              fillOpacity = 1, 
              weight = 0.3) %>%
  addProviderTiles(providers$Hydda.RoadsAndLabels) 

Ultimately, I'ld like to do this with addTiles (instead of addProviderTiles as in the above code) using a custom MapBox, but I can't figure out how to make that reproducible for this example... given that you need a key to access custom MapBox tiles (BTW, I've created a custom MapBox tile that should be transparent except for roads and labels, so the underlying polygons should "show thru.")

Here is one way to do add a tile on top of a circle with the non-R version of leaflet: http://jsfiddle.net/dcu9pz2w/, but I don't see how to make that work in my context. I think adding "panes" may be the way to go, but I don't see that functionality in R leaflet. Also, I explored z-index values, but that seemed to be a dead end.

Any help is much appreciated!

Answer 1

R leaflet now includes addMapPane function. The solution to this problem is to first set up pane order and then add tiles/polygons. Reproducible example:

library(leaflet)
library(geojsonio)

# get polygon data
# https://github.com/simonepri/geo-maps/blob/master/info/countries-land.md
world <- geojson_read(
  "https://github.com/simonepri/geo-maps/releases/download/v0.6.0/countries-land-10km.geo.json", 
  what = "sp"
)

# generate random values
world@data$value <- runif(nrow(world@data))

# get color palette
color_pal <- colorNumeric(palette = "YlOrRd", domain = NULL)

# get leaflet map
leaflet() %>%
  setView(lat = 50, lng = 15, zoom = 4) %>%
  addMapPane("background_map", zIndex = 410) %>%  # Level 1: bottom
  addMapPane("polygons", zIndex = 420) %>%        # Level 2: middle
  addMapPane("labels", zIndex = 430) %>%          # Level 3: top
  addProviderTiles(
    providers$Esri.WorldTerrain,
    options = pathOptions(pane = "background_map")
  ) %>%
  addPolygons(
    data = world, stroke = FALSE, smoothFactor = 0.2,
    fillOpacity = 0.6, fillColor = ~color_pal(value),
    options = pathOptions(pane = "polygons")
  ) %>%
  addProviderTiles(
    providers$Stamen.TonerLabels,
    options = pathOptions(pane = "labels")
  )