Remove unused GEOID in geo_join

Question

I am attempting to plot profitability on top of counties in Minnesota, Iowa, and Nebraska. Using leaflet and tigris, I have been able to plot ALL counties, whether or not I have data for it. This leaves me with a few counties with colors and the rest labeled as NA. Is there a way for me to remove all NA's from my geo_join data so that it just isn't used ala unused Wisconsin areas? I have tried using fortify, but I can't figure out how to determine what county boundaries I'm looking at when I merge the TIGER boundary lines with my County FIPS file in order to remove them.

Here is what my leaflet currently looks like:

My code to get the map is this:

library(tigris)
library(leaflet)

pal <- colorNumeric(c("yellow","dark red"),county$Construction.Cost,na.color="white")
IA_counties <- counties(state="IA", cb=TRUE, resolution ="20m")
MN_counties <- counties(state="MN",cb=TRUE,resolution="20m")
NE_counties <- counties(state="NE",cb=TRUE,resolution="20m")
IA_merged <- geo_join(IA_counties,county,"GEOID", "GEOID")
MN_merged <- geo_join(MN_counties,county,"GEOID","GEOID")
NE_merged <- geo_join(NE_counties,county,"GEOID","GEOID")
popupIA <- paste0("County Projects: ", as.character(paste('$',formatC(format(round(IA_merged$Construction.Cost, 0), big.mark=',', format = 'f')))))
popupMN <- paste0("County Projects: ", as.character(paste('$',formatC(format(round(MN_merged$Construction.Cost, 0), big.mark=',', format = 'f')))))
popupNE <- paste0("County Projects: ", as.character(paste('$',formatC(format(round(NE_merged$Construction.Cost, 0), big.mark=',', format = 'f')))))


leaflet() %>%
      addProviderTiles("MapQuestOpen.OSM") %>%
      addLegend(pal = pal, 
                values = IA_merged$Construction.Cost, 
                position = "bottomright", 
                title = "County Projects",
                labFormat=labelFormat(prefix="$")) %>%
      addCircles(lng=yup2$lon, lat=yup2$lat,weight=.75,fillOpacity=0.01,color="red",
                 radius = 96560) %>%
      addCircles(lng=yup2$lon, lat=yup2$lat,weight=.75,fillOpacity=0.01,color="blue",
                 radius = 193121) %>%
      addPolygons(data = IA_counties, 
                  fillColor = ~pal(IA_merged$Construction.Cost), 
                  layerId=1,
                  fillOpacity = .25, 
                  weight = 0.05, 
                  popup = popupIA)%>%
      addPolygons(data=MN_counties,
                  fillColor=~pal(MN_merged$Construction.Cost),
                  fillOpacity=0.25,
                  weight=0.05, 
                  popup = popupMN) %>%
      addPolygons(data=NE_counties,
                  fillColor=~pal(NE_merged$Construction.Cost),
                  fillOpacity=0.25,
                  weight=0.05, 
                  popup = popupNE) 

I apologize for not including reproducible data, but if needed, please ask. I'm hoping that this is more of a simple na.color= formula solution. The map looks "okay" as of now, but I'd like it if it's possible to not have to make the fillOpacity so light so the NA counties don't stand out.

Thanks for any and all help and please, let me know if you have any questions!

Answer 1

So, embarrassingly, the answer to this question was as simple as I had hoped. I tweaked the following na.color code and it worked exactly as I wanted.

pal <- colorNumeric(c("yellow","dark red"),county$Construction.Cost,na.color="transparent")