Plotting polygons with rasters in base R, ggplot2 or levelplot - r

Question

I am trying to plot in R a raster layer with lines/polygon objects in R and each time I fail miserably with errors. I tried to do this in base R, ggplot2 and using levelplot but can't get the right result.
Source data can be found here.
What I need to do in the plot (all in one plot) is to:
1) zoom in a certain area defined as NIG. T
2) Display raster r values on a scale with cuts intervals.
3) Plot the country boundaries(shpAfr in base R and ggplot2 or world.outlines.spin levelplot). 4) Finally, include shpWater polygon layer (with col="blue" fill and contours).
library(raster)
library(maptools)
library(rasterVis)
library(viridis)
library(sf)
library(rgdal)
library(ggplot2)
r <- raster("raster_example.tif")
crs(r) <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +to wgs84=0,0,0"
NIG <- c(2,14.5,4,14)
Reg_name <- "Nigeria"
shpAfr <- readOGR(dsn="Africa.shp")
proj4string(shpAfr) # describes data’s current coordinate reference system
#st_read(system.file("shape/nc.shp", package="sf"))
# Import water polygon
shpWater <- readOGR(dsn="waterbodies_africa.shp")
shpWater.count <- nrow(shpWater#data)
shpWater$id <- 1:shpWater.count
shpWater.fort <- fortify(shpWater, region='id')
# Import Africa admin map
shpAfr <- readOGR(dsn="Africa.shp")
shpAfr.count <- nrow(shpAfr#data)
shpAfr$id <- 1:shpAfr.count
shpAfr.fort <- fortify(shpAfr, region='id')
# Set colour intervals for plotting:
cuts=seq(0,1,0.1) #set breaks
Trying in base R, my problem is I can get the water shape fill in the right colour (fill and contour should be blue). If I try to plot both wrld_simpl and shpWater as polygon() I get into even bigger troubles.
plot(r, xlim = NIG[1:2], ylim = NIG[3:4],
breaks=cuts, col = rev(plasma(11)))
lines(wrld_simpl,lwd = 1.5)
lines(shpWater, col="blue") # works but cannot fill the polygon
polygon(shpWater, col = "blue", border = "blue") # getting error here
Error in as.double(y) :
cannot coerce type 'S4' to vector of type 'double'
Ok, so now I try ggplot2, but I can't find a way to include a raster here without getting an error.
lon <- seq(r#extent#xmin,r#extent#xmax,
(r#extent#xmax-r#extent#xmin)/r#ncols)
lat <- seq(r#extent#ymin,r#extent#ymax,
(r#extent#ymax-r#extent#ymin)/r#nrows)
Plot1 <- ggplot()+
geom_polygon(aes(x = long, y = lat, group=id),
data = shpAfr.fort, color ="grey27", fill ="grey",
alpha = .4, size = .2)+
geom_raster(data = test, aes(fill=values))+ ## here it goes bad
#geom_tile(data=test_df, aes(x=x, y=y, fill=value), alpha=0.8) +
#scale_fill_viridis() +
geom_polygon(aes(x = long, y = lat, group=id),
data = shpWater.fort, color ="lightskyblue2", fill ="lightskyblue2",
size = .2)+coord_equal()+
theme_minimal()+
coord_map(xlim = Region[[3]][1:2],ylim = Region[[3]][3:4])
plot(Plot1)
Finally, I tried the levelplot and AGAIN failed.
mapTheme <- rasterTheme(region = rev(brewer.pal(10, "RdBu")))
# Get world outlines:
world.outlines <- map("world", plot=FALSE)
world.outlines.sp <- map2SpatialLines(world.outlines, proj4string = CRS("+proj=longlat"))
# Plot raster and polygon:
Plot2 <- levelplot(r,par.settings = mapTheme,pretty=TRUE,margin = F,
xlim = NIG[1:2],ylim = NIG[3:4],
col.regions=colorRampPalette(c("light blue","blue", "red")),
main=paste0("test")) + layer(sp.lines(world.outlines.sp, col = "black", lwd = 0.5))
plot(Plot2 + layer(sp.lines(world.outlines.sp, col = "black", lwd = 0.5))
#Error: Attempted to create layer with no stat.
My results so far:
1) first image does not have the polygons filled with blue
2) second image has clearly world outlines not in the right location
:

Answer 1

You would have probably have had answers a lot earlier if you had made a simple reprex, e.g. like this
library(raster)
r <- raster(res=1/12)
values(r) <- sample(100, ncell(r), replace=TRUE)
filename <- system.file("external/lux.shp", package="raster")
v <- shapefile(filename)
zoom in a certain area
One way to zoom is to use crop (alternatively use the ext argument in plot)
x <- crop(r, v)
Display raster r values on a scale with cuts intervals
cuts <- c(0,20,60,100)
plot(x, breaks=cuts, col=rainbow(3))
or
y <- cut(x, cuts)
Plot the country boundaries
lines(v)
Finally, include polygon layer (with col="blue" fill and contours).
plot(v[c(1,3),], col="blue", border="red", lwd=2, add=TRUE)

Answer 2

6 months later but I feel this question. My two thoughts are (1) I have had luck with plotting geom_sf and geom_stars together. You have to change your raster to a df before changing to a geom_stars. and (2) regardless of method, you need all datasets in the same projection - check with crs() and set all to the same with st_transform()
I didn't actually test this with your data but something like:
make raster into a df
test.df = as.data.frame (test, xy=TRUE) # Convert to data.frame, keeping the
coordinates
class(test.df)
convert to geom_stars
test.stars = st_as_stars(test.df)
try your plot
Plot1 <- ggplot()+
geom_stars(data = test, aes(fill=values))+ #need to plot raster first I think?
scale_fill_identity( name = "", breaks = cuts,labels = "")+
geom_sf(data = shpAfr.fort, color ="grey27", size = .2)+
geom_sf(data = shpWater.fort, color ="lightskyblue2", fill
="lightskyblue2", size = .2)+
theme_minimal()+
coord_sf( xlim = NIG[1:2], ylim = NIG[3:4]),expand = FALSE)
Plot1