In edzer/sp: Classes and Methods for Spatial Data

Plotting maps with `sp`

This document shows example images created with objects represented by one of the classes for spatial data in packages sp.

Loading data and packages

The Meuse data set is loaded using a demo script in package sp,

library(sp)
demo(meuse, ask = FALSE, echo = FALSE) # loads the meuse data sets
class(meuse)

The North Carolina SIDS (sudden infant death syndrome) data set is available from package sf, and is loaded by

library(sf)
nc <- as(st_read(system.file("gpkg/nc.gpkg", package="sf")), "Spatial")

Using base plot

The basic plot command on a Spatial object gives just the geometry, without axes:

plot(meuse)

axes can be added when axes=TRUE is given; plot elements can be added incrementally:

plot(meuse, pch = 1, cex = sqrt(meuse$zinc)/12, axes = TRUE)
v = c(100,200,400,800,1600)
legend("topleft", legend = v, pch = 1, pt.cex = sqrt(v)/12)
plot(meuse.riv, add = TRUE, col = grey(.9, alpha = .5))

For local projection systems, such as in this case

proj4string(meuse)

the aspect ratio is set to 1, to make sure that one unit north equals one unit east. Even if the data are in long/lat degrees, an aspect ratio is chosen such that in the middle of the plot one unit north approximates one unit east. For small regions, this works pretty well; also note the degree symbols in the axes tic marks:

crs.longlat = CRS("+init=epsg:4326")
meuse.longlat = spTransform(meuse, crs.longlat)
plot(meuse.longlat, axes = TRUE)

which looks different from the plot where one degree north (latitude) equals one degree east (longitude):

par(mar = rep(0,4))
plot(meuse.longlat, asp = 1)

Graticules

Instead of axes with ticks and tick marks, maps often have graticules, a grid with constant longitude and latitude lines. sp provides several helper functions to add graticules, either in the local reference system, or in long/lat. Here is an example of the local reference system:

par(mar = c(0, 0, 1, 0))
library(methods) # as
plot(as(meuse, "Spatial"), expandBB = c(.05, 0, 0, 0))
plot(gridlines(meuse), add = TRUE, col = grey(.8))
plot(meuse, add = TRUE)
text(labels(gridlines(meuse)), col = grey(.7))
title("default gridlines with Meuse projected data")

par(mar = c(0, 0, 1, 0))
grd <- gridlines(meuse.longlat)
grd_x <- spTransform(grd, CRS(proj4string(meuse)))
plot(as(meuse, "Spatial"), expandBB = c(.05, 0, 0, 0))
plot(grd_x, add=TRUE, col = grey(.8))
plot(meuse, add = TRUE)
text(labels(grd_x, crs.longlat), col = grey(.7))
title("longitude latitude gridlines and labels")

These lines look pretty straight, because it concerns a small area. For

# demonstrate axis labels with angle, both sides:

maps2sp = function(xlim, ylim, l.out = 100, clip = TRUE) {
    stopifnot(require(maps))
    m = map(xlim = xlim, ylim = ylim, plot = FALSE, fill = TRUE)
    as(st_as_sf(m), "Spatial")
}
par(mar = c(0, 0, 1, 0))
m = maps2sp(c(-100,-20), c(10,55))
sp = SpatialPoints(rbind(c(-101,9), c(-101,55), c(-19,9), c(-19,55)), CRS("+init=epsg:4326"))
laea = CRS("+proj=laea +lat_0=30 +lon_0=-40")
m.laea = spTransform(m, laea)
sp.laea = spTransform(sp, laea)
plot(as(m.laea, "Spatial"), expandBB = c(.1, 0.05, .1, .1))
plot(m.laea, col = grey(.8), add = TRUE)
gl = gridlines(sp, easts = c(-100,-80,-60,-40,-20), norths = c(20,30,40,50))
gl.laea = spTransform(gl, laea)
plot(gl.laea, add = TRUE)
text(labels(gl.laea, crs.longlat))
text(labels(gl.laea, crs.longlat, side = 3:4), col = 'red')
title("curved text label demo")

# polar:
par(mar = c(0, 0, 1, 0))
pts=SpatialPoints(rbind(c(-180,-70),c(0,-70),c(180,-89),c(180,-70)), CRS("+init=epsg:4326"))
gl = gridlines(pts, easts = seq(-180,180,20), ndiscr = 100)
polar = CRS("+init=epsg:3031")
plot(spTransform(pts, polar), expandBB = c(.05, 0, .05, 0))
gl.polar = spTransform(gl, polar)
lines(gl.polar)
l = labels(gl.polar, crs.longlat, side = 3)
l$pos = NULL # pos is too simple, use adj:
text(l, adj = c(0.5, -0.5), cex = .8) 
l = labels(gl.polar, crs.longlat, side = 4)
l$srt = 0 # otherwise they end up upside-down
text(l, cex = .8)
title("grid line labels on polar projection, epsg 3031")

par(mar = c(0, 0, 1, 0))
m = maps2sp(xlim = c(-180,180), ylim = c(-90,-70), clip = FALSE)
gl = gridlines(m, easts = seq(-180,180,20))
polar = CRS("+init=epsg:3031")
gl.polar = spTransform(gl, polar)
plot(as(gl.polar, "Spatial"), expandBB = c(.05, 0, .05, 0))
plot(gl.polar, add = TRUE)
plot(spTransform(m, polar), add = TRUE, col = grey(0.8, 0.8))
l = labels(gl.polar, crs.longlat, side = 3)
# pos is too simple here, use adj:
l$pos = NULL 
text(l, adj = c(0.5, -0.3), cex = .8)
l = labels(gl.polar, crs.longlat, side = 2)
l$srt = 0 # otherwise they are upside-down
text(l, cex = .8)
title("grid line labels on polar projection, epsg 3031")

Other spatial objects in base plot

The following plot shows polygons with county name as labels at their center point:

par(mar = c(0, 0, 1, 0))
plot(nc)
invisible(text(coordinates(nc), labels=as.character(nc$NAME), cex=0.4))

This plot of a SpatialPolygonsDataFrame uses grey shades:

names(nc)
rrt <- nc$SID74/nc$BIR74
brks <- quantile(rrt, seq(0,1,1/7))
cols <- grey((length(brks):2)/length(brks))
dens <- (2:length(brks))*3
par(mar = c(0, 0, 1, 0))
plot(nc, col=cols[findInterval(rrt, brks, all.inside=TRUE)])

The following plot shows a SpatialPolygonsDataFrame, using line densities

rrt <- nc$SID74/nc$BIR74
brks <- quantile(rrt, seq(0,1,1/7))
cols <- grey((length(brks):2)/length(brks))
dens <- (2:length(brks))*3
par(mar = rep(0,4))
plot(nc, density=dens[findInterval(rrt, brks, all.inside=TRUE)])

Plot/image of a grid file, using base plot methods:

image(meuse.grid)

plot(meuse.grid["dist"])
points(meuse, col = 'green')

plot(meuse.grid["dist"], zlim = c(0,1))
plot(geometry(meuse.grid), add = TRUE, col = grey(.8))

Read this blog post to find out more about the options available (and limitations) for plotting gridded data with base plot methods in sp.

using lattice plot (spplot)

The following plot colours points with a legend in the plotting area and adds scales:

spplot(meuse, "zinc", do.log = TRUE,
    key.space=list(x = 0.1, y = 0.95, corner = c(0, 1)),
    scales=list(draw = TRUE))

The following plot has coloured points plot with legend in plotting area and scales; it has a non-default number of cuts with user-supplied legend entries:

spplot(meuse, "zinc", do.log = TRUE,
    key.space=list(x=0.2,y=0.9,corner=c(0,1)),
    scales=list(draw = TRUE), cuts = 3,
    legendEntries = c("low", "intermediate", "high"))

The following plot adds a scale bar and north arrow:

scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
    offset = c(178600,332490), scale = 500, fill=c("transparent","black"))
text1 = list("sp.text", c(178600,332590), "0")
text2 = list("sp.text", c(179100,332590), "500 m")
arrow = list("SpatialPolygonsRescale", layout.north.arrow(), 
    offset = c(178750,332000), scale = 400)
spplot(meuse, "zinc", do.log=T,
    key.space=list(x=0.1,y=0.93,corner=c(0,1)),
    sp.layout=list(scale,text1,text2,arrow),
    main = "Zinc (top soil)")

The following plot has north arrow and text outside panels

rv = list("sp.polygons", meuse.riv, fill = "lightblue")
scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
    offset = c(180500,329800), scale = 500, fill=c("transparent","black"), which = 1)
text1 = list("sp.text", c(180500,329900), "0", which = 1)
text2 = list("sp.text", c(181000,329900), "500 m", which = 1)
arrow = list("SpatialPolygonsRescale", layout.north.arrow(), 
    offset = c(178750,332500), scale = 400)
spplot(meuse["zinc"], do.log = TRUE,
    key.space = "bottom", 
    sp.layout = list(rv, scale, text1, text2),
    main = "Zinc (top soil)",
    legend = list(right = list(fun = mapLegendGrob(layout.north.arrow()))))

The same plot; north arrow now inside panel, with custom panel function instead of sp.layout

spplot(meuse, "zinc", panel = function(x, y, ...) {
        sp.polygons(meuse.riv, fill = "lightblue")
        SpatialPolygonsRescale(layout.scale.bar(), offset = c(179900,329600), 
            scale = 500, fill=c("transparent","black"))
        sp.text(c(179900,329700), "0")
        sp.text(c(180400,329700), "500 m")
        SpatialPolygonsRescale(layout.north.arrow(), 
            offset = c(178750,332500), scale = 400)
        panel.pointsplot(x, y, ...)
    },
    do.log = TRUE, cuts = 7,
    key.space = list(x = 0.1, y = 0.93, corner = c(0,1)),
    main = "Top soil zinc concentration (ppm)")

A multi-panel plot, scales + north arrow only in last plot: using the which argument in a layout component (if which=4 was set as list component of sp.layout, the river would as well be drawn only in that (last) panel)

rv = list("sp.polygons", meuse.riv, fill = "lightblue")
scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
    offset = c(180500,329800), scale = 500, fill=c("transparent","black"), which = 4)
text1 = list("sp.text", c(180500,329900), "0", cex = .5, which = 4)
text2 = list("sp.text", c(181000,329900), "500 m", cex = .5, which = 4)
arrow = list("SpatialPolygonsRescale", layout.north.arrow(), 
    offset = c(181300,329800), 
    scale = 400, which = 4)
cuts = c(.2,.5,1,2,5,10,20,50,100,200,500,1000,2000)
spplot(meuse, c("cadmium", "copper", "lead", "zinc"), do.log = TRUE,
    key.space = "right", as.table = TRUE,
    sp.layout=list(rv, scale, text1, text2, arrow), # note that rv is up front!
    main = "Heavy metals (top soil), ppm", cex = .7, cuts = cuts)

Comparing four kriging varieties in a multi-panel plot with shared scale:

rv = list("sp.polygons", meuse.riv, fill = "blue", alpha = 0.1)
pts = list("sp.points", meuse, pch = 3, col = "grey", alpha = .5)
text1 = list("sp.text", c(180500,329900), "0", cex = .5, which = 4)
text2 = list("sp.text", c(181000,329900), "500 m", cex = .5, which = 4)
scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
    offset = c(180500,329800), scale = 500, fill=c("transparent","black"), which = 4)
library(gstat)
v.ok = variogram(log(zinc)~1, meuse)
ok.model = fit.variogram(v.ok, vgm(1, "Exp", 500, 1))
# plot(v.ok, ok.model, main = "ordinary kriging")
v.uk = variogram(log(zinc)~sqrt(dist), meuse)
uk.model = fit.variogram(v.uk, vgm(1, "Exp", 300, 1))
# plot(v.uk, uk.model, main = "universal kriging")
meuse[["ff"]] = factor(meuse[["ffreq"]])
meuse.grid[["ff"]] = factor(meuse.grid[["ffreq"]])
v.sk = variogram(log(zinc)~ff, meuse)
sk.model = fit.variogram(v.sk, vgm(1, "Exp", 300, 1))
# plot(v.sk, sk.model, main = "stratified kriging")
zn.ok = krige(log(zinc)~1,          meuse, meuse.grid, model = ok.model, debug.level = 0)
zn.uk = krige(log(zinc)~sqrt(dist), meuse, meuse.grid, model = uk.model, debug.level = 0)
zn.sk = krige(log(zinc)~ff,         meuse, meuse.grid, model = sk.model, debug.level = 0)
zn.id = krige(log(zinc)~1,          meuse, meuse.grid, debug.level = 0)

zn = zn.ok
zn[["a"]] = zn.ok[["var1.pred"]]
zn[["b"]] = zn.uk[["var1.pred"]]
zn[["c"]] = zn.sk[["var1.pred"]]
zn[["d"]] = zn.id[["var1.pred"]]
spplot(zn, c("a", "b", "c", "d"), 
    names.attr = c("ordinary kriging", "universal kriging with dist to river", 
        "stratified kriging with flood freq", "inverse distance"), 
    as.table = TRUE, main = "log-zinc interpolation",
    sp.layout = list(rv, scale, text1, text2)
)

Reuse these results; universal kriging standard errors; grid plot with point locations and polygon (river):

rv = list("sp.polygons", meuse.riv, fill = "blue", alpha = 0.1)
pts = list("sp.points", meuse, pch = 3, col = "grey", alpha = .7)
spplot(zn.uk, "var1.pred",
    sp.layout = list(rv, scale, text1, text2, pts),
    main = "log(zinc); universal kriging using sqrt(dist to Meuse)")
zn.uk[["se"]] = sqrt(zn.uk[["var1.var"]])
spplot(zn.uk, "se", sp.layout = list(rv, pts),
    main = "log(zinc); universal kriging standard errors")

arrow = list("SpatialPolygonsRescale", layout.north.arrow(),
    offset = c(-76,34), scale = 0.5, which = 2)
spplot(nc, c("SID74", "SID79"), names.attr = c("1974","1979"),
    colorkey=list(space="bottom"), scales = list(draw = TRUE),
    main = "SIDS (sudden infant death syndrome) in North Carolina",
    sp.layout = list(arrow), as.table = TRUE)

arrow = list("SpatialPolygonsRescale", layout.north.arrow(), 
    offset = c(-76,34), scale = 0.5, which = 2)
#scale = list("SpatialPolygonsRescale", layout.scale.bar(), 
#   offset = c(-77.5,34), scale = 1, fill=c("transparent","black"), which = 2)
#text1 = list("sp.text", c(-77.5,34.15), "0", which = 2)
#text2 = list("sp.text", c(-76.5,34.15), "1 degree", which = 2)
# create a fake lines data set:
## multi-panel plot with coloured lines: North Carolina SIDS
spplot(nc, c("SID74","SID79"), names.attr = c("1974","1979"),
    colorkey=list(space="bottom"),
    main = "SIDS (sudden infant death syndrome) in North Carolina",
    sp.layout = arrow, as.table = TRUE)

Bubble plots for cadmium and zinc:

b1 = bubble(meuse, "cadmium", maxsize = 1.5, main = "cadmium concentrations (ppm)",
    key.entries = 2^(-1:4))
b2 = bubble(meuse, "zinc", maxsize = 1.5, main = "zinc concentrations (ppm)",
    key.entries =  100 * 2^(0:4))
print(b1, split = c(1,1,2,1), more = TRUE)
print(b2, split = c(2,1,2,1), more = FALSE)

Factor variables using spplot:

# create two dummy factor variables, with equal labels:
set.seed(31)
nc$f = factor(sample(1:5, 100,replace = TRUE),labels=letters[1:5])
nc$g = factor(sample(1:5, 100,replace = TRUE),labels=letters[1:5])
library(RColorBrewer)
## Two (dummy) factor variables shown with qualitative colour ramp; degrees in axes
spplot(nc, c("f","g"), col.regions=brewer.pal(5, "Set3"), scales=list(draw = TRUE))

maps using ggplot2

(it is recommended to migrate to sf, and use geom_sf() for this)

Interactive maps: leaflet, mapview

R packages leaflet and mapview provide interactive, browser-based maps building upon the leaflet javascript library. Example with points, grid and polygons follow:

library(mapview)
mapview(meuse, zcol = c("zinc", "lead"), legend = TRUE)

mapview(meuse.grid, zcol = c("soil", "dist"), legend = TRUE)

mapview(nc, zcol = c("SID74", "SID79"), alpha.regions = 1.0, legend = TRUE)

Mapview also allows grids of view that are synced

m1 <- mapview(meuse, zcol = "soil", burst = TRUE, legend = TRUE)
m2 <- mapview(meuse, zcol = "lead", legend = TRUE)
m3 <- mapview(meuse, zcol = "landuse", map.types = "Esri.WorldImagery", legend = TRUE)
m4 <- mapview(meuse, zcol = "dist.m", legend = TRUE)
sync(m1, m2, m3, m4) # 4 panels synchronised
# latticeView(m1, m2, m3, m4) # 4 panels