Plotting spatial points data in R?

Question

I have some kind of noob question: how do I plot spatialpoints dataframe in R using spplot (or ggmap) based on column values?

let's say we have this:

library(sp)
data(meuse)

v <- SpatialPointsDataFrame(meuse, coords = meuse[,1:2])

How would I plot 'copper' column here (with triangles pointed up or down based on a random threshold - let's say 31.0)?

I couldn't find a specific anwser so far.

Or how do I do that using proportional symbols?

Answer 1

Converting the data to an sf object, you can either use ggplot as the answer before or ggmap in the following way:

library(sp)
library(sf)
#> Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
library(dplyr, warn.conflicts = F)
library(ggmap, quietly = T)

data('meuse')
coordinates(meuse) <- ~x+y
proj4string(meuse) <- CRS("+init=epsg:28992")

meuse <- st_as_sf(meuse,coords = 1:2)

meuse <- meuse %>% 
  st_transform(crs = 4326)

meuse_map <- get_stamenmap(
   bbox = unname(st_bbox(meuse)),
   zoom = 13, maptype = 'toner-lite', source = 'stamen'
 ) %>% ggmap()
#> Map from URL : http://tile.stamen.com/toner-lite/13/4226/2742.png
#> Map from URL : http://tile.stamen.com/toner-lite/13/4227/2742.png
#> Map from URL : http://tile.stamen.com/toner-lite/13/4226/2743.png
#> Map from URL : http://tile.stamen.com/toner-lite/13/4227/2743.png
#> Map from URL : http://tile.stamen.com/toner-lite/13/4226/2744.png
#> Map from URL : http://tile.stamen.com/toner-lite/13/4227/2744.png

meuse_map + 
  geom_sf(
    data = meuse, 
    aes(size = copper), 
    color = 'red', alpha = 0.5,
    show.legend = 'point', inherit.aes = F
  )
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.

meuse <- meuse %>% mutate(copper.shape = ifelse(copper > 31, '> 31', '<= 31'))

meuse_map + 
  geom_sf(
    data = meuse, 
    aes(shape = copper.shape, fill = copper.shape), 
    inherit.aes = F
  ) +
  scale_shape_manual(values = c(25,24), guide = F) +
  scale_fill_manual(values = c('green','red'))
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.

Answer 2

For threshold:

plot(v[v$copper>31,], pch = 2, col="blue")
points(v[v$copper<=31,], pch = 6, col="red")

For proportional:

plot(v, cex=(3*(v$copper)/max(v$copper)), pch=16)

Apologies; ggplot for shape:

v@data$threshold = ifelse(v$copper > 31, "a", "b")
ggplot(data=v@data,
       aes(x=x,y=y, shape = threshold)) +
  geom_point() +
  scale_shape_manual(values=c(2,6))

ggplot code for proportional:

ggplot(data=v@data,
       aes(x=x,y=y, size = copper)) +
  geom_point()

Upon reflection, I think you'd be better off making a call to the coordinates slot rather than x and y from v. This is because x and y are fixed in the dataframe part of the SpatialPointsDataFrame. Instead, doing something like what I have below plots based on the spatial part of things and is robust to transformations on the object.

# Assume a sample spatial argument for the dataframe
proj4string(v) = CRS("+proj=utm +zone=10 +ellps=GRS80 +datum=NAD83 +units=m +no_defs")
proj4string(v)
# spatial transformation
v2 = spTransform(v,
                 CRSobj = CRS("+init=epsg:4326"))
proj4string(v2)

# Plotting this way enables plotting based on transformations
ggplot(data=v2@data,
       aes(x=coordinates(v2)[,1],y=coordinates(v2)[,2], 
           shape = threshold)) +
  geom_point() +
  scale_shape_manual(values=c(2,6))