plot contour in different panels of sp plot - r

Question

I have 3 different rasters in a stack. I need to plot a panel plot and add different shapefiles on each panel. So far I managed to do the following;
## read the libraries
library(raster)
library(rgdal)
library(sp)
library(rworldmap)
library(OceanView)
##random raster object
r <- raster(ncol=40, nrow=20)
r[] <- rnorm(n=ncell(r))
# Create a RasterStack object with 3 layers
s <- stack(x=c(r, r*2, r**2))
##coordinate system
wgs<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
##reading the additional shape files
w <- spTransform(getMap(), wgs)
poly <- list(list("sp.lines", as(w, 'SpatialLines'), lwd =
0.5,col="black"))
##plotting with spplot
plot(spplot(s,layout=c(3,1),sp.layout=poly,
colorkey =list(space = "right"),
names.attr = c("a","b","c")))
so far I plotted the 3 rasters with a shapefile overlayed on it. Now I need to plot the 3 different contours one each on the panel plot. And also need to plot the windspeed arrows on each of the plot. I know to do this I need to use contour() and quiver() functions. However, I am unable to plot these.
## different raster stack for the contour plot
s1 <- stack(x=c(r/2, r*10, r**5))
##differnt wind components
lat= matrix(rep(seq(-90,90,length.out=20),each=20), ncol=20, byrow=TRUE)
lon=matrix(rep(seq(-180,180,length.out=20),each=20), ncol=20, byrow=F)
u=matrix(rep(sample(seq(-2,2,length.out=1000),20),each=20), ncol=20, byrow=TRUE)
v=matrix(rep(sample(seq(-2,2,length.out=1000),20),each=20), ncol=20, byrow=TRUE)
##plot the arrows
quiver2D(u = u,v=v,x = lon, y = lat,add=T,type="simple")
can any one help me with this? Any help would be appreciated.

Answer 1

First you need to figure out which function in the lattice paradigm is being called. That requires either looking at the ?spplot` help page (which I stupidly failed to do first), or following the classes and functions along the calling tree (which is what I actually did). And then look at the help page of the final function to see if there is a parameter you can pass to add contour lines:
showMethods("spplot",class="Raster", includeDefs=TRUE) # last argument need to see code
Function: spplot (package sp)
obj="Raster"
function (obj, ...)
{
.local <- function (obj, ..., maxpixels = 50000, as.table = TRUE,
zlim)
{
obj <- sampleRegular(obj, maxpixels, asRaster = TRUE,
useGDAL = TRUE)
if (!missing(zlim)) {
if (length(zlim) != 2) {
warning("zlim should be a vector of two elements")
}
if (length(zlim) >= 2) {
obj[obj < zlim[1] | obj > zlim[2]] <- NA
}
}
obj <- as(obj, "SpatialGridDataFrame")
spplot(obj, ..., as.table = as.table)
}
.local(obj, ...)
}
> showMethods("spplot",class="SpatialGridDataFrame",includeDefs=TRUE)
Function: spplot (package sp)
obj="SpatialGridDataFrame"
function (obj, ...)
spplot.grid(as(obj, "SpatialPixelsDataFrame"), ...)
> showMethods("spplot.grid",class="SpatialPixelsDataFrame",includeDefs=TRUE)
Function "spplot.grid":
<not an S4 generic function>
> spplot.grid
Error: object 'spplot.grid' not found
> getAnywhere(spplot.grid)
A single object matching ‘spplot.grid’ was found
It was found in the following places
namespace:sp
with value
function (obj, zcol = names(obj), ..., names.attr, scales = list(draw = FALSE),
xlab = NULL, ylab = NULL, aspect = mapasp(obj, xlim, ylim),
panel = panel.gridplot, sp.layout = NULL, formula, xlim = bbox(obj)[1,
], ylim = bbox(obj)[2, ], checkEmptyRC = TRUE, col.regions = get_col_regions())
{
if (is.null(zcol))
stop("no names method for object")
if (checkEmptyRC)
sdf = addNAemptyRowsCols(obj)
else sdf = as(obj, "SpatialPointsDataFrame")
if (missing(formula))
formula = getFormulaLevelplot(sdf, zcol)
if (length(zcol) > 1) {
sdf = spmap.to.lev(sdf, zcol = zcol, names.attr = names.attr)
zcol2 = "z"
}
else zcol2 = zcol
if (exists("panel.levelplot.raster")) {
opan <- lattice.options("panel.levelplot")[[1]]
lattice.options(panel.levelplot = "panel.levelplot.raster")
}
scales = longlat.scales(obj, scales, xlim, ylim)
args = append(list(formula, data = as(sdf, "data.frame"),
aspect = aspect, panel = panel, xlab = xlab, ylab = ylab,
scales = scales, sp.layout = sp.layout, xlim = xlim,
ylim = ylim, col.regions = col.regions), list(...))
if (all(unlist(lapply(obj#data[zcol], is.factor)))) {
args$data[[zcol2]] = as.numeric(args$data[[zcol2]])
if (is.null(args$colorkey) || (is.logical(args$colorkey) &&
args$colorkey) || (is.list(args$colorkey) && is.null(args$colorkey$at) &&
is.null(args$colorkey$labels))) {
if (!is.list(args$colorkey))
args$colorkey = list()
ck = args$colorkey
args$colorkey = NULL
args = append(args, colorkey.factor(obj[[zcol[1]]],
ck))
}
else args = append(args, colorkey.factor(obj[[zcol[1]]],
ck, FALSE))
}
ret = do.call(levelplot, args)
if (exists("panel.levelplot.raster"))
lattice.options(panel.levelplot = opan)
ret
}
<bytecode: 0x7fae5e6b7878>
<environment: namespace:sp>
You can see that it supports additional arguments passed via , list(...)). As it happens it's therefore fairly easy to add contour lines to a levelplot with contour=TRUE although that only appears in the Arguments list, but not in the named arguments in the Usage section for levelplot. Nonetheless testing in the example on ?levelplot page shows that it succeeds. Your example is not a particularly good one to illustrate with, since it is so fine-grained and has no pattern of ascending or descending levels. Nonetheless adding contour=TRUE, to the arguments to spplot does produce black contour lines. (The timestamp is due to lattice code in my Rprofile setup so won't show up on your device).
png(); plot(spplot(s,layout=c(3,1),sp.layout=poly, contour=TRUE,
colorkey =list(space = "right"),
names.attr = c("a","b","c"))) ; dev.off()
If one gets around to hacking spplot.grid or perhaps sp::panel.gridplot, then this material from the author of levelplot might be of use:
https://markmail.org/search/?q=list%3Aorg.r-project.r-help+lattice+add+contours+to+levelplot#query:list%3Aorg.r-project.r-help%20lattice%20add%20contours%20to%20levelplot%20from%3A%22Deepayan%20Sarkar%22+page:1+mid:w7q4l7dh6op2lfmt+state:results