Overlaying world map on a image plot in R - r

I am trying to plot a global map using latitude, longitude and grid data in R. For this I am using image and image.plot functions. Additionally I need to overlay global coastline for land area. However I am not sure how to place the map exactly over my image of gridded data. Map is appearing bit shifted to the left in the console and that part is not visible either. See sample code below with random grid data.
remove(list=ls())
library(fields)
library(maps)
grid_lon<-c(0.5:1:359.5)
grid_lat<-c(-89.5:89.5)
temp1<-matrix(data = rexp(200, rate = 10), nrow = 360, ncol = 180)#random matrix
zlim=c(0,0.25)
par(oma=c( 3,0,0,0))# c(bottom, left, top, right)#plot margins
image(grid_lon,grid_lat,temp1,axes=FALSE,xlab='',ylab='')
map("world", fill=TRUE, col="white", bg="white", ylim=c(-90, 90),add=TRUE)
title(main ='Main title')
image.plot(zlim=zlim,legend.only=TRUE,horizontal=TRUE,legend.mar=0.4,legend.shrink=0.4,legend.width=0.4,nlevel=64,axis.args = list(cex.axis =1,at=zlim, labels=zlim,mgp=c(1, 0, 0),tck=0),smallplot=c(.25,.72, 0,.030),
legend.args=list( text=expression(textstyle(atop('anomaly',
paste('(meters)')),cex.main=1.2)),cex=1.2, side=1, line=1.6)
)#end image.plot
box()

In general, when working with maps it is preferable to use spatial objects, for which a projection method can be defined. The coherence with the map is then better guaranteed. Since you are working with a filled grid, an obvious choice is to use a raster from package raster. Your code would then become:
require (raster)
require (maps)
temp1<-matrix(data = rexp(180*360, rate = 10), nrow = 360, ncol = 180) #random matrix
r<-raster(temp1,xmn=-179.5,xmx=179.5,ymn=-89.5,ymx=89.5,crs="+proj=longlat +datum=WGS84")
plot(r)
map("world",add=T,fill=TRUE, col="white", bg="white")
EDIT
This code does not take into account that the data comes as a 360*180 matrix, while it is desirable to plot (map) a 180*360 matrix. Transposing is risky because it may result in an upside-down image. In order to be sure that the right coordinates are associated with the right values, we can explicitly associate them, and afterwards transform into a spatial object. The for-loop doing this is in the code below is slow, maybe it can be made more efficient, but it does the job.
require (raster)
require (maps)
# basic data, as in code given
grid_lon<-seq(0.5,359.5,1)
grid_lat<-seq(-89.5,89.5,1)
temp1<-matrix(data = rexp(200, rate = 10), nrow = 360, ncol = 180)#random matrix
# transform into data frame, where coords are associated to values
tt<-data.frame(lon=rep(NA,64800),lat=rep(NA,64800),z=rep(NA,64800))
ct<-0
for (i in 1:360){
for (j in 1:180){
ct<-ct+1
tt$lon[ct]<-grid_lon[i]
tt$lat[ct]<-grid_lat[j]
tt$z[ct]<-temp1[i,j]
}
}
# transform to spatial structure
coordinates(tt)<- ~lon+lat
# make spatial structure gridded
gridded(tt)<-TRUE
# transform to raster
r<-raster(tt)
projection(r)<-crs("+proj=longlat +datum=WGS84")
# plot
plot(r)
map("world2",add=T,fill=TRUE, col="white", bg="white")

I found the answer after few attempts and a tip from colleague. What needs to be done is shift the longitude grid from 0:359 to -179.5:179.5 using following commands after grid_lon is declared:
indexes_to_shift<-180
grid_lon[grid_lon>=180]<-grid_lon[grid_lon>=180]-360
grid_lon<-c(tail(grid_lon, indexes_to_shift), head(grid_lon, indexes_to_shift))

Related

How do i get mapview to plot my raster image with the same colors as plotRGB or plot

I have a raster file that I have exported from ArcGIS as a georeferenced tif file.
The raster will be used as a background map in mapview because the mapview background layers CartoDB.Positron, CartoDB.DarkMatter, OpenStreetMap , Esri.WorldImagery and OpenTopoMapdont dont give the required background at the zoom level i need.
First I read my raster brick into R using the raster package and then I plot using plotRGB.
library(raster)
library(mapview)
r<-brick("KYENGERA2.tif")#raster exported from Arcgis read. has 4 bands
r<-subset(r,1:3) #Retain only layers/bands with RGB
plotRGB(r, 1,2,3, stretch='lin')
The result is as expected
I then create a new raster r2 with values 0 - 255 and assign a colortable based on the rgb values in r. I plot it in two difefrent ways and i get the same result.
pct <- rgdal::SGDF2PCT(as(r, "SpatialGridDataFrame"))
r2 <- setValues(raster(r), pct$idx-1) #create a new raster with values 0 - 255
colortable(r2) <- pct$ct #define 256 colors
plotRGB(r, 1,2,3, stretch='lin')
plot(r2)#plot(r2,col=r2#legend#colortable)
Here is the result and it is much better
However when I try mapview, the result is not as expected.
mapview(r2, col.regions = pct$ct,na.col="transparent")
Can anyone help me solve this issue with mapview?
I have taken a look at this but i couldnt figure out a solution.
You can simply use mapview::viewRGB()
viewRGB(r, 1, 2, 3, method = "ngb", quantiles = c(0, 1), maxpixels = ncell(r))

projectRaster results in different output when projecting with its own crs

For a function I want to reproject a raster input - itself the output after using crop and mask - using a user set CRS. I thought that projecting with the existing crs would do nothing and simply return the input raster. To my surprise this was not the case. Below a reproducible example
Create dummy raster:
library(raster)
# Download country polygin, in this case Malawi
mwi <- raster::getData("GADM", country = "MWI", level = 0)
# Create dummy raster
grid <- raster::raster() # 1 degree raster
grid <- raster::disaggregate(grid, fact = 12) # 5 arcmin
grid <- raster::crop(grid, mwi)
values(grid) <- rep(1, ncell(grid)) # Set a value
# The input raster with dimensions 94,39,3666
grid <- raster::mask(grid, mwi)
plot(grid)
grid
# Reproject the raster using its own crs. I use ngb as it is a categorical variable.
# This raster has dimensions 102, 47, 4794 so it seems a lot of white space (NA) is added.
own_crs <- crs(grid)
grid_reproj <- raster::projectRaster(grid, crs = own_crs, method = "ngb")
plot(grid_reproj)
grid_reproj
# To remove the white space I use trim
# This results in a waster with dimensions 93, 39, 3627
grid_trim <- raster::trim(grid_reproj)
plot(grid_trim)
grid_trim
# I also decided to compare the maps visually with mapview
library(mapview)
# There seems to be a trim function in mapview which I set to FALSE
# Also use the browser for easy viewing
options(viewer = NULL)
mapviewOptions(trim = FALSE)
mapviewGetOption("trim")
mapview(grid, col.regions = "green", legend = F) +
mapview(grid_reproj, col.regions = "red", legend = F) +
mapview(grid_trim, col.regions = "blue", legend = F)
Comparing the maps I observe two things:
(1) grid and grid_trim are nearly identical apart from a single grid cell
on top. Perhaps this is due to rounding,
(2) grid_reproj has a much larger dimensions and different extent. It also
seems as if the map is slightly shifted in comparison to the other maps. This
is corrected by trim, so I assume that these are in fact NA cells and the difference might be
related how mapview displays the maps.
Hence, my main question is, what is happening when rasterProject projects with
the same extent? And why does the result differ, even after trim?
To project raster data the right way you must supply another Raster* object, and not a only crs.
If you supply a crs, a new extent is computed, a bit larger than what is expected to be needed to avoid loosing data. Of course in this odd case where the crs is actually the same it would make sense to return the input unchanged.

How to properly project and plot raster in R

I have a raster in an equal area Behrmann projection and I would like to project it to the Mollweide projection and plot.
When I do this with the following code, however, the plotting doesn't seem right, as the map extends to the sides, and there are outlines of various landmasses where I wouldn't expect them.Also, the map extends beyond the plot window.
Can anyone please help me get this to plot nicely?
Thanks!
The data file used can be downloaded from this link.
Here is the code I have so far:
require(rgdal)
require(maptools)
require(raster)
data(wrld_simpl)
mollCRS <- CRS('+proj=moll')
behrmannCRS <- CRS('+proj=cea +lat_ts=30')
sst <- raster("~/Dropbox/Public/sst.tif", crs=behrmannCRS)
sst_moll <- projectRaster(sst, crs=mollCRS)
wrld <- spTransform(wrld_simpl, mollCRS)
plot(sst_moll)
plot(wrld, add=TRUE)
Alright, since the example at this page seems to work, I tried to mimic it as much as possible. I think problems arise because the far left and far right side of the raster image overlap. Cropping and an intermediate reprojection to Lat-Lon as in the example seem to solve your problem.
Perhaps this workaround can be a basis for a more elegant solution that directly addresses the problem, as it is not benificial to reproject a raster twice.
# packages
library(rgdal)
library(maptools)
library(raster)
# define projections
mollCRS <- CRS('+proj=moll')
behrmannCRS <- CRS('+proj=cea +lat_ts=30')
# read data
data(wrld_simpl)
sst <- raster("~/Downloads/sst.tif", crs=behrmannCRS)
# crop sst to extent of world to avoid overlap on the seam
world_ext = projectExtent(wrld_simpl, crs = behrmannCRS)
sst_crop = crop(x = sst, y=world_ext, snap='in')
# convert sst to longlat (similar to test file)
# somehow this gets rid of the unwanted pixels outside the ellipse
sst_longlat = projectRaster(sst_crop, crs = ('+proj=longlat'))
# then convert to mollweide
sst_moll <- projectRaster(sst_longlat, crs=mollCRS, over=T)
wrld <- spTransform(wrld_simpl, mollCRS)
# plot results
plot(sst_moll)
plot(wrld, add=TRUE)

How to plot contours on a map with ggplot2 when data is on an irregular grid?

Sorry for the wall of text, but I explain the question, include the data, and provide some code :)
QUESTION:
I have some climate data that I want to plot using R. I am working with data that is on an irregular, 277x349 grid, where (x=longitude, y=latitude, z=observation). Say z is a measure of pressure (500 hPa height (m)). I tried to plot contours (or isobars) on top of a map using the package ggplot2, but I am having some trouble due to the structure of the data.
The data comes from a regular, evenly spaced out 277x349 grid on a Lambert conformal projection, and for each grid point we have the actual longitude, latitude, and pressure measurement. It is a regular grid on the projection, but if I plot the data as points on a map using the actual longitude and latitude where the observations were recorded, I get the following:
I can make it look a little nicer by translating the rightmost piece to the left (maybe this can be done with some function, but I did this manually) or by ignoring the rightmost piece. Here is the plot with the right piece translated to the left:
(An aside) Just for fun, I tried my best to re-apply the original projection. I have some of the parameters for applying the projection from the data source, but I do not know what these parameters mean. Also, I do not know how R handles projections (I did read the help files...), so this plot was produced through some trial and error:
I tried to add the contour lines using the geom_contour function in ggplot2, but it froze my R. After trying it on a very small subset of the data, I found that out after some googling that ggplot was complaining because the data was on an irregular grid. I also found out that that is the reason geom_tile was not working. I am guessing that I have to make my grid of points evenly spaced out - probably by projecting it back into the original projection (?), or by evenly spacing out my data by either sampling a regular grid (?) or by extrapolating between points (?).
My questions are:
How can I draw contours on top of the map (preferably using ggplot2) for my data?
Bonus questions:
How do I transform my data back to a regular grid on the Lambert conformal projection? The parameters of the projection according to the data file include (mpLambertParallel1F=50, mpLambertParallel2F=50, mpLambertMeridianF=253, corners, La1=1, Lo1=214.5, Lov=253). I have no idea what these are.
How do I center my maps so that one side is not clipped (like in the first map)?
How do I make the projected plot of the map look nice (without the unnecessary parts of the map hanging around)? I tried adjusting the xlim and ylim, but it seems to apply the axes limits before projecting.
DATA:
I uploaded the data as rds files on Google drive. You can read in the files using the readRDS function in R.
lat2d: The actual latitude for the observations on the 2d grid
lon2d: The actual longitude for the observations on the 2d grid
z500: The observed height (m) where pressure is 500 millibars
dat: The data arranged in a nice data frame (for ggplot2)
I am told that the data is from the North American Regional Reanalysis data base.
MY CODE (THUS FAR):
library(ggplot2)
library(ggmap)
library(maps)
library(mapdata)
library(maptools)
gpclibPermit()
library(mapproj)
lat2d <- readRDS('lat2d.rds')
lon2d <- readRDS('lon2d.rds')
z500 <- readRDS('z500.rds')
dat <- readRDS('dat.rds')
# Get the map outlines
outlines <- as.data.frame(map("world", plot = FALSE,
xlim = c(min(lon2d), max(lon2d)),
ylim = c(min(lat2d), max(lat2d)))[c("x","y")])
worldmap <-geom_path(aes(x, y), inherit.aes = FALSE,
data = outlines, alpha = 0.8, show_guide = FALSE)
# The layer for the observed variable
z500map <- geom_point(aes(x=lon, y=lat, colour=z500), data=dat)
# Plot the first map
ggplot() + z500map + worldmap
# Fix the wrapping issue
dat2 <- dat
dat2$lon <- ifelse(dat2$lon>0, dat2$lon-max(dat2$lon)+min(dat2$lon), dat2$lon)
# Remake the outlines
outlines2 <- as.data.frame(map("world", plot = FALSE,
xlim = c(max(min(dat2$lon)), max(dat2$lon)),
ylim = c(min(dat2$lat), max(dat2$lat)))[c("x","y")])
worldmap2 <- geom_path(aes(x, y), inherit.aes = FALSE,
data = outlines2, alpha = 0.8, show_guide = FALSE)
# Remake the variable layer
ggp <- ggplot(aes(x=lon, y=lat), data=dat2)
z500map2 <- geom_point(aes(colour=z500), shape=15)
# Try a projection
projection <- coord_map(projection="lambert", lat0=30, lat1=60,
orientation=c(87.5,0,255))
# Plot
# Without projection
ggp + z500map2 + worldmap2
# With projection
ggp + z500map + worldmap + projection
Thanks!
UPDATE 1
Thanks to Spacedman's suggestions, I think I have made some progress. Using the raster package, I can directly read from an netcdf file and plot the contours:
library(raster)
# Note: ncdf4 may be a pain to install on windows.
# Try installing package 'ncdf' if this doesn't work
library(ncdf4)
# band=13 corresponds to the layer of interest, the 500 millibar height (m)
r <- raster(filename, band=13)
plot(r)
contour(r, add=TRUE)
Now all I need to do is get the map outlines to show under the contours! It sounds easy, but I'm guessing that the parameters for the projection need to be inputted correctly to do things properly.
The file in netcdf format, for those that are interested.
UPDATE 2
After much sleuthing, I made some more progress. I think I have the proper PROJ4 parameters now. I also found the proper values for the bounding box (I think). At the very least, I am able to roughly plot the same area as I did in ggplot.
# From running proj +proj=lcc +lat_1=50.0 +lat_2=50.0 +units=km +lon_0=-107
# in the command line and inputting the lat/lon corners of the grid
x2 <- c(-5628.21, -5648.71, 5680.72, 5660.14)
y2 <- c( 1481.40, 10430.58,10430.62, 1481.52)
plot(x2,y2)
# Read in the data as a raster
p4 <- "+proj=lcc +lat_1=50.0 +lat_2=50.0 +units=km +lon_0=-107 +lat_0=1.0"
r <- raster(nc.file.list[1], band=13, crs=CRS(p4))
r
# For some reason the coordinate system is not set properly
projection(r) <- CRS(p4)
extent(r) <- c(range(x2), range(y2))
r
# The contour map on the original Lambert grid
plot(r)
# Project to the lon/lat
p <- projectRaster(r, crs=CRS("+proj=longlat"))
p
extent(p)
str(p)
plot(p)
contour(p, add=TRUE)
Thanks to Spacedman for his help. I will probably start a new question about overlaying shapefiles if I can't figure things out!
Ditch the maps and ggplot packages for now.
Use package:raster and package:sp. Work in the projected coordinate system where everything is nicely on a grid. Use the standard contouring functions.
For map background, get a shapefile and read into a SpatialPolygonsDataFrame.
The names of the parameters for the projection don't match up with any standard names, and I can only find them in NCL code such as this
whereas the standard projection library, PROJ.4, wants these
So I think:
p4 = "+proj=lcc +lat_1=50 +lat_2=50 +lat_0=0 +lon_0=253 +x_0=0 +y_0=0"
is a good stab at a PROJ4 string for your data.
Now if I use that string to reproject your coordinates back (using rgdal:spTransform) I get a pretty regular grid, but not quite regular enough to transform to a SpatialPixelsDataFrame. Without knowing the original regular grid or the exact parameters that NCL uses we're a bit stuck for absolute precision here. But we can blunder on a bit with a good guess - basically just take the transformed bounding box and assume a regular grid in that:
coordinates(dat)=~lon+lat
proj4string(dat)=CRS("+init=epsg:4326")
dat2=spTransform(dat,CRS(p4))
bb=bbox(dat2)
lonx=seq(bb[1,1], bb[1,2],len=277)
laty=seq(bb[2,1], bb[2,2],len=349)
r=raster(list(x=laty,y=lonx,z=md))
plot(r)
contour(r,add=TRUE)
Now if you get a shapefile of your area you can transform it to this CRS to do a country overlay... But I would definitely try and get the original coordinates first.

How to get RGB raster image with UTM coordinates

I have a three layer raster with red, green, and blue channel values in it. I can plot the image with raster::plotRGB, but I need to add axes with UTM coordinates. Coordinates can be added with axes=TRUE, but they are floating in space and look bad. I would like to get the coordinates as they show up in plots created with the raster plot method, or better yet as they appear when using rasterVis::levelplot.
Ultimately, I need to create a raster image with UTM coordinates, a scale bar, and north arrow. This needs to be done using the plotRGB function in the raster package of R, or something with a similar functionality, as I need to assign the colour of each pixel by hand (no colour ramps).
This is an ancient post, but it's a good question so I'll give it an answer.
I'll give an example of how this might be done with rasterVis::levelplot, using the 3-channel R logo raster data that comes with raster.
library(rasterVis)
b <- brick(system.file("external/rlogo.grd", package="raster"))
Plotting three-channel RGB rasters with levelplot
Create an empty raster with the same dimensions and extent as the brick.
r <- raster(b)
Calculate the hexadecimal colours corresponding to the values of the RGB channels, and coerce to factor.
cols <- factor(rgb(b[], maxColorValue=255))
Assign these factor values to the raster's cells.
r[] <- cols
Plot with levelplot, extracting the hexadecimal colours from the levels of cols and passing them to col.regions.
levelplot(r, col.regions=as.character(levels(cols)), colorkey=FALSE)
Adding north arrow and scale bar
For the north arrow and the scale bar, we will look to #OscarPerpiñán's docs.
levelplot(r, col.regions=as.character(levels(cols)), colorkey=FALSE) +
layer(SpatialPolygonsRescale(layout.north.arrow(), offset = c(5, 10), scale = 10)) +
layer({
xs <- seq(5, 25, by=5)
grid.rect(x=xs, y=5,
width=5, height=2,
gp=gpar(fill=rep(c('transparent', 'black'), 2)),
default.units='native')
grid.text(x=xs-2.5, y=8, seq(0, 400, by=100),
gp=gpar(cex=0.7),
default.units='native')
})
I'll leave it up to you to calculate the true distance (passed to grid.text) associated with the width, in map units, of the rectangles.

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