Plotting netcdf in R with correct grid

Question

My goal is to plot nitrate (no3) data on a world map, using the correct longitude and latitude for these data.

There are two netcdf files:
1. with the data
2. with the grid information

Summary info on the data: no3 is an array of length x*y*sigma no3_df is 'x*y obs. of 3 variables' x = integer [180] y = integer [193] sigma = array[53]

I want to look at sigma ('depth') 20. I therefore did the following:

# Load the needed libraries to handle netcdf files
library(ncdf)
library(akima)

# Open data and grid files
file1 <- open.ncdf(file.choose())
grid  <- open.ncdf(file.choose())

# Read relevant variables/parameters from data file1
x <- get.var.ncdf(file1,varid="x")
y <- get.var.ncdf(file1,varid="y")
sigma <- get.var.ncdf(file1,varid="sigma")
no3 <- get.var.ncdf(file1,varid="no3")
sigma_plot <- no3[,,sigma=20]

# Read relevant variables/parameters from grid file
plon <- get.var.ncdf(grid,varid="plon")
plat <- get.var.ncdf(grid,varid="plat")

# Each cell of sigma_plot corresponds to one cell of plon and plat.
A <- array(c(plon,plat,sigma_plot),dim=c(180,193,3))

# Now B is an array containing for each row: (longitude, latitude, value).
B <- apply(A, 3, cbind)

# But it is not a regular grid, so interpolate to a regular grid. akima library
C <- interp(B[,1],B[,2],B[,3], 
            xo=seq(-180,180,1),yo=seq(-90,90,by=1), # tweak here the resolution
            duplicate='mean') # extra y values are duplicates

#########
# PLOTTING
#########

# This one works, but doesn't have a correct longitude and latitude:
filled.contour(x,y,sigma_plot, col=rich.colors(18))

# Try to plot with lon and lat
filled.contour(C, col=rich.colors(30))

Since the filled.contour plot doesn't have correct longitude and latitude, I would like to use ggplot. However, I don't know how to do this...

# And the plotting with ggplot
ggplot(aes(x=plon_datafrm,y=plat_datafrm),data=no3_df) +
  geom_raster() +
  coord_equal() +
  scale_fill_gradient()

This doesn't seem to work. I am net to ggplot so that might be the reason, I would truly appreciate any help.

Answer 1

library(ncdf)
data <- open.ncdf(file1)
no3 <- get.var.ncdf(data,varid="no3")
sigma_plot <- no3[,,20]
grid <- open.ncdf(file2)
plon <- get.var.ncdf(grid,varid="plon")
plat <- get.var.ncdf(grid,varid="plat")

Contrary to what I previously understood, each cell of sigma_plot corresponds to one cell of plon and plat.

A <- array(c(plon,plat,a),dim=c(180,193,3))
B <- apply(A, 3, cbind)

Now B is an array containing for each row: (longitude, latitude, value). But it is not a regular grid, so you need to interpolate a regular grid. Easiest way would be using interp from package akima :

library(akima)
C <- interp(B[,1],B[,2],B[,3], 
            xo=seq(-180,180,1),yo=seq(-90,90,by=1), #you can tweak here the resolution
            duplicate='mean') #for some reasons some entries are duplicates, i don t know how you want to handle it.

image(C) #for instance, or filled.contour if you prefer
library(maptools)
data(wrld_simpl)
plot(wrld_simpl, add=TRUE, col="white") #To add a simple world map on top