How to plot a spatially explicit hdf5 file? - r - raster - r

Question

I have an hdf5 data file that has lat/long and a dozen of values, for example temperature. I would like to plot so I can visualize the data in a map style so with lat/long in the axis. Is there a direct way to do it? I only found a very complicated way on a blog. With netcdf data I can just use plot(ncvariable) and it will work, not with a hdf5 file.
I am using the rhdf5. If I read the h5 file and a specific value I only get a vector
> library(rhdf5)
> ncep<-h5read("CB_OL1_1979OCT.h5", "sh")
> head(ncep)
[1] 1.03953242 0.79024571 2.29503083 0.43957919 0.36909071 -0.04498866
I am attaching the file. I am not sure you would call it a 3d, it's a simple raster with x,y,value.
h5 file

Answer 1

It's been some time since you asked, but in case you did not found a solution yet, I'd like to provide two approaches on how to handle this.
Since your hdf5 file is not available anymore, I just picked a random file provided here for illustration.
On the one hand, you could simply use plot(grid = TRUE) from {terra} after having read your hdf5 file using rast():
library(terra)
#> terra 1.6.17
# read netcdf file
r <- rast("AMSR_E_L3_DailyOcean_V04_20020619.hdf")
# get layer names
names(r)
#> [1] "Very_low_res_sst" "Low_res_sst" "Low_res_wind" "Med_res_wind"
#> [5] "Med_res_vapor" "High_res_cloud" "RFI_angle"
# subset dataset by layer name
rs <- r[["Med_res_vapor"]]
rs
#> class : SpatRaster
#> dimensions : 720, 1440, 1 (nrow, ncol, nlyr)
#> resolution : 0.25, 0.25 (x, y)
#> extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat Unknown datum based upon the Clarke 1866 ellipsoid
#> source : AMSR_E_L3_DailyOcean_V04_20020619.hdf:GlobalGrid:Med_res_vapor
#> varname : AMSR_E_L3_DailyOcean_V04_20020619
#> name : Med_res_vapor
plot(rs, grid = TRUE)
Or you could go for the little bit more complex solution, generating graticules manually using sf::st_graticules() first, followed by making use of {tidyterra} to be able to use {ggplot2} with SpatRaster and SpatVector objects from {terra}:
library(sf)
#> Linking to GEOS 3.9.1, GDAL 3.4.3, PROJ 7.2.1; sf_use_s2() is TRUE
library(ggplot2)
library(tidyterra)
grat <- st_graticule(lon = seq(-180, 180, 30),
lat = seq(-90, 90, 30),
ndiscr = 100) |>
st_transform("epsg:4326") |>
vect()
ggplot() +
geom_spatraster(data = rs) +
geom_spatvector(data = grat, color = alpha("grey60", 0.5)) +
coord_sf(expand = FALSE) +
scale_x_continuous(breaks = seq(-180, 180, 30)) +
scale_y_continuous(breaks = seq(-90, 90, 30))
#> SpatRaster resampled to ncells = 5e+05