Untitled

library(ncdf4)
library(lattice)
library(raster)

## Loading required package: sp

library(leaflet) # install.packages("leaflet")

nc <- "/mbon/data_big/satellite/chlor_a/clim/A20032007_chlor_a_CLIM_MO_GLOB_9km.nc"

ncdf <- nc_open(nc)

lon <- ncvar_get(ncdf, "longitude")[,1]
lat <- ncvar_get(ncdf, "latitude")[1,]

r = raster(nc, varname="January_chlor_a_clim") # , ext=extent(min(lon), max(lon), min(lat), max(lat)))

r <- flip(r, direction="y")
r <- setExtent(r, extent(min(lon), max(lon), min(lat), max(lat)))
crs(r) <- "+proj=longlat +datum=WGS84 +no_defs"
plot(r)

r

## class       : RasterLayer 
## dimensions  : 2160, 4320, 9331200  (nrow, ncol, ncell)
## resolution  : 0.08333333, 0.08333333  (x, y)
## extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
## coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 
## data source : in memory
## names       : layer 
## values      : 0.010876, 96.51842  (min, max)

r_l = leaflet::projectRasterForLeaflet(r)

## Warning in rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[, :
## 106 projected point(s) not finite

## Warning in rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[, :
## 106 projected point(s) not finite

pal <- colorNumeric(
  "Greens",  # RColorBrewer::display.brewer.all()
  values(r), na.color = "transparent")

leaflet() %>% 
  addProviderTiles("Stamen.TonerLite") %>%
  addRasterImage(r_l, colors = pal, opacity = 0.8) %>%
  addLegend(pal = pal, values = values(r),
    title = "Chl")