Plotting NCAR MUSICA outputs using R

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library(ncdf4)

library(colorout)

library(ggplot2)

library(cptcity)


fc <- list.files(path = "/glade/scratch/sibarra/SAAP/run",

                 pattern = "SAAP.cam.h0.2014",

                 full.names = T)

nc <- list.files(path = "/glade/scratch/sibarra/SAAP/run",

                 pattern = "SAAP.cam.h0.2014")


dates <- as.Date(nc, format = "SAAP.cam.h0.%Y-%m-%d-00000.nc")


nd <- paste0(strftime(dates, "%Y%m%d"), ".nc")


mi <- map_data('world', wrap=c(0,360))



# geo ####
lat <- ncvar_get(nc1, varid = "lat")
lon <- ncvar_get(nc1, varid = "lon")


#PM25 ####

x <- ncvar_get(nc1, varid = "PM25")

dtx <- data.table::data.table(
  lat = lat,
  lon = lon,
  x = x[, 32]*1e9
)

summary(dtx)

rc <- classInt::classIntervals(var = dtx$x,
                               n = 100, 
                               style = "quantile")$brks

ggplot(dtx, 
       aes(x = lon, 
           y = lat, 
           colour = x),
       alpha = 0.3) +
  geom_point() +
  scale_colour_gradientn(expression(PM[2.5]~mu*g*m^{-3}),
                         colours = cpt(rev = T), 
                         values = rc/max(rc)) +
  geom_polygon(data = mi, 
               aes(x = long,
                   y = lat,
                   group = group),
               fill = NA, 
               colour = "grey50") +
  coord_quickmap() +
  labs(x = NULL, y = NULL, 
       title = paste0("NCAR MUSICA South America ", nc[32])) +
  scale_x_continuous(expand = c(0, 0)) +
  scale_y_continuous(expand = c(0, 0)) +
  theme(text = element_text(size = 20),
        legend.key.height = unit(4, "lines"),
        plot.title = element_text(hjust = 0.5))



rc <- classInt::classIntervals(var = dtx[lon > 250 & lon < 350 &
                                           lat > -60 & lat < 15]$x,
                               n = 100, 
                               style = "sd")$brks

ggplot(dtx[lon > 250 & lon < 350 &
             lat > -60 & lat < 15], 
       aes(x = lon, 
           y = lat, 
           colour = x),
       alpha = 0.3) +
  geom_point(size = 3) +
  scale_colour_gradientn(expression(PM[2.5]~mu*g*m^{-3}),
                         colours = lucky(rev = T), 
                         values = rc/max(rc)) +
  geom_polygon(data = mi, 
               aes(x = long,
                   y = lat,
                   group = group),
               fill = NA, 
               colour = "grey50") +
  coord_quickmap(xlim = c(250, 350), 
                 ylim = c(-60, 15), 
                 expand = c(0,0)) +
  labs(x = NULL, y = NULL, 
       title = paste0("NCAR MUSICA South America ", nc[32])) +
  theme(text = element_text(size = 20),
        legend.key.height = unit(4, "lines"),
        plot.title = element_text(hjust = 0.5))





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