This lesson is being piloted (Beta version)

Plot Raster Data in R

Overview

Teaching: 20 min
Exercises: 10 min
Questions
  • How can I create categorized or customized maps of raster data?

  • How can I customize the color scheme of a raster image?

  • How can I layer raster data in a single image?

Objectives
  • Build customized plots for a single band raster using the ggplot2 package.

  • Layer a raster dataset on top of a hillshade to create an elegant basemap.

Things You’ll Need To Complete This Episode

See the lesson homepage for detailed information about the software, data, and other prerequisites you will need to work through the examples in this episode.

Plot Raster Data in R

This episode covers how to plot a raster in R using the ggplot2 package with customized coloring schemes. It also covers how to layer a raster on top of a hillshade to produce an eloquent map. We will continue working with the Digital Surface Model (DSM) raster for the NEON Harvard Forest Field Site.

Plotting Data Using Breaks

In the previous episode, we viewed our data using a continuous color ramp. For clarity and visibility of the plot, we may prefer to view the data “symbolized” or colored according to ranges of values. This is comparable to a “classified” map. To do this, we need to tell ggplot how many groups to break our data into, and where those breaks should be. To make these decisions, it is useful to first explore the distribution of the data using a bar plot. To begin with, we will use dplyr’s mutate() function combined with cut() to split the data into 3 bins.

DSM_HARV_df <- DSM_HARV_df %>%
                mutate(fct_elevation = cut(HARV_dsmCrop, breaks = 3))

ggplot() +
    geom_bar(data = DSM_HARV_df, aes(fct_elevation))

plot of chunk histogram-breaks-ggplot

If we want to know the cutoff values for the groups, we can ask for the unique values of fct_elevation:

unique(DSM_HARV_df$fct_elevation)
[1] (379,416] (342,379] (305,342]
Levels: (305,342] (342,379] (379,416]

And we can get the count of values in each group using dplyr’s group_by() and summarize() functions:

DSM_HARV_df %>%
        group_by(fct_elevation) %>%
        summarize(counts = n())
# A tibble: 3 x 2
  fct_elevation  counts
  <fct>           <int>
1 (305,342]      418891
2 (342,379]     1530073
3 (379,416]      370835

We might prefer to customize the cutoff values for these groups. Lets round the cutoff values so that we have groups for the ranges of 301–350 m, 351–400 m, and 401–450 m. To implement this we will give mutate() a numeric vector of break points instead of the number of breaks we want.

custom_bins <- c(300, 350, 400, 450)

DSM_HARV_df <- DSM_HARV_df %>%
  mutate(fct_elevation_2 = cut(HARV_dsmCrop, breaks = custom_bins))

unique(DSM_HARV_df$fct_elevation_2)
[1] (400,450] (350,400] (300,350]
Levels: (300,350] (350,400] (400,450]

Data Tips

Note that when we assign break values a set of 4 values will result in 3 bins of data.

The bin intervals are shown using ( to mean exclusive and ] to mean inclusive. For example: (305, 342] means “from 306 through 342”.

And now we can plot our bar plot again, using the new groups:

ggplot() +
  geom_bar(data = DSM_HARV_df, aes(fct_elevation_2))

plot of chunk histogram-custom-breaks

And we can get the count of values in each group in the same way we did before:

DSM_HARV_df %>%
  group_by(fct_elevation_2) %>%
  summarize(counts = n())
# A tibble: 3 x 2
  fct_elevation_2  counts
  <fct>             <int>
1 (300,350]        741815
2 (350,400]       1567316
3 (400,450]         10668

We can use those groups to plot our raster data, with each group being a different color:

ggplot() +
  geom_raster(data = DSM_HARV_df , aes(x = x, y = y, fill = fct_elevation_2)) + 
  coord_quickmap()

plot of chunk raster-with-breaks

The plot above uses the default colors inside ggplot for raster objects. We can specify our own colors to make the plot look a little nicer. R has a built in set of colors for plotting terrain, which are built in to the terrain.colors() function. Since we have three bins, we want to create a 3-color palette:

terrain.colors(3)
[1] "#00A600FF" "#ECB176FF" "#F2F2F2FF"

The terrain.colors() function returns hex colors - each of these character strings represents a color. To use these in our map, we pass them across using the scale_fill_manual() function.

ggplot() +
 geom_raster(data = DSM_HARV_df , aes(x = x, y = y,
                                      fill = fct_elevation_2)) + 
    scale_fill_manual(values = terrain.colors(3)) + 
    coord_quickmap()

plot of chunk ggplot-breaks-customcolors

More Plot Formatting

If we need to create multiple plots using the same color palette, we can create an R object (my_col) for the set of colors that we want to use. We can then quickly change the palette across all plots by modifying the my_col object, rather than each individual plot.

We can label the x- and y-axes of our plot too using xlab and ylab. We can also give the legend a more meaningful title by passing a value to the name argument of the scale_fill_manual() function.

my_col <- terrain.colors(3)

ggplot() +
 geom_raster(data = DSM_HARV_df , aes(x = x, y = y,
                                      fill = fct_elevation_2)) + 
    scale_fill_manual(values = my_col, name = "Elevation") + 
    coord_quickmap()

plot of chunk add-ggplot-labels

Or we can also turn off the labels of both axes by passing element_blank() to the relevant part of the theme() function.

ggplot() +
 geom_raster(data = DSM_HARV_df , aes(x = x, y = y,
                                      fill = fct_elevation_2)) + 
    scale_fill_manual(values = my_col, name = "Elevation") +
    theme(axis.title = element_blank()) + 
    coord_quickmap()

plot of chunk turn-off-axes

Challenge: Plot Using Custom Breaks

Create a plot of the Harvard Forest Digital Surface Model (DSM) that has:

  1. Six classified ranges of values (break points) that are evenly divided among the range of pixel values.
  2. Axis labels.
  3. A plot title.

Answers

DSM_HARV_df <- DSM_HARV_df  %>%
               mutate(fct_elevation_6 = cut(HARV_dsmCrop, breaks = 6)) 

 my_col <- terrain.colors(6)

ggplot() +
    geom_raster(data = DSM_HARV_df , aes(x = x, y = y,
                                      fill = fct_elevation_6)) + 
    scale_fill_manual(values = my_col, name = "Elevation") + 
    ggtitle("Classified Elevation Map - NEON Harvard Forest Field Site") +
    xlab("UTM Westing Coordinate (m)") +
    ylab("UTM Northing Coordinate (m)") + 
    coord_quickmap()

plot of chunk challenge-code-plotting

Layering Rasters

We can layer a raster on top of a hillshade raster for the same area, and use a transparency factor to create a 3-dimensional shaded effect. A hillshade is a raster that maps the shadows and texture that you would see from above when viewing terrain. We will add a custom color, making the plot grey.

First we need to read in our DSM hillshade data and view the structure:

DSM_hill_HARV <-
  raster("data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_DSMhill.tif")

DSM_hill_HARV
class       : RasterLayer 
dimensions  : 1367, 1697, 2319799  (nrow, ncol, ncell)
resolution  : 1, 1  (x, y)
extent      : 731453, 733150, 4712471, 4713838  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0 
data source : /home/travis/build/datacarpentry/r-raster-vector-geospatial/_episodes_rmd/data/NEON-DS-Airborne-Remote-Sensing/HARV/DSM/HARV_DSMhill.tif 
names       : HARV_DSMhill 
values      : -0.7136298, 0.9999997  (min, max)

Next we convert it to a dataframe, so that we can plot it using ggplot2:

DSM_hill_HARV_df <- as.data.frame(DSM_hill_HARV, xy = TRUE) 

str(DSM_hill_HARV_df)
'data.frame':	2319799 obs. of  3 variables:
 $ x           : num  731454 731454 731456 731456 731458 ...
 $ y           : num  4713838 4713838 4713838 4713838 4713838 ...
 $ HARV_DSMhill: num  NA NA NA NA NA NA NA NA NA NA ...

Now we can plot the hillshade data:

ggplot() +
  geom_raster(data = DSM_hill_HARV_df,
              aes(x = x, y = y, alpha = HARV_DSMhill)) + 
  scale_alpha(range =  c(0.15, 0.65), guide = "none") + 
  coord_quickmap()

plot of chunk raster-hillshade

Data Tips

Turn off, or hide, the legend on a plot by adding guide = "none" to a scale_something() function or by setting theme(legend.position = "none").

The alpha value determines how transparent the colors will be (0 being transparent, 1 being opaque).

We can layer another raster on top of our hillshade by adding another call to the geom_raster() function. Let’s overlay DSM_HARV on top of the hill_HARV.

ggplot() +
  geom_raster(data = DSM_HARV_df , 
              aes(x = x, y = y, 
                  fill = HARV_dsmCrop)) + 
  geom_raster(data = DSM_hill_HARV_df, 
              aes(x = x, y = y, 
                  alpha = HARV_DSMhill)) +  
  scale_fill_viridis_c() +  
  scale_alpha(range = c(0.15, 0.65), guide = "none") +  
  ggtitle("Elevation with hillshade") +
  coord_quickmap()

plot of chunk overlay-hillshade

Challenge: Create DTM & DSM for SJER

Use the files in the NEON_RemoteSensing/SJER/ directory to create a Digital Terrain Model map and Digital Surface Model map of the San Joaquin Experimental Range field site.

Make sure to:

  • include hillshade in the maps,
  • label axes on the DSM map and exclude them from the DTM map,
  • include a title for each map,
  • experiment with various alpha values and color palettes to represent the data.

Answers

# CREATE DSM MAPS

# import DSM data
DSM_SJER <- raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_dsmCrop.tif")
# convert to a df for plotting
DSM_SJER_df <- as.data.frame(DSM_SJER, xy = TRUE)

# import DSM hillshade
DSM_hill_SJER <- raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_dsmHill.tif")
# convert to a df for plotting
DSM_hill_SJER_df <- as.data.frame(DSM_hill_SJER, xy = TRUE)

# Build Plot
ggplot() +
    geom_raster(data = DSM_SJER_df , 
                aes(x = x, y = y, 
                     fill = SJER_dsmCrop,
                     alpha = 0.8)
                ) + 
    geom_raster(data = DSM_hill_SJER_df, 
                aes(x = x, y = y, 
                  alpha = SJER_dsmHill)
                ) +
    scale_fill_viridis_c() +
    guides(fill = guide_colorbar()) +
    scale_alpha(range = c(0.4, 0.7), guide = "none") +
    # remove grey background and grid lines
    theme_bw() + 
    theme(panel.grid.major = element_blank(), 
          panel.grid.minor = element_blank()) +
    xlab("UTM Westing Coordinate (m)") +
    ylab("UTM Northing Coordinate (m)") +
    ggtitle("DSM with Hillshade") +
    coord_quickmap()

plot of chunk challenge-hillshade-layering

# CREATE DTM MAP
# import DTM
DTM_SJER <- raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DTM/SJER_dtmCrop.tif")
DTM_SJER_df <- as.data.frame(DTM_SJER, xy = TRUE)

# DTM Hillshade
DTM_hill_SJER <- raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DTM/SJER_dtmHill.tif")
DTM_hill_SJER_df <- as.data.frame(DTM_hill_SJER, xy = TRUE)

ggplot() +
    geom_raster(data = DTM_SJER_df ,
                aes(x = x, y = y,
                     fill = SJER_dtmCrop,
                     alpha = 2.0)
                ) +
    geom_raster(data = DTM_hill_SJER_df,
                aes(x = x, y = y,
                  alpha = SJER_dtmHill)
                ) +
    scale_fill_viridis_c() +
    guides(fill = guide_colorbar()) +
    scale_alpha(range = c(0.4, 0.7), guide = "none") +
    theme_bw() +
    theme(panel.grid.major = element_blank(), 
          panel.grid.minor = element_blank()) +
    theme(axis.title.x = element_blank(),
          axis.title.y = element_blank()) +
    ggtitle("DTM with Hillshade") +
    coord_quickmap()

plot of chunk challenge-hillshade-layering

Key Points

  • Continuous data ranges can be grouped into categories using mutate() and cut().

  • Use built-in terrain.colors() or set your preferred color scheme manually.

  • Layer rasters on top of one another by using the alpha aesthetic.