Sampling Stations Figure for Manuscript

Alexis Provencal

Author: Alexis Provencal

Resources

Objective

The objective is to reproduce the figure below. The figure is a combination of a base map, a locator map, labels, and a scale bar and north arrow. We can reproduce these items using sf, ggplot2, and ggspatial.

Example Figure

Citation: Wiegner TN, Mead LH, Molloy SL (2012) A Comparison of Water Quality Between Low- and High-Flow River Conditions in a Tropical Estuary, Hilo Bay, Hawaii. Estuar Coasts 36:319-333

Notes

When preparing figures for export, size matters. To render a plot in the size you are planning on exporting it in, put fig.height=3 in the chunk options. 3 is the height of the rendered figure in inches. What are chunk options? ```{r, chunkOptions}

Install packages

# install.packages("sf")
library(sf)
# install.packages("ggplot2")
library(ggplot2)
# install.packages("ggspatial")
library(ggspatial)

Importing data

Data was obtained from the Hawaii Statewide GIS Data website. The layers downloaded were “Coastlines” and “Streams”. The original CRS was found in the metadata file of each respective layer. The files uploaded to the working directory were the .shp and .shx files of each respective layer.

library(sf)

# Read in files
streams_raw_shp <- sf::st_read(dsn = "streams_dar.shp", stringsAsFactors = FALSE)

## Reading layer `streams_dar' from data source 
##   `/Users/alexisprovencal/Desktop/survey_area_figrure/streams_dar.shp' 
##   using driver `ESRI Shapefile'
## Simple feature collection with 10785 features and 0 fields
## Geometry type: LINESTRING
## Dimension:     XY
## Bounding box:  xmin: 375192.1 ymin: 2095488 xmax: 925123.5 ymax: 2458275
## CRS:           NA

original_crs <- sf::st_crs("+proj=utm +zone=4 +datum=NAD83 +units=m +no_defs")
sf::st_crs(streams_raw_shp) <- original_crs
streams <- sf::st_transform(streams_raw_shp, crs = 4326)
# plot(st_geometry(streams), axes = TRUE) # check

coastline_raw_shp <- sf::st_read(dsn = "coast_n83.shp", stringsAsFactors = FALSE)

## Reading layer `coast_n83' from data source 
##   `/Users/alexisprovencal/Desktop/survey_area_figrure/coast_n83.shp' 
##   using driver `ESRI Shapefile'
## Simple feature collection with 13 features and 0 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: 371124.5 ymin: 2094231 xmax: 940278.9 ymax: 2458612
## CRS:           NA

original_crs <- sf::st_crs("+proj=utm +zone=4 +datum=NAD83 +units=m +no_defs")
sf::st_crs(coastline_raw_shp) <- original_crs
coastlines <- sf::st_transform(coastline_raw_shp, crs = 4326)
# plot(st_geometry(coastlines), axes = TRUE, lwd = 3) # check

Plotting Hilo Bay with `ggplot2`

Make base map

library(ggplot2)
library(ggspatial)

# Map coastline layer and stream layer overlay
base_map_0 <- ggplot() +
  ggplot2::geom_sf(data=coastlines, fill = "gray80", color = "black", lwd = 0.5) +
  ggplot2::geom_sf(data=streams, color = "black", lwd = 0.25) +
  ggplot2::coord_sf(datum=st_crs(streams))

# Zoom in to Hilo Bay, Hawaii 
base_map_1 <- base_map_0 +
  scale_x_continuous(limits = c(-155.1025, -155.04), 
                     breaks = c(-155.09)) +
  scale_y_continuous(limits = c(19.707, 19.760), 
                     breaks = c(19.75)) 

# Add map labels
base_map_2 <- base_map_1 +
  geom_text(aes(x = -155.075, y = 19.75, label = "Pacific Ocean"),
            size = 5, color = "black", 
            fontface = "italic", family = "times") +
  geom_text(aes(x = -155.065, y = 19.718, label = "Wailoa River"),
            size = 3, color = "black", 
            fontface = "bold", family = "times") +
  geom_text(aes(x = -155.097256, y = 19.728130, label = "Wailuku River"),
            size = 3, color = "black", 
            fontface = "bold", family = "times")

# # Add station labels
# base_map_2_a <- base_map_2 +
#   geom_text(data = station_locations,
#             aes(x = Long, y = Lat, label = Station),
#             size = 2.7, color = "black",
#             family = "times")

# Add scale bar and north arrow
base_map_3 <- base_map_2 +
  ggspatial::annotation_scale(
    style = "ticks",
    location = "br",
    text_family = "times",
    text_cex = 1
  ) +
  ggspatial::annotation_north_arrow(
    which_north = "true",
    location = "tl",
    pad_x = unit(1.1, "in"), 
    pad_y = unit(0.1, "in"),
    height = unit(0.25, "in"),
    width = unit(0.15, "in"),
    style = ggspatial::north_arrow_orienteering(
      line_width = 0.8,
      line_col = "black",
      fill = c("white", "black"),
      text_col = "black",
      text_family = "times",
      text_face = NULL,
      text_size = 5,
      text_angle = 0)
    ) 

# Theme base map
base_map_4 <- base_map_3 +
  theme(panel.border = element_rect(color = "black", fill = NA, size = 1),
        text = element_text(family = "times"),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        axis.text.y = element_text(angle = 90, vjust = 0.5, hjust = 0.5, size = 12,
                                   color = "black", family = "times"),
        axis.text.x = element_text(size = 12, color = "black", family = "times"),
        panel.background = element_rect(fill = "white"))

base_map <- base_map_4

base_map

Make locator map

# Define the bounding box coordinates
hawaii_island_xlim <- c(-156.368408, -154.335938)
hawaii_island_ylim <- c(18.583776, 20.344627)

# Specify the box parameters
box_xlim <- c(-155.13, -154.975891)
box_ylim <- c(19.678798, 19.810638)

# Create an st_bbox object
big_island <- st_bbox(c(
  xmin = hawaii_island_xlim[1], 
  xmax = hawaii_island_xlim[2], 
  ymin = hawaii_island_ylim[1], 
  ymax = hawaii_island_ylim[2]), 
  crs = 4326)

# Zoom in to Hawaii Island
locator_map_base <- st_crop(coastlines, big_island)

# Create the base locator map
locator_map_0 <- ggplot() +
  geom_sf(data = locator_map_base, fill = "gray90", color = "black")

# Add box to resemble zoomed in map area
locator_map_1 <- locator_map_0 +
  geom_rect(
    aes(
      xmin = box_xlim[1],
      xmax = box_xlim[2],
      ymin = box_ylim[1],
      ymax = box_ylim[2]
      ),
    color = "black", fill = NA, size = 0.25) 

# Label
locator_map_2 <- locator_map_1 +
  geom_text(aes(x = -155.55, y = 19.55, 
                label = "Island of\nHawai'i"),
            size = 3, color = "black", family = "times") 

# Theme
locator_map_3 <- locator_map_2 +
  theme_void()+
  theme(panel.border = element_rect(color = "black", fill = NA, size = 1),
        panel.background = element_rect(fill = "white"))

locator_map <- locator_map_3

locator_map

Inset the locator map in the base map

# Inset the locator map into the base map
final_map <- base_map + annotation_custom(grob = ggplotGrob(locator_map), 
                            xmin = -155.052, xmax = -155.0375,
                            ymin = 19.74325, ymax = 19.764875)
final_map

Saving the plot

library(ggplot2)

ggplot2::ggsave(filename = "survey_area.png", 
                plot = final_map,
                device = "png",
                dpi = 320,
                path = NULL,
                height = 4,
                units = "in")

## Saving 10 x 4 in image

How to overlay shapefiles in Base R

# Plot coastlines with axes
plot(st_geometry(coastlines), axes = TRUE, lwd = 1, col = "gray",
     xlim = c(-155.1, -155.04),
     ylim = c(19.72, 19.760))

# Overlay streams on the existing plot
plot(st_geometry(streams), add = TRUE,
     xlim = c(-155.1, -155.04),
     ylim = c(19.72, 19.760))