Maps with Satelite Imagery

Introduction

Building maps of a study area using R is straight forward, flexible, and easily adaptable. For this example I am going to make a map of the region where my PhD research takes place in the SAVA region of Madagascar. Maps like these are in my Astrovirus paper and Leptospira in small mammals paper.

Data set up

The data needed to build these maps is just the locations of each of the villages and a shapefile of the boundary of Marojejy National Park. The shapefile is publicly available from Protected Planet. The geodata package has country and regional boarders. To work with spatial data the sf package is needed.

## coord reference desired (this matches the basemaps)
crs_desired <- 3857

## Village locations
village_locs <- data.frame(
  ## regional notes if this is a major city in the region
  regional = c(0, 0, 0, 0, 1, 1),
  village = c("Andatsakala", "Ampandrana", "Mandena", "Sarahandrano",
              "Sambava", "Andapa"),
  lat = c(-14.39810, -14.40613, -14.47705, -14.60757,
          -14.26652, -14.66350),
  lon = c(49.88619, 49.87721, 49.81470, 49.64776,
          50.16664, 49.65145)
) %>% 
  mutate(regional = as.factor(regional)) %>% 
  ## make spatial (currently WGS 84)
  st_as_sf(coords = c("lon", "lat"), crs=4326) %>% 
  ## re project
  st_transform(crs = crs_desired)

## national park shape file
national_park <- st_read("C:/Users/Kayla/Documents/marojejy_polygon/marojejy polygon/marojejy_polygon.shp")

Reading layer `marojejy_polygon' from data source 
  `C:\Users\Kayla\Documents\marojejy_polygon\marojejy polygon\marojejy_polygon.shp' 
  using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 0 fields
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: 49.53831 ymin: -14.61449 xmax: 49.8818 ymax: -14.29655
Geodetic CRS:  WGS 84

## re project
national_park <- national_park %>% 
  st_transform(crs = crs_desired)

## madagascar and sava region 
mada <- geodata::gadm(country = "Madagascar", level = 4, path=".")

mada <- st_as_sf(mada) %>% 
  st_transform(mada, crs=crs_desired)

## group the entire country geometry
madagascar <- mada %>% 
  group_by(COUNTRY) %>% 
  st_union()

## just sava region
sava <- mada %>% 
  filter(NAME_2 == "Sava") %>% 
  st_union()

Plot defaults

## use theme void to not get grid lines or axis labels
theme_set(theme_void())
theme_update(plot.title = element_text(hjust = 0.5),
             plot.subtitle = element_text(hjust = 0.5))

Making the maps

Country/region inset

Having an inset of the country and region is helpful for orienting readers to where in the world a map is located. For this I’ll just the country, region, and national park shapes. The ggspatial package has nice tools to get scale bars and north arrows.

## make inset maps of madagascar with Sava highlighted
ggplot() +
  ## country
  geom_sf(data = madagascar, 
          fill = "white", 
          col = "black") +
  ## region
  geom_sf(data = sava, 
          col = "black", 
          fill = "grey90") +
  ## park boundary
  geom_sf(data=national_park, 
          fill = "darkgreen", 
          col="grey20", 
          linewidth = 0.5)+
  ## north arrow
  annotation_north_arrow(location = "tl", which_north = "true", 
                         style = north_arrow_fancy_orienteering)

Including a box for the next inset around the study area would be helpful

## A 15km buffer around the villages for zoomed in inset
study_ext <- village_locs %>% 
  ## because projection is utm, dist units are m
  st_buffer(dist=15000) %>% 
  ## bounding box around that area
  st_bbox() %>% 
  st_as_sfc()

## update the previous map
(country_wide <- ggplot() +
  ## country
  geom_sf(data = madagascar, 
          fill = "white", 
          col = "black") +
  ## region
  geom_sf(data = sava, 
          col = "black", 
          fill = "grey70") +
  ## park boundary
  geom_sf(data=national_park, 
          fill = "darkgreen", 
          col="grey20", 
          linewidth = 0.5)+
    ## box of map extent
    geom_sf(data=study_ext, 
            col="black", 
            fill="transparent",
            linewidth = 0.75) +
  ## north arrow
  annotation_north_arrow(location = "tl", which_north = "true", 
                         style = north_arrow_fancy_orienteering)
)

Study area inset

It would be helpful to also have an inset with the study area.

## entire study area with a 2.5km buffer around each village 
study_ext_small <- village_locs %>% 
  ## just the villages in the study
  filter(regional == 0) %>% 
  ## because projection is utm, dist units are m
  st_buffer(dist=2500) %>% 
  ## bounding box around that area
  st_bbox() %>% 
  st_as_sfc()

## crop the sava region to that bigger buffer
sava_crop <- st_crop(sava, study_ext)

## plot that inset
ggplot() +
    ## regional crop
    geom_sf(data = sava_crop, 
            col = "black", 
            fill = "grey90") +
    ## box of map extent
    geom_sf(data=study_ext, 
            col="black", 
            fill="transparent", 
            linewidth = 1) +
    ## park boundary
    geom_sf(data = national_park, 
            fill = "darkgreen", 
            col="grey20")+
    ## study area
    # geom_sf(data = study_ext_small, 
    #         fill="transparent", 
    #         col="grey20", 
    #         linewidth = 1) +
    ## village locations if in study or regional city
    geom_sf(data = village_locs, 
            aes(col=regional, shape=regional)) +
    geom_sf_text(data = village_locs, 
                 aes(label = village),
                 ## this took some messing to figure out a good place for each
                 nudge_x = c(11000, 10000, 8000, 11000, -5000, 0),
                 nudge_y = c(1700, rep(-1500, 3), -1800, -1800)
                 ) +
    ## shapes and colors of points
    scale_color_manual(values = c("coral1", "maroon")) +
    scale_shape_manual(values = c(16, 15))+
    ## I don't need a legend for the cities
    theme(legend.position = "none") +
  labs(x=NULL, y=NULL)

For this to be clearer in the panels below use A, B, C instead

village_text <- village_locs %>% 
  mutate(inset_label = case_when(regional == 1 ~ village,
                                 village %in% c("Ampandrana",
                                                "Andatsakala") ~ "A",
                                 village == "Mandena" ~ "B",
                                 village == "Sarahandrano" ~ "C"))
(regional_inset <- ggplot() +
    ## regional crop
    geom_sf(data = sava_crop, 
            col = "black", 
            fill = "grey90") +
    ## box of map extent
    geom_sf(data=study_ext, 
            col="black", 
            fill="transparent", 
            linewidth = 1) +
    ## park boundary
    geom_sf(data = national_park, 
            fill = "darkgreen", 
            col="grey20")+
    ## study area
    # geom_sf(data = study_ext_small, 
    #         fill="transparent", 
    #         col="grey20", 
    #         linewidth = 1) +
    ## village locations if in study or regional city
    geom_sf(data = village_locs, 
            aes(col=regional, shape=regional)) +
    geom_sf_text(data = village_text, 
                 check_overlap = TRUE, #this removes duplicate A
                 aes(label = inset_label),
                 ## this took some messing to figure out a good place for each
                 nudge_x = c(rep(1500, 4), -5000, 0),
                 nudge_y = c(rep(-1000, 4), -1800, -1800)
                 ) +
    ## shapes and colors of points
    scale_color_manual(values = c("coral1", "maroon")) +
    scale_shape_manual(values = c(16, 15))+
    ## I don't need a legend for the cities
    theme(legend.position = "none") +
  labs(x=NULL, y=NULL))

Satellite imagery for each village

The basemaps package is useful for downloading publically available imagery.

## list availabale base map types
# get_maptypes()

## set defaults for the basemaps
set_defaults(map_service = "esri", map_type = "world_imagery")

The two most north eastern can go together.

## subset to those two villages
v_sub <- village_locs %>% 
  filter(village %in% c("Andatsakala", "Ampandrana"))  

## make a buffer 2.5km around that area
v_ext <- v_sub %>% 
  st_buffer(dist = 2500)

## because I want include the park boundary, also crop that to the area
park_crop <- st_crop(national_park, v_ext)

## basemap downloads as a ggplot
## this take
(p1 <- basemap_ggplot(v_ext, verbose = FALSE) +
  ## park boundary
  geom_sf(data = park_crop, 
          fill="transparent", 
          col="grey80", 
          linewidth  = 0.75,
          linetype = 2) +
  ## villages
    geom_sf(data = v_sub, 
            shape=16, 
            col="coral1", 
            size=2) +
    geom_sf_text(data = v_sub, 
                 aes(label = village),
                 color = "white",
                 nudge_y = -200) +
  ## scale bar 
  annotation_scale(location="br", 
                   pad_x = unit(1, "cm"), 
                   pad_y = unit(1, "cm"), 
                   text_col = "white",
                   text_cex = 1) +
  ## plot area formatting
  labs(x=NULL, y=NULL))

The next village

## subset to those two villages
v_sub <- village_locs %>% 
  filter(village %in% c("Mandena"))  

## make a buffer 2.5km around that area
v_ext <- v_sub %>% 
  st_buffer(dist = 2500)

## because I want include the park boundary, also crop that to the area
park_crop <- st_crop(national_park, v_ext)

## basemap downloads as a ggplot
## this take
(p2 <- basemap_ggplot(v_ext, verbose = FALSE) +
  ## park boundary
  geom_sf(data = park_crop, 
          fill="transparent", 
          col="grey80", 
          linewidth = 0.75,
          linetype = 2) +
  ## villages
    geom_sf(data = v_sub, 
            shape=16, 
            col="coral1", 
            size=2) +
    geom_sf_text(data = v_sub, 
                 aes(label = village),
                 color = "white",
                 nudge_y = -200) +
  ## scale bar 
  annotation_scale(location="br", 
                   pad_x = unit(1, "cm"), 
                   pad_y = unit(1, "cm"), 
                   text_col = "white",
                   text_cex = 1) +
  ## plot area formatting
  labs(x=NULL, y=NULL))

The southern most village

## subset to those two villages
v_sub <- village_locs %>% 
  filter(village %in% c("Sarahandrano"))  

## make a buffer 2.5km around that area
v_ext <- v_sub %>% 
  st_buffer(dist = 2500)

## because I want include the park boundary, also crop that to the area
park_crop <- st_crop(national_park, v_ext)

## basemap downloads as a ggplot
## this take
(p3 <- basemap_ggplot(v_ext, verbose = FALSE) +
  ## park boundary
  geom_sf(data = park_crop, 
          fill="transparent", 
          col="grey80", 
          linewidth = 0.75,
          linetype = 2) +
  ## villages
    geom_sf(data = v_sub, 
            shape=16, 
            col="coral1", 
            size=2) +
    geom_sf_text(data = v_sub, 
                 aes(label = village),
                 color = "white",
                 nudge_y = -200) +
  ## scale bar 
  annotation_scale(location="br", 
                   pad_x = unit(1, "cm"), 
                   pad_y = unit(1, "cm"), 
                   text_col = "white",
                   text_cex = 1) +
  ## plot area formatting
  labs(x=NULL, y=NULL))

Combined figure

Both the patchwork and cowplot packages are useful for combining ggplot into one figure. I’m going to use patchwork here. This involves choosing the size you want the final image to be then saving and making adjustments, then resaving. For example, the final plot below would benifit from a larger sized font in the text labels.

## plots west to east
plot_spacer() + p1 + p3 + p2  +
  plot_annotation(tag_levels = "A")
ggsave("village-panels.png", 
       dpi = 600, width = 8, height = 8, units = "in")

ggsave("regional-inset.png", plot = regional_inset,
       dpi = 600, width = 4, height = 4, units = "in")

ggsave("mada-studyarea.png", plot = country_wide,
       dpi = 600, width = 2, height = 3, units = "in")

The final touches can be put on in any simple formatting software, such as powerpoint. Here is the final figure.

--- title: "Maps with Satelite Imagery" description: "Making maps in R" author: - name: Kayla Kauffman url: https://https://kmkauffm.github.io/ orcid: 0000-0002-4897-9428 format: html: toc: true toc-location: left message: false warning: false code-fold: false code-tools: true theme: sandstone date: 2024-09-04 categories: [R, code, spatial] # self-defined categories image: areal-figure.png draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready! --- ```{r} #| echo: false #| message: false library(tidyverse) library(patchwork) library(sf) library(ggspatial) library(basemaps) ``` ## Introduction Building maps of a study area using R is straight forward, flexible, and easily adaptable. For this example I am going to make a map of the region where my PhD research takes place in the SAVA region of Madagascar. Maps like these are in my [Astrovirus](publications.qmd#section-1) paper and [Leptospira in small mammals](publications.qmd) paper. ## Data set up The data needed to build these maps is just the locations of each of the villages and a shapefile of the boundary of Marojejy National Park. The shapefile is publicly available from [Protected Planet](https://www.protectedplanet.net/2305). The `geodata` package has country and regional boarders. To work with spatial data the `sf` package is needed. ```{r} ## coord reference desired (this matches the basemaps) crs_desired <- 3857 ## Village locations village_locs <- data.frame( ## regional notes if this is a major city in the region regional = c(0, 0, 0, 0, 1, 1), village = c("Andatsakala", "Ampandrana", "Mandena", "Sarahandrano", "Sambava", "Andapa"), lat = c(-14.39810, -14.40613, -14.47705, -14.60757, -14.26652, -14.66350), lon = c(49.88619, 49.87721, 49.81470, 49.64776, 50.16664, 49.65145) ) %>% mutate(regional = as.factor(regional)) %>% ## make spatial (currently WGS 84) st_as_sf(coords = c("lon", "lat"), crs=4326) %>% ## re project st_transform(crs = crs_desired) ## national park shape file national_park <- st_read("C:/Users/Kayla/Documents/marojejy_polygon/marojejy polygon/marojejy_polygon.shp") ## re project national_park <- national_park %>% st_transform(crs = crs_desired) ## madagascar and sava region mada <- geodata::gadm(country = "Madagascar", level = 4, path=".") mada <- st_as_sf(mada) %>% st_transform(mada, crs=crs_desired) ## group the entire country geometry madagascar <- mada %>% group_by(COUNTRY) %>% st_union() ## just sava region sava <- mada %>% filter(NAME_2 == "Sava") %>% st_union() ``` Plot defaults ```{r} ## use theme void to not get grid lines or axis labels theme_set(theme_void()) theme_update(plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5)) ``` ## Making the maps ### Country/region inset Having an inset of the country and region is helpful for orienting readers to where in the world a map is located. For this I'll just the country, region, and national park shapes. The `ggspatial` package has nice tools to get scale bars and north arrows. ```{r} ## make inset maps of madagascar with Sava highlighted ggplot() + ## country geom_sf(data = madagascar, fill = "white", col = "black") + ## region geom_sf(data = sava, col = "black", fill = "grey90") + ## park boundary geom_sf(data=national_park, fill = "darkgreen", col="grey20", linewidth = 0.5)+ ## north arrow annotation_north_arrow(location = "tl", which_north = "true", style = north_arrow_fancy_orienteering) ``` Including a box for the next inset around the study area would be helpful ```{r} ## A 15km buffer around the villages for zoomed in inset study_ext <- village_locs %>% ## because projection is utm, dist units are m st_buffer(dist=15000) %>% ## bounding box around that area st_bbox() %>% st_as_sfc() ## update the previous map (country_wide <- ggplot() + ## country geom_sf(data = madagascar, fill = "white", col = "black") + ## region geom_sf(data = sava, col = "black", fill = "grey70") + ## park boundary geom_sf(data=national_park, fill = "darkgreen", col="grey20", linewidth = 0.5)+ ## box of map extent geom_sf(data=study_ext, col="black", fill="transparent", linewidth = 0.75) + ## north arrow annotation_north_arrow(location = "tl", which_north = "true", style = north_arrow_fancy_orienteering) ) ``` ### Study area inset It would be helpful to also have an inset with the study area. ```{r} ## entire study area with a 2.5km buffer around each village study_ext_small <- village_locs %>% ## just the villages in the study filter(regional == 0) %>% ## because projection is utm, dist units are m st_buffer(dist=2500) %>% ## bounding box around that area st_bbox() %>% st_as_sfc() ## crop the sava region to that bigger buffer sava_crop <- st_crop(sava, study_ext) ## plot that inset ggplot() + ## regional crop geom_sf(data = sava_crop, col = "black", fill = "grey90") + ## box of map extent geom_sf(data=study_ext, col="black", fill="transparent", linewidth = 1) + ## park boundary geom_sf(data = national_park, fill = "darkgreen", col="grey20")+ ## study area # geom_sf(data = study_ext_small, # fill="transparent", # col="grey20", # linewidth = 1) + ## village locations if in study or regional city geom_sf(data = village_locs, aes(col=regional, shape=regional)) + geom_sf_text(data = village_locs, aes(label = village), ## this took some messing to figure out a good place for each nudge_x = c(11000, 10000, 8000, 11000, -5000, 0), nudge_y = c(1700, rep(-1500, 3), -1800, -1800) ) + ## shapes and colors of points scale_color_manual(values = c("coral1", "maroon")) + scale_shape_manual(values = c(16, 15))+ ## I don't need a legend for the cities theme(legend.position = "none") + labs(x=NULL, y=NULL) ``` For this to be clearer in the panels below use A, B, C instead ```{r} village_text <- village_locs %>% mutate(inset_label = case_when(regional == 1 ~ village, village %in% c("Ampandrana", "Andatsakala") ~ "A", village == "Mandena" ~ "B", village == "Sarahandrano" ~ "C")) (regional_inset <- ggplot() + ## regional crop geom_sf(data = sava_crop, col = "black", fill = "grey90") + ## box of map extent geom_sf(data=study_ext, col="black", fill="transparent", linewidth = 1) + ## park boundary geom_sf(data = national_park, fill = "darkgreen", col="grey20")+ ## study area # geom_sf(data = study_ext_small, # fill="transparent", # col="grey20", # linewidth = 1) + ## village locations if in study or regional city geom_sf(data = village_locs, aes(col=regional, shape=regional)) + geom_sf_text(data = village_text, check_overlap = TRUE, #this removes duplicate A aes(label = inset_label), ## this took some messing to figure out a good place for each nudge_x = c(rep(1500, 4), -5000, 0), nudge_y = c(rep(-1000, 4), -1800, -1800) ) + ## shapes and colors of points scale_color_manual(values = c("coral1", "maroon")) + scale_shape_manual(values = c(16, 15))+ ## I don't need a legend for the cities theme(legend.position = "none") + labs(x=NULL, y=NULL)) ``` ### Satellite imagery for each village The `basemaps` package is useful for downloading publically available imagery. ```{r} ## list availabale base map types # get_maptypes() ## set defaults for the basemaps set_defaults(map_service = "esri", map_type = "world_imagery") ``` The two most north eastern can go together. ```{r} ## subset to those two villages v_sub <- village_locs %>% filter(village %in% c("Andatsakala", "Ampandrana")) ## make a buffer 2.5km around that area v_ext <- v_sub %>% st_buffer(dist = 2500) ## because I want include the park boundary, also crop that to the area park_crop <- st_crop(national_park, v_ext) ## basemap downloads as a ggplot ## this take (p1 <- basemap_ggplot(v_ext, verbose = FALSE) + ## park boundary geom_sf(data = park_crop, fill="transparent", col="grey80", linewidth = 0.75, linetype = 2) + ## villages geom_sf(data = v_sub, shape=16, col="coral1", size=2) + geom_sf_text(data = v_sub, aes(label = village), color = "white", nudge_y = -200) + ## scale bar annotation_scale(location="br", pad_x = unit(1, "cm"), pad_y = unit(1, "cm"), text_col = "white", text_cex = 1) + ## plot area formatting labs(x=NULL, y=NULL)) ``` The next village ```{r} ## subset to those two villages v_sub <- village_locs %>% filter(village %in% c("Mandena")) ## make a buffer 2.5km around that area v_ext <- v_sub %>% st_buffer(dist = 2500) ## because I want include the park boundary, also crop that to the area park_crop <- st_crop(national_park, v_ext) ## basemap downloads as a ggplot ## this take (p2 <- basemap_ggplot(v_ext, verbose = FALSE) + ## park boundary geom_sf(data = park_crop, fill="transparent", col="grey80", linewidth = 0.75, linetype = 2) + ## villages geom_sf(data = v_sub, shape=16, col="coral1", size=2) + geom_sf_text(data = v_sub, aes(label = village), color = "white", nudge_y = -200) + ## scale bar annotation_scale(location="br", pad_x = unit(1, "cm"), pad_y = unit(1, "cm"), text_col = "white", text_cex = 1) + ## plot area formatting labs(x=NULL, y=NULL)) ``` The southern most village ```{r} ## subset to those two villages v_sub <- village_locs %>% filter(village %in% c("Sarahandrano")) ## make a buffer 2.5km around that area v_ext <- v_sub %>% st_buffer(dist = 2500) ## because I want include the park boundary, also crop that to the area park_crop <- st_crop(national_park, v_ext) ## basemap downloads as a ggplot ## this take (p3 <- basemap_ggplot(v_ext, verbose = FALSE) + ## park boundary geom_sf(data = park_crop, fill="transparent", col="grey80", linewidth = 0.75, linetype = 2) + ## villages geom_sf(data = v_sub, shape=16, col="coral1", size=2) + geom_sf_text(data = v_sub, aes(label = village), color = "white", nudge_y = -200) + ## scale bar annotation_scale(location="br", pad_x = unit(1, "cm"), pad_y = unit(1, "cm"), text_col = "white", text_cex = 1) + ## plot area formatting labs(x=NULL, y=NULL)) ``` ## Combined figure Both the `patchwork` and `cowplot` packages are useful for combining ggplot into one figure. I'm going to use `patchwork` here. This involves choosing the size you want the final image to be then saving and making adjustments, then resaving. For example, the final plot below would benifit from a larger sized font in the text labels. ```{r, eval=FALSE} ## plots west to east plot_spacer() + p1 + p3 + p2 + plot_annotation(tag_levels = "A") ggsave("village-panels.png", dpi = 600, width = 8, height = 8, units = "in") ggsave("regional-inset.png", plot = regional_inset, dpi = 600, width = 4, height = 4, units = "in") ggsave("mada-studyarea.png", plot = country_wide, dpi = 600, width = 2, height = 3, units = "in") ``` The final touches can be put on in any simple formatting software, such as powerpoint. Here is the final figure. ![](areal-figure.png){fig-align="center"}