# Introduction

This post is to simply introduce how to make a map in R environment, or more officially, geographic/spatial visualisation. However, I just found numerous methods to do this in R, depending on which data type you have. So this post will not introduce the basic of R and GIS. After all, I am also not an expert in this.

To make a map, at least two types of data are needed:

• Geographic Information System (GIS) data for position
• Research data per se for value

Sometimes these two are combined to a unified data (e.g., population data as an attribute in a shapefile). However, in most cases for those who are not studying geography (like me), we have to join the research data (in csv, netCDF) to GIS fields based on shared “key/id column”. The relevant GIS data probably can be found in third-party packages such as maps or mapdata, but for more demands like custom resolution, one have to download in other sources.

# CSV file with lat and long columns

There are two methods to plot a csv data frame on a map:

• plot layers using ggplot2

• transform to sf

Because the latter one is same to sections below, so I will introduce ggplot2, which is very (but not limitedly) proficient at analysing data frames.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  library(ggplot2) library(maps) # outline data for continents,countries library(mapdata) # extra map datasets library(mapproj) # map projection #library(maptools) # a quickest method to plot a global map # map("world") # Here I create a simple dataframe, which can be replaced to your data by read.csv() toy_df <- data.frame(city = c("Bristol", "Shangrao"), long = c(51.45, 28.45), lat = c(-2.59, 117.94)) world <- map_data("world") # a ggplot2 function to get a world data.frame,see also borders # notice x is lat and y is long, which differs normal impression ggplot(world) + geom_polygon(aes(x = long, y = lat, group=group)) + geom_label(data= toy_df, aes(lat, long, label=city)) + coord_map("mollweide", xlim=c(-180,180)) + # change the projection theme_minimal() 

Actuallyggfortify provides the autoplot function, which is a quicker wrapper for ggplot2. So we can do the same by using less command.

 1 2 3 4 5  library(ggfortify) world <- map('world', plot = FALSE, fill = TRUE) autoplot(world, geom = 'polygon') + geom_point(data = toy_df, aes(lat, long), color="red", size=2) 

There is another geom type: geom_map in ggplot. The difference between geom_map and geom_polygon is that the latter just plot the polygon (or position) and does not care about the value, but the geom_map contains both position and value information. Therefore, there must be a id columns shared by both polygon and value data frames, but no need to add lat/long in aes().

An example

 1 2 3 4 5 6 7 8  fr_map <- map_data("france") fr_data <- data.frame(region = unique(fr_map$region), value = rnorm(length(unique(fr_map$region)))) ggplot(fr_data, aes(map_id = region)) + geom_map(aes(fill = value), map=fr_map) + expand_limits(x = fr_map$long, y = fr_map$lat) + coord_fixed() 

# sf object + geom_sf

shp file can be read in R through sf or rgal, and then plot using ggplot .

 1 2  #from https://r-spatial.org/r/2018/10/25/ggplot2-sf.htm library(sf) 
 1  ## Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 8.2.1; sf_use_s2() is TRUE 
 1 2 3 4 5 6  library(rnaturalearth) #another public map data package #library(rnaturalearthdata) it_data =st_as_sf(map("italy", plot = FALSE, fill = TRUE)) #polygons it_sf <- ne_countries(scale = "medium", country="italy",returnclass = "sf") #an outline ggplot(it_sf)+geom_sf()+geom_sf(data = it_data, fill = NA) 
 1 2  #and you can add more geom_sf() based on data in your hand #plot(uk_sf$geometry) #uk_sf$geometry equals st_geomety(uk_sf) 

# sf object + tmap

tmap has a similar layer-based syntax to plot map, but should be more professional and specilised than ggplot2.

  1 2 3 4 5 6 7 8 9 10 11  #from https://geocompr.robinlovelace.net/adv-map.html library(spData) #library(spDataLarge) library(tmap) library(sf) world <- spData::world toy_sf <- st_as_sf(toy_df, coords = c("lat", "long"), crs=4326) #WGS84 tm_shape(world)+tm_borders()+tm_fill()+ tm_shape(toy_sf) + tm_dots(size=.5) 

# ggmap

ggmap is another friendly package for people from other research background, it provides a function get_map() to download some map data from google, open street map and so on.

 1 2 3 4 5 6 7 8 9  library(ggmap) #downloading raster data by get_map(). REQUIRE GOOGLE API gmap <- get_stamenmap(bbox = c(left = -10, bottom = 50, right = 5, top = 60), zoom = 6, maptype='watercolor', messaging = FALSE) ggmap(gmap) + theme_void() 

# raster + levelplot/geom_raster

netCDF data can be transformed to raster format.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15  library(ncdf4) library(terra) library(rasterVis) # an example file from UCAR # https://www.unidata.ucar.edu/software/netcdf/examples/files.html nc <- nc_open("tos_O1_2001-2002.nc") #names(nc\$var) # print all variables sst_K <- ncvar_get(nc, varid="tos") #in Kelvin sst <- sst_K - 273.15 #in Celsius #dim(sst) # check dimension #image(sst[,,1]) sst_raster <- flip(rast(t(sst[,,1]))) plot(sst_raster) 

We can also use ggplot to do the plotting. But notice that the array from netCDF is not containing CRS data, that’s why we have x-y axis with 0-1 range.

 1 2 3 4 5 6  library(ggplot2) #to use geom_raster/geom_tile, we should transfer raster to a data.frame sst_df <- sst_raster |> terra::as.data.frame(xy=TRUE) #pipe requires R > 4.1, otherwise use %>% in tidyverse names(sst_df)[3] <- "sst" ggplot(sst_df) + geom_raster(aes(x=x, y=y, fill=sst)) + theme_light() + scale_fill_viridis_c() 
 1 2  # what's the difference between |> and %>%? #https://stackoverflow.com/questions/67633022/what-are-the-differences-between-rs-new-native-pipe-and-the-magrittr-pipe 

As for the difference between geom_tile, geom_raster, let’s see the offical answer:

geom_rect() and geom_tile() do the same thing, but are parameterised differently: geom_rect() uses the locations of the four corners (xmin, xmax, ymin and ymax), while geom_tile() uses the center of the tile and its size (x, y, width, height). geom_raster() is a high performance special case for when all the tiles are the same size.

# More resources

• rworldmap for extra intersting data
• cowplot for subplot added on ggplot objects
• gganimate for animated plot
• leaflet for interactive map