Author: Gilles Colling
Date: 2026-02-28

# Visualization

#### Gilles Colling

#### 2026-02-28

This vignette covers hexify’s visualization functions in detail: customizing appearance, showing points, creating heatmaps, and working with ggplot2.

## Sample Data

We’ll use European cities throughout:

    cities <- data.frame(
      name = c("Vienna", "Paris", "Madrid", "Berlin", "Rome",
               "Warsaw", "Prague", "Brussels", "Amsterdam", "Lisbon"),
      lon = c(16.37, 2.35, -3.70, 13.40, 12.50,
              21.01, 14.42, 4.35, 4.90, -9.14),
      lat = c(48.21, 48.86, 40.42, 52.52, 41.90,
              52.23, 50.08, 50.85, 52.37, 38.72)
    )

    grid <- hex_grid(area_km2 = 10000)
    result <- hexify(cities, lon = "lon", lat = "lat", grid = grid)

## Base R Plotting with plot()

The `plot()` method provides quick visualization with sensible defaults.

### Basic Plot

    plot(result, main = "European Cities")

    #> Spherical geometry (s2) switched on

### Customizing Colors and Styling

    plot(result,
         grid_fill = "steelblue",
         grid_border = "darkblue",
         grid_alpha = 0.6,
         basemap_fill = "ivory",
         basemap_border = "gray50",
         main = "Custom Styling")

    #> Spherical geometry (s2) switched on

### Disabling the Basemap

    plot(result,
         basemap = FALSE,
         grid_fill = "forestgreen",
         grid_border = "darkgreen",
         main = "No Basemap")

### Setting Map Extent

To control the map extent, use `crop = TRUE` with `crop_expand` to add padding:

    plot(result,
         crop = TRUE,
         crop_expand = 0.2,
         main = "Custom Extent (20% padding)")

    #> Spherical geometry (s2) switched on

## Showing Points

Points can be displayed on top of hexagon cells. By default, points are jittered within their assigned cell to avoid overplotting.

### Basic Points

    plot(result,
         show_points = TRUE,
         point_color = "red",
         main = "Cities with Points")

    #> Spherical geometry (s2) switched on

### Point Size Presets

The `point_size` parameter accepts presets that define what fraction of a hex cell a single point covers:

Preset | Coverage
--- | ---
`"tiny"` | ~2% of cell
`"small"` | ~5% of cell
`"normal"` / `"auto"` | ~10% of cell
`"large"` | ~20% of cell
`"very large"` | ~35% of cell

    oldpar <- par(mfrow = c(2, 2))

    plot(result, show_points = TRUE, point_size = "small",
         point_color = "red", main = "small (~5%)")
    #> Spherical geometry (s2) switched on
    plot(result, show_points = TRUE, point_size = "normal",
         point_color = "red", main = "normal (~10%)")
    #> Spherical geometry (s2) switched on
    plot(result, show_points = TRUE, point_size = "large",
         point_color = "red", main = "large (~20%)")
    #> Spherical geometry (s2) switched on
    plot(result, show_points = TRUE, point_size = "very large",
         point_color = "red", main = "very large (~35%)")

    #> Spherical geometry (s2) switched on

    par(oldpar)

### Custom Point Styling

    plot(result,
         show_points = TRUE,
         point_size = "small",
         point_color = "darkblue",
         point_alpha = 0.8,
         grid_fill = "lightyellow",
         grid_border = "orange",
         main = "Custom Point Styling")
    #> Warning in plot.window(...): "point_alpha" is not a graphical parameter
    #> Warning in plot.xy(xy, type, ...): "point_alpha" is not a graphical parameter
    #> Warning in axis(side = side, at = at, labels = labels, ...): "point_alpha" is
    #> not a graphical parameter
    #> Warning in axis(side = side, at = at, labels = labels, ...): "point_alpha" is
    #> not a graphical parameter
    #> Warning in box(...): "point_alpha" is not a graphical parameter
    #> Warning in title(...): "point_alpha" is not a graphical parameter

    #> Spherical geometry (s2) switched on

### Disabling Jitter

For exact point locations (no randomization):

    plot(result,
         show_points = TRUE,
         jitter = FALSE,
         point_color = "red",
         main = "Points at Cell Centers (No Jitter)")
    #> Warning in plot.window(...): "jitter" is not a graphical parameter
    #> Warning in plot.xy(xy, type, ...): "jitter" is not a graphical parameter
    #> Warning in axis(side = side, at = at, labels = labels, ...): "jitter" is not a
    #> graphical parameter
    #> Warning in axis(side = side, at = at, labels = labels, ...): "jitter" is not a
    #> graphical parameter
    #> Warning in box(...): "jitter" is not a graphical parameter
    #> Warning in title(...): "jitter" is not a graphical parameter

    #> Spherical geometry (s2) switched on

## ggplot2 with hexify_heatmap()

For ggplot2 users, `hexify_heatmap()` returns a ggplot object that can be further customized.

### Basic ggplot

    hexify_heatmap(result, basemap = "world", title = "European Cities")
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

### Customizing with ggplot2

Since `hexify_heatmap()` returns a ggplot object, you can add layers and modify themes:

    hexify_heatmap(result, basemap = "world") +
      labs(
        title = "Major European Cities",
        subtitle = "Assigned to ISEA hexagonal grid cells",
        caption = "Data: Sample cities"
      ) +
      theme_minimal() +
      theme(
        plot.title = element_text(face = "bold", size = 14),
        panel.grid = element_blank()
      )
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

### Adding Custom Layers

    # Get the city coordinates
    city_points <- st_as_sf(cities, coords = c("lon", "lat"), crs = 4326)

    hexify_heatmap(result, basemap = "world", title = "Cities with Labels") +
      geom_sf(data = city_points, color = "red", size = 2) +
      geom_sf_text(data = city_points, aes(label = name),
                   nudge_y = 0.8, size = 3, color = "darkgray") +
      coord_sf(xlim = c(-5, 25), ylim = c(45, 55))
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on
    #> Coordinate system already present.
    #> ℹ Adding new coordinate system, which will replace the existing one.
    #> Warning in st_point_on_surface.sfc(sf::st_zm(x)): st_point_on_surface may not
    #> give correct results for longitude/latitude data

## Heatmaps with Value Mapping

For choropleth-style visualizations with aggregated data, pass a `value` column to `hexify_heatmap()`.

### Creating Aggregated Data

    # Simulate observation data with counts
    set.seed(42)
    n_obs <- 100
    obs_data <- data.frame(
      lon = c(rnorm(60, 10, 8), rnorm(40, 0, 10)),
      lat = c(rnorm(60, 48, 5), rnorm(40, 52, 6)),
      count = rpois(n_obs, lambda = 50)
    )

    # Hexify
    grid <- hex_grid(area_km2 = 10000)
    obs_hex <- hexify(obs_data, lon = "lon", lat = "lat", grid = grid)

### Basic Heatmap

    hexify_heatmap(
      obs_hex,
      value = "count",
      title = "Observation Counts"
    )
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

### Customizing Colors

    hexify_heatmap(
      obs_hex,
      value = "count",
      colors = "YlOrRd",
      title = "Yellow-Orange-Red Palette"
    )
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

Available color palettes include any from `scale_fill_viridis_c()` or `scale_fill_distiller()`:

- Viridis options: `"viridis"`, `"magma"`, `"plasma"`, `"inferno"`, `"cividis"`, `"mako"`, `"rocket"`, `"turbo"`

- ColorBrewer sequential: `"YlOrRd"`, `"YlGnBu"`, `"Blues"`, `"Greens"`, `"Reds"`, `"Purples"`, etc.

    p1 <- hexify_heatmap(obs_hex, value = "count", colors = "viridis",
                         title = "viridis", xlim = c(-20, 35), ylim = c(35, 65))
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on
    p2 <- hexify_heatmap(obs_hex, value = "count", colors = "YlGnBu",
                         title = "YlGnBu", xlim = c(-20, 35), ylim = c(35, 65))
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

    gridExtra::grid.arrange(p1, p2, ncol = 2)

### Setting Map Extent

    hexify_heatmap(
      obs_hex,
      value = "count",
      xlim = c(-20, 35),
      ylim = c(35, 65),
      title = "Zoomed to Region",
      legend_title = "Count"
    )
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

### Basemap Options

    # With world basemap (default)
    hexify_heatmap(
      obs_hex,
      value = "count",
      basemap = "world",
      xlim = c(-20, 35),
      ylim = c(35, 65),
      title = "With World Basemap"
    )
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

    # Without basemap
    hexify_heatmap(
      obs_hex,
      value = "count",
      basemap = NULL,
      xlim = c(-20, 35),
      ylim = c(35, 65),
      title = "No Basemap"
    )
    #> Spherical geometry (s2) switched off
    #> Spherical geometry (s2) switched on

## World Map Helper

`plot_world()` provides a quick way to draw a world basemap:

    plot_world(fill = "lightgray", border = "gray50")

### Customizing the World Map

    plot_world(
      fill = "antiquewhite",
      border = "sienna",
      xlim = c(-30, 50),
      ylim = c(30, 70)
    )

## Pentagon Cell Visualization

The ISEA grid contains 12 pentagonal cells at the icosahedron vertices. Here’s how to visualize them:

    # Pentagon locations (icosahedron vertices in standard ISEA orientation)
    pentagon_coords <- data.frame(
      type = c("Pole", "Pole", rep("Vertex", 10)),
      lon = c(0, 0, seq(0, 324, by = 36)),
      lat = c(90, -90, rep(c(26.57, -26.57), 5))
    )

    # Assign to grid and get polygons
    grid <- hex_grid(area_km2 = 500000)
    pentagon_cells <- lonlat_to_cell(pentagon_coords$lon, pentagon_coords$lat, grid)

    pentagon_polys <- cell_to_sf(pentagon_cells, grid)

    ggplot() +
      geom_sf(data = hexify_world, fill = "gray95", color = "gray70", linewidth = 0.2) +
      geom_sf(data = pentagon_polys, fill = alpha("purple", 0.6),
              color = "purple", linewidth = 0.8) +
      labs(
        title = "Pentagon Cell Locations",
        subtitle = "12 pentagonal cells at icosahedron vertices (area = 5/6 of hexagons)"
      ) +
      theme_minimal() +
      theme(axis.text = element_blank(), axis.ticks = element_blank())

## Random Sampling Visualization

Visualizing uniformly sampled cells across Earth:

    # Grid parameters (coarse for faster build)
    grid <- hex_grid(area_km2 = 200000, aperture = 3)
    max_cell <- 10 * (3^grid@resolution) + 2

    # Sample random cell IDs
    set.seed(123)
    N <- 50
    random_cells <- sample(1:max_cell, N, replace = FALSE)

    # Generate polygons for sampled cells
    sample_polys <- cell_to_sf(random_cells, grid)

    ggplot() +
      geom_sf(data = hexify_world, fill = "gray95", color = "gray70", linewidth = 0.2) +
      geom_sf(data = sample_polys, fill = alpha("forestgreen", 0.5),
              color = "darkgreen", linewidth = 0.4) +
      labs(title = sprintf("Random Sample of %d Cells (~%.0f km2 each)", N, grid@area_km2)) +
      theme_minimal() +
      theme(axis.text = element_blank(), axis.ticks = element_blank())

## Building Custom Visualizations

For full control, generate polygons directly and use ggplot2:

    # Create data with a numeric variable
    set.seed(456)
    stations <- data.frame(
      lon = runif(50, -10, 30),
      lat = runif(50, 35, 60),
      temperature = rnorm(50, mean = 15, sd = 5)
    )

    # Hexify (coarser grid for faster build)
    grid <- hex_grid(area_km2 = 20000)
    stations_hex <- hexify(stations, lon = "lon", lat = "lat", grid = grid)

    # Aggregate temperature by cell
    stations_df <- as.data.frame(stations_hex)
    stations_df$cell_id <- stations_hex@cell_id
    cell_temps <- aggregate(temperature ~ cell_id, data = stations_df, FUN = mean)

    # Generate polygons and merge data
    cell_polys <- cell_to_sf(cell_temps$cell_id, grid)
    cell_polys <- merge(cell_polys, cell_temps, by = "cell_id")

    # Custom visualization
    europe <- hexify_world[hexify_world$continent == "Europe", ]

    ggplot() +
      geom_sf(data = europe, fill = "gray95", color = "gray60", linewidth = 0.2) +
      geom_sf(data = cell_polys, aes(fill = temperature),
              color = "white", linewidth = 0.2) +
      scale_fill_gradient2(
        low = "blue", mid = "white", high = "red",
        midpoint = 15, name = "Temp (°C)"
      ) +
      coord_sf(xlim = c(-10, 30), ylim = c(35, 60)) +
      labs(
        title = "Mean Temperature by Grid Cell",
        subtitle = "Diverging color scale centered at 15°C"
      ) +
      theme_minimal() +
      theme(
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        panel.grid = element_line(color = "gray90")
      )

## Function Reference

Function | Description
--- | ---
`plot()` | Base R plot method for HexData objects
`hexify_heatmap()` | ggplot2 visualization, returns modifiable ggplot object
`plot_world()` | Quick world basemap
`cell_to_sf()` | Generate sf polygons from cell IDs

## See Also

- `vignette("quickstart")` - Getting started with hexify

- `vignette("workflows")` - Complete analysis workflows