Plots for spatial elements — SpatImagePlot (original) (raw)

# \donttest{
set.seed(8525)
# --- SpatImagePlot ---
# Generate a sample SpatRaster
r <- terra::rast(
    nrows = 50, ncols = 40, vals = runif(2000),
    xmin = 0, xmax = 40, ymin = 0, ymax = 50,
    crs = ""
)
SpatImagePlot(r)

SpatImagePlot(r, raster = TRUE, raster_dpi = 20)

SpatImagePlot(r, alpha = 0.5, theme = "theme_blank",
    theme_args = list(add_coord = FALSE), fill_name = "value")

SpatImagePlot(r, ext = c(0, 10, 0, 10), flip_y = FALSE, palette = "viridis")


# --- SpatMasksPlot ---
m <- terra::rast(
   nrows = 50, ncols = 40,
   vals = sample(c(1:5, NA), 2000, replace = TRUE, prob = c(rep(0.04, 5), 0.8)),
   xmin = 0, xmax = 40, ymin = 0, ymax = 50,
   crs = ""
)
SpatMasksPlot(m, border_color = "red")

SpatMasksPlot(m, ext = c(0, 15, 0, 20), add_border = FALSE,
    palette_reverse = TRUE, fill_name = "value")
#> Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
#> ℹ Consider using `geom_tile()` instead.


# --- SpatShapesPlot ---
polygons <- data.frame(
   id = paste0("poly_", 1:10),
   cat = sample(LETTERS[1:3], 10, replace = TRUE),
   feat1 = rnorm(10),
   feat2 = rnorm(10),
   geometry = c(
       'POLYGON((64.6 75.3,66.0 70.5,66.4 70.2,67.0 69.8,72.8 70.4,64.6 75.3))',
       'POLYGON((56.7 63.0,52.3 65.6,48.0 63.2,51.2 55.7,57.1 59.2,56.7 63.0))',
       'POLYGON((9.9 16.5,9.3 15.9,8.0 13.1,11.5 7.8,17.8 11.3,9.9 16.5))',
       'POLYGON((64.9 37.2,60.3 37.4,57.6 31.7,58.9 29.3,64.0 28.1,64.9 37.2))',
       'POLYGON((30.5 49.1,22.4 46.5,22.4 43.9,30.9 41.9,31.6 42.9,30.5 49.1))',
       'POLYGON((78.3 57.8,70.5 61.6,71.6 52.7,72.2 52.5,77.4 54.5,78.3 57.8))',
       'POLYGON((41.8 23.8,41.3 25.9,41.0 26.4,36.5 28.7,35.8 28.6,41.8 23.8))',
       'POLYGON((15.7 75.9,14.2 74.4,15.7 67.5,23.0 69.8,23.4 71.7,15.7 75.9))',
       'POLYGON((80.7 37.4,75.3 31.3,77.1 28.5,82.5 28.0,83.1 28.5,80.7 37.4))',
       'POLYGON((15.5 37.8,14.4 38.6,7.3 32.6,8.3 30.9,15.1 30.2,15.5 37.8))'
   )
)

polygons <- terra::vect(polygons, crs = "EPSG:4326", geom = "geometry")

SpatShapesPlot(polygons)

SpatShapesPlot(polygons, ext = c(0, 20, 0, 20))

SpatShapesPlot(polygons, highlight = 'cat == "A"', highlight_color = "red2")

SpatShapesPlot(polygons, border_color = "red", border_size = 2)

SpatShapesPlot(polygons, fill_by = "cat", fill_name = "category")

# Let border color be determined by fill
SpatShapesPlot(polygons, fill_by = "cat", alpha = 0.6, border_color = TRUE)

SpatShapesPlot(polygons, fill_by = "feat1")

SpatShapesPlot(polygons, fill_by = c("feat1", "feat2"), palette = "RdYlBu")


# --- SpatPointsPlot ---
# create some random points in the above polygons
points <- data.frame(
  id = paste0("point_", 1:30),
  gene = sample(LETTERS[1:3], 30, replace = TRUE),
  feat1 = runif(30, 0, 100),
  feat2 = runif(30, 0, 100),
  size = runif(30, 1, 5),
  x = c(
    61.6, 14.3, 12.7, 49.6, 74.9, 58.9, 13.9, 24.7, 16.9, 15.6,
    72.4, 60.1, 75.4, 14.9, 80.3, 78.8, 16.7, 27.6, 48.9, 52.5,
    12.9, 11.8, 50.4, 25.6, 10.4, 51.9, 73.4, 26.8, 50.4, 60.0
  ),
  y = c(
    32.1, 12.8, 33.2, 59.9, 57.8, 31.9, 10.1, 46.8, 75.3, 69.0,
    60.0, 29.4, 54.2, 34.2, 35.3, 33.1, 74.7, 48.0, 63.2, 59.2,
    9.2, 15.1, 64.5, 47.1, 11.4, 60.1, 54.1, 44.5, 61.9, 30.3
  )
)

SpatPointsPlot(points)

SpatPointsPlot(points, color_by = "gene", size_by = "size", shape = 22,
  border_size = 1)

SpatPointsPlot(points, raster = TRUE, raster_dpi = 30, color_by = "feat1")

SpatPointsPlot(points, color_by = c("feat1", "feat2"), size_by = "size")

SpatPointsPlot(points, color_by = "feat1", hex = TRUE)

SpatPointsPlot(points, color_by = "gene", label = TRUE)

SpatPointsPlot(points, color_by = "gene", highlight = 1:20,
  highlight_color = "red2", highlight_stroke = 0.8)


# --- Graph/Network functionality ---
# Create a simple adjacency matrix for demonstration
set.seed(8525)
graph_mat <- matrix(0, nrow = 30, ncol = 30)
# Add some random connections with weights
for(i in 1:30) {
  neighbors <- sample(setdiff(1:30, i), size = sample(2:5, 1))
  graph_mat[i, neighbors] <- runif(length(neighbors), 0.1, 1)
}
rownames(graph_mat) <- colnames(graph_mat) <- rownames(points)
attr(points, "graph") <- graph_mat

SpatPointsPlot(points, color_by = "gene", graph = "@graph",
  edge_color = "grey60", edge_alpha = 0.3)

SpatPointsPlot(points, color_by = "feat1", graph = graph_mat,
  edge_size = c(0.1, 1), edge_alpha = 0.5)


# --- Use the `return_layer` argument to get the ggplot layers
ext = c(0, 40, 0, 50)
ggplot2::ggplot() +
  SpatImagePlot(r, return_layer = TRUE, alpha = 0.2, ext = ext) +
  SpatShapesPlot(polygons, return_layer = TRUE, ext = ext, fill_by = "white") +
  SpatPointsPlot(points, return_layer = TRUE, ext = ext, color_by = "feat1") +
  theme_box() +
  ggplot2::coord_sf(expand = 0) +
  ggplot2::scale_y_continuous(labels = function(x) -x)


# }