Add functions to compute tile colors

R/ternary_density.R

@@ -92,7 +92,8 @@ coordinates_kde <- function(x, y, z, h = NULL, n = 25,
     y = ratio[, 2],
     h = h,
     n = n,
-    lims = c(lims, lims) # x and y range should be same
+    xlim = lims, # x and y range should be same
+    ylim = lims
   )
 
   ## Compute contours
@@ -106,10 +107,11 @@ coordinates_kde <- function(x, y, z, h = NULL, n = 25,
 }
 
 ## Adapted from MASS::kde2d
-kde <- function(x, y, h = NULL, n = 25, lims = c(range(x), range(y))) {
+kde <- function(x, y, h = NULL, n = 25, gx = NULL, gy = NULL,
+                xlim = range(x), ylim = range(y)) {
   n <- rep(n, length.out = 2L)
-  gx <- seq(lims[1L], lims[2L], length.out = n[1L])
-  gy <- seq(lims[3L], lims[4L], length.out = n[2L])
+  if (is.null(gx)) gx <- seq(xlim[1L], xlim[2L], length.out = n[1L])
+  if (is.null(gy)) gy <- seq(ylim[1L], ylim[2L], length.out = n[2L])
 
   if (is.null(h)) {
     h <- c(bandwidth(x), bandwidth(y))

R/ternary_image.R

@@ -13,31 +13,90 @@ setMethod(
     tri <- .triangle_center(n)
     xyz <- coordinates_cartesian(tri$x, tri$y)
     val <- f(xyz$x, xyz$y, xyz$z, ...)
+    ok <- seq_along(tri$x)
 
     if (isFALSE(palette)) {
       color <- val
     }
     if (is.null(palette)) {
-     palette <- function(x) {
-       x <- (x - min(x)) / (max(x) - min(x)) # Rescale to [0,1]
-       col <- grDevices::hcl.colors(256L, palette = "viridis")
-       grDevices::rgb(grDevices::colorRamp(col)(x), maxColorValue = 255)
-     }
+      palette <- function(x) {
+        x <- (x - min(x)) / (max(x) - min(x)) # Rescale to [0,1]
+        col <- grDevices::hcl.colors(256L, palette = "viridis")
+        grDevices::rgb(grDevices::colorRamp(col)(x), maxColorValue = 255)
+      }
     }
     if (is.function(palette)) {
-      color <- palette(val)
+      ok <- is.finite(val) # Remove NA/Inf (if any)
+      color <- palette(val[ok])
     }
 
     .triangle_tile(
-      x = tri$x,
-      y = tri$y,
-      direction = tri$direction,
+      x = tri$x[ok],
+      y = tri$y[ok],
+      direction = tri$direction[ok],
       resolution = tri$resolution,
       col = color
     )
   }
 )
 
+xyz_density <- function(x, y, z) {
+  ## ILR
+  coda <- cbind(x, y, z)
+  ratio <- ilr(coda)
+
+  ## Compute KDE
+  function(x, y, z) {
+    xyz <- cbind(x, y, z)
+    xy <- ilr(xyz)
+    dens <- kde(
+      x = ratio[, 1],
+      y = ratio[, 2],
+      gx = sort(unique(xy[, 1])),
+      gy = sort(unique(xy[, 2]))
+    )
+
+    i <- as.numeric(as.factor(rank(xy[, 1])))
+    j <- as.numeric(as.factor(rank(xy[, 2])))
+
+    dens$z[cbind(i, j)]
+  }
+}
+
+xyz_interpolate <- function(x, y, z, value, method = "linear", ...) {
+  ## Validation
+  if (!requireNamespace("interp", quietly = TRUE)) {
+    msg <- "The interp package is required. Please install it."
+    stop(msg, call. = FALSE)
+  }
+  assert_length(value, length(x))
+
+  ## ILR
+  coda <- cbind(x, y, z)
+  ratio <- ilr(coda)
+
+  ## Compute KDE
+  function(x, y, z) {
+    xyz <- cbind(x, y, z)
+    xy <- ilr(xyz)
+
+    interp <- interp::interp(
+      x = ratio[, 1],
+      y = ratio[, 2],
+      z = value,
+      xo = sort(unique(xy[, 1])),
+      yo = sort(unique(xy[, 2])),
+      method = method,
+      ...
+    )
+
+    i <- as.numeric(as.factor(rank(xy[, 1])))
+    j <- as.numeric(as.factor(rank(xy[, 2])))
+
+    interp$z[cbind(i, j)]
+  }
+}
+
 .triangle_center <- function(resolution) {
 
   offset <- 1 / resolution / 2L

inst/tinytest/test_geometry.R

@@ -74,18 +74,4 @@ if (at_home()) {
     ternary_text(coda, col = "red")
   }
   expect_snapshot_plot(geom_text, "geom_text")
-
-  # Image ======================================================================
-  f <- function(x, y, z) x - z + (3 * x * y) + (50 * x * y * z)
-  image_function <- function() {
-    ternary_plot(NULL)
-    ternary_image(f = f, n = 48)
-  }
-  expect_snapshot_plot(image_function, "image_function")
-
-  image_rgb <- function() {
-    ternary_plot(NULL, xlab = "Red", ylab = "Green", zlab = "Blue")
-    ternary_image(f = grDevices::rgb, n = 20, palette = FALSE)
-  }
-  expect_snapshot_plot(image_rgb, "image_rgb")
 }

inst/tinytest/test_statistics.R

@@ -64,41 +64,35 @@ if (at_home()) {
     ternary_pca(lava, axis = 1)
   }
   expect_snapshot_plot(pca_1, "pca_1")
-}
-if (at_home() && requireNamespace("interp", quietly = TRUE)) {
-  using("tinysnapshot")
-  options(tinysnapshot_device = "svglite")
-  options(tinysnapshot_height = 7) # inches
-  options(tinysnapshot_width = 7)
-  options(tinysnapshot_tol = 200) # pixels
-  options(tinysnapshot_os = "Linux")
 
   # Contour ====================================================================
-  a <- matrix(rep(seq(0, 1, length = 50), each = 50), nrow = 50, byrow = TRUE)
-  b <- matrix(rep(seq(0, 1, length = 50), each = 50), nrow = 50, byrow = FALSE)
-  mask <- a + b <= 1
-  a <- a[mask]
-  b <- b[mask]
-  coords <- cbind(b, 1 - a - b, a)
-  value <- sin(3.2 * pi * (a + b)) + sin(3 * pi * (a - b))
+  if (requireNamespace("interp", quietly = TRUE)) {
+    a <- matrix(rep(seq(0, 1, length = 50), each = 50), nrow = 50, byrow = TRUE)
+    b <- matrix(rep(seq(0, 1, length = 50), each = 50), nrow = 50, byrow = FALSE)
+    mask <- a + b <= 1
+    a <- a[mask]
+    b <- b[mask]
+    coords <- cbind(b, 1 - a - b, a)
+    value <- sin(3.2 * pi * (a + b)) + sin(3 * pi * (a - b))
 
-  # col <- colorRamp(c("blue", "red"))(scales::rescale_mid(value))
-  # col <- rgb(col[, 1], col[, 2], col[, 3], maxColorValue = 255)
-  # ternary_plot(coords, panel.first = ternary_grid(), pch = 16, col = col)
+    # col <- colorRamp(c("blue", "red"))(scales::rescale_mid(value))
+    # col <- rgb(col[, 1], col[, 2], col[, 3], maxColorValue = 255)
+    # ternary_plot(coords, panel.first = ternary_grid(), pch = 16, col = col)
 
-  ## Contour ILR
-  contour_ilr <- function() {
-    ternary_plot(NULL)
-    ternary_contour(coords, value = value, n = 100, nlevels = 10, ilr = TRUE)
-  }
-  expect_snapshot_plot(contour_ilr, "contour_ilr")
+    ## Contour ILR
+    contour_ilr <- function() {
+      ternary_plot(NULL)
+      ternary_contour(coords, value = value, n = 100, nlevels = 10, ilr = TRUE)
+    }
+    expect_snapshot_plot(contour_ilr, "contour_ilr")
 
-  ## Contour Cartesian
-  contour_cartesian <- function() {
-    ternary_plot(NULL)
-    suppressWarnings( # Remove warnings (collinear points)
-      ternary_contour(coords, value = value, n = 100, nlevels = 10, ilr = FALSE)
-    )
+    ## Contour Cartesian
+    contour_cartesian <- function() {
+      ternary_plot(NULL)
+      suppressWarnings( # Remove warnings (collinear points)
+        ternary_contour(coords, value = value, n = 100, nlevels = 10, ilr = FALSE)
+      )
+    }
+    expect_snapshot_plot(contour_cartesian, "contour_cartesian")
   }
-  expect_snapshot_plot(contour_cartesian, "contour_cartesian")
 }

inst/tinytest/test_tiles.R

@@ -0,0 +1,35 @@
+if (at_home()) {
+  using("tinysnapshot")
+  options(tinysnapshot_device = "svglite")
+  options(tinysnapshot_height = 7) # inches
+  options(tinysnapshot_width = 7)
+  options(tinysnapshot_tol = 200) # pixels
+  options(tinysnapshot_os = "Linux")
+
+  # Image ======================================================================
+  image_rgb <- function() {
+    ternary_plot(NULL, xlab = "Red", ylab = "Green", zlab = "Blue")
+    ternary_image(f = grDevices::rgb, n = 20, palette = FALSE)
+  }
+  expect_snapshot_plot(image_rgb, "image_rgb")
+
+  # Density ====================================================================
+  f <- isopleuros:::xyz_density(lava[, 1], lava[, 2], lava[, 3])
+  image_density <- function() {
+    ternary_plot(NULL)
+    ternary_image(f = f, n = 24)
+    ternary_points(lava, col = "red", pch = 16)
+  }
+  expect_snapshot_plot(image_density, "image_density")
+
+  # Interpolation ==============================================================
+  if (requireNamespace("interp", quietly = TRUE)) {
+    f <- isopleuros:::xyz_interpolate(arctic[, 1], arctic[, 2], arctic[, 3], value = arctic$depth)
+    image_interpolate <- function() {
+      ternary_plot(NULL)
+      ternary_image(f = f, n = 24)
+      ternary_points(arctic, col = "red", pch = 16)
+    }
+    expect_snapshot_plot(image_interpolate, "image_interpolate")
+  }
+}