implement multiscale label visualization

Author: Artur-man

NAMESPACE

@@ -27,7 +27,7 @@ importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_polygon)
-importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_raster)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)

R/plotImage.R

@@ -159,24 +159,11 @@ plotSpatialData <- \() ggplot() + scale_y_reverse() + .theme
     return(NULL)
 }
 
-.guess_scale <- \(x, w, h) {
-    n <- length(dim(x))
-    i <- ifelse(n == 3, -1, TRUE)
-    d <- vapply(x@data, dim, numeric(n))
-    d <- apply(d, 2, \(.) sum(abs(.[i]-c(h, w))))
-    which.min(d)
-}
-
-.get_img_data <- \(x, k=NULL, w=800, h=800) {
-    if (!is.null(k)) return(data(x, k))
-    data(x, .guess_scale(x, w, h))
-}
-
 #' @importFrom methods as
 #' @importFrom grDevices rgb
 #' @importFrom DelayedArray realize
 .df_i <- \(x, k=NULL, ch=NULL, c=NULL, cl=NULL) {
-    a <- .get_img_data(x, k)
+    a <- .get_multiscale_data(x, k)
     ch <- .ch_idx(x, ch)
     if (!.is_rgb(x))
         a <- a[ch, , , drop=FALSE]

R/plotLabel.R

@@ -45,13 +45,13 @@ NULL
 #' @importFrom methods as
 #' @importFrom ggplot2 
 #'   scale_fill_manual scale_fill_gradientn
-#'   aes geom_tile theme unit guides guide_legend
+#'   aes geom_raster theme unit guides guide_legend
 #' @export
 setMethod("plotLabel", "SpatialData", \(x, i=1, c=NULL, 
     a=0.5, pal=c("red", "green"), nan=NA, assay=1) {
     if (is.numeric(i)) i <- labelNames(x)[i]
     i <- match.arg(i, labelNames(x))
-    y <- as.matrix(as(data(label(x, i)), "DelayedArray"))
+    y <- as.matrix(.get_multiscale_data(label(x, i)))
     df <- data.frame(x=c(col(y)), y=c(row(y)), z=c(y))
     aes <- aes(.data[["x"]], .data[["y"]])
     if (!is.null(c)) {
@@ -81,5 +81,5 @@ setMethod("plotLabel", "SpatialData", \(x, i=1, c=NULL,
             theme(legend.position="none"),
             scale_fill_manual(NULL, values=pal))
     }
-    list(thm, do.call(geom_tile, list(data=df, mapping=aes, alpha=a)))
+    list(thm, do.call(geom_raster, list(data=df, mapping=aes, alpha=a)))
 })

R/utils.R

@@ -45,4 +45,19 @@
 .DTYPE_MAX_VALUES <- c("uint8" = 255,
                        "uint16" = 65535,
                        "uint32" = 4294967295,
-                       "uint64" = 2^64 - 1)
+                       "uint64" = 2^64 - 1)
+
+# guess scale of image or label
+.guess_scale <- \(x, w, h) {
+  n <- length(dim(x))
+  i <- ifelse(n == 3, -1, TRUE)
+  d <- vapply(x@data, dim, numeric(n))
+  d <- apply(d, 2, \(.) sum(abs(.[i]-c(h, w))))
+  which.min(d)
+}
+
+# get multiscale
+.get_multiscale_data <- \(x, k=NULL, w=800, h=800) {
+  if (!is.null(k)) return(data(x, k))
+  data(x, .guess_scale(x, w, h))
+}

tests/testthat/Rplots.pdf

@@ -22,11 +22,11 @@ test_that(".guess_scale", {
             dim <- lapply(c(6, 3), \(.) c(3, rep(., 2))), \(.) 
             array(sample(seq_len(255), prod(.), replace=TRUE), dim=.)))
     # manual scale
-    expect_identical(.get_img_data(img, k=1), lys[[1]]) 
-    expect_identical(.get_img_data(img, k=2), lys[[2]])
+    expect_identical(.get_multiscale_data(img, k=1), lys[[1]]) 
+    expect_identical(.get_multiscale_data(img, k=2), lys[[2]])
     # automatic scale
-    expect_identical(.get_img_data(img, k=NULL, w=5, h=7), lys[[1]]) 
-    expect_identical(.get_img_data(img, k=NULL, w=2, h=2), lys[[2]])
+    expect_identical(.get_multiscale_data(img, k=NULL, w=5, h=7), lys[[1]]) 
+    expect_identical(.get_multiscale_data(img, k=NULL, w=2, h=2), lys[[2]])
 })
 
 test_that("plotImage()", {