add k argument for plotLabel, selecting custom scales from multiscales

Author: Artur-man

R/plotLabel.R

@@ -3,6 +3,9 @@
 #' 
 #' @param x \code{SpatialData} object.
 #' @param i character string or index; the label element to plot.
+#' @param k index of the scale of an image; by default (NULL), will auto-select 
+#'   scale in order to minimize memory-usage and blurring for a target size of 
+#'   800 x 800px; use Inf to plot the lowest resolution available.
 #' @param c the default, NULL, gives a binary image of whether or not 
 #'   a given pixel is non-zero; alternatively, a character string specifying
 #'   a \code{colData} column or row name in a \code{table} annotating \code{i}.
@@ -47,11 +50,11 @@ NULL
 #'   scale_fill_manual scale_fill_gradientn
 #'   aes geom_raster theme unit guides guide_legend
 #' @export
-setMethod("plotLabel", "SpatialData", \(x, i=1, c=NULL, 
+setMethod("plotLabel", "SpatialData", \(x, i=1, k=NULL, 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(.get_multiscale_data(label(x, i)))
+    y <- as.matrix(.get_multiscale_data(label(x, i), k))
     df <- data.frame(x=c(col(y)), y=c(row(y)), z=c(y))
     aes <- aes(.data[["x"]], .data[["y"]])
     if (!is.null(c)) {

man/plotLabel.Rd

@@ -66,6 +66,5 @@ test_that("plotLabel()", {
     expect_identical(q$layers[[1]]$aes_params$alpha, a)
     expect_error(show(plotSpatialData() + plotLabel(x, i, a=".....")))
     expect_error(show(plotSpatialData() + plotLabel(x, i, a=c(1, 2))))
-    # TODO: use 'annotation_raster'
-    # TODO: multiscale plotting
+    # TODO: should we use 'annotation_raster' ?
 })

tests/testthat/Rplots.pdf

@@ -93,8 +93,8 @@ pal_d <- hcl.colors(10, "Spectral")
 pal_c <- hcl.colors(9, "Inferno")[-9]
 
 a <- p + plotLabel(x, i) # simple binary image
-b <- p + plotLabel(x, i, "id", pal=pal_d) # 'colData'
-c <- p + plotLabel(x, i, "channel_1_sum", pal=pal_c) + 
+b <- p + plotLabel(x, i, c = "id", pal=pal_d) # 'colData'
+c <- p + plotLabel(x, i, c = "channel_1_sum", pal=pal_c) + 
     theme(legend.key.width=unit(1, "lines")) # 'assay'
 
 (a | b | c) + 
@@ -236,7 +236,7 @@ pa <- unzip_spd_demo(
 pal <- hcl.colors(8, "Spectral")
 wrap_plots(nrow=1, lapply(seq(3), \(.)
     plotSpatialData() + plotImage(x, .) +
-    plotLabel(x, ., "Cluster", pal=pal))) +
+    plotLabel(x, ., c = "Cluster", pal=pal))) +
     plot_layout(guides="collect")
 ```
 
@@ -337,7 +337,7 @@ x <- mask(x, "blobs_image", i, fun=mean)
 (t <- getTable(x, i))
 # visualize side-by-side
 ps <- lapply(paste(seq_len(3)), \(.) 
-    plotSpatialData() + plotLabel(x, i, .) + 
+    plotSpatialData() + plotLabel(x, i, c = .) + 
     ggtitle(paste("channel", ., "sum"))) 
 wrap_plots(ps, nrow=1) & theme(
     legend.position="bottom",