r cmd checking

Author: HelenaLC

DESCRIPTION

@@ -45,6 +45,7 @@ Imports:
     Rarr,
     rlang,
     reticulate,
+    scales,
     sfarrow,
     S4Vectors,
     SingleCellExperiment,

NAMESPACE

@@ -70,9 +70,11 @@ importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,rainbow)
 importFrom(grDevices,rgb)
 importFrom(methods,as)
+importFrom(methods,initialize)
 importFrom(methods,is)
 importFrom(methods,slot)
 importFrom(rlang,.data)
+importFrom(scales,alpha)
 importFrom(sfarrow,read_sf_dataset)
 importFrom(utils,.DollarNames)
 importFrom(utils,unzip)

R/class.R

@@ -14,6 +14,7 @@
 #'   For \code{Shape/PointFrame}s, an \code{arrow} Table or derivative.
 #' @param zattrs \code{Zattrs} objects; used to represent .zattrs.
 #' @param metadata (option) list of free-form extra data.
+#' @param x \code{SpatialData} object.
 #' 
 #' @return \code{SpatialData}
 #' 
@@ -32,7 +33,7 @@
 #' @importFrom S7 new_class new_generic method class_list check_is_S7 
 #' @importFrom SingleCellExperiment int_metadata
 #' @importFrom SummarizedExperiment colData
-#' @importFrom methods is
+#' @importFrom methods is initialize
 #' @export
 SpatialData <- new_class("SpatialData",
     properties=list(

R/data.R

@@ -20,9 +20,11 @@
 #' # bucket for zipped .zarr archives for various platforms
 #' Sys.setenv(AWS_REGION="us-east-1")
 #' if (requireNamespace("paws")) sd_osn_list()
-#'
+#' 
+#' \donttest{
 #' # retrieve dataset & ingest
 #' (sd <- sd_osn_load("merfish"))
+#' }
 NULL
 
 .require <- \(x) if (!requireNamespace(x, quietly=TRUE)) 
@@ -137,6 +139,10 @@ sd_osn_load <- \(patt,
     readSpatialData(dir(td, full.names=TRUE))
 }
 
+#' @name spatialdata-io
+#' @title Writing .zarr
+#' 
+#' @description
 #' Use Python's 'spatialdata-io' to transform manufacturer 
 #' output to .zarr with specific folder structure.
 #' 
@@ -186,7 +192,7 @@ sd_make <- \(platform, srcdir, dest, env) {
     }
 }
 
-#' @rdname sd_data
+#' @rdname spatialdata-io
 #' @export
 sdio_list <- \(env) {
     .require("basilisk")

R/plot-label.R

@@ -6,6 +6,7 @@
 #'   specifies which \code{labels} to plot.
 #' @param c character vector of colors to use;
 #'   if NULL (default), using \code{rainbow()}.
+#' @param alpha scalar numeric; controls opacity.
 #' @param k resolution; if NULL (default), picking 
 #'   best for given \code{w}idth and \code{h}eight.
 #' @param w,h render width and height in pixel.
@@ -22,10 +23,11 @@
 #' sd_plot() + sd_plot_label(sd, c=c("lavender", "blue"))
 #' 
 #' @importFrom methods as
+#' @importFrom scales alpha
 #' @importFrom DelayedArray realize
 #' @importFrom grDevices rgb rainbow colorRampPalette
 #' @export
-sd_plot_label <- \(x, i=1, c=NULL, k=NULL, w=800, h=800) {
+sd_plot_label <- \(x, i=1, c=NULL, alpha=1, k=NULL, w=800, h=800) {
     la <- x@labels[[i]]
     if (is.null(k)) 
         k <- .guess_scale(la, w, h)
@@ -38,13 +40,10 @@ sd_plot_label <- \(x, i=1, c=NULL, k=NULL, w=800, h=800) {
     } else if (n > length(c)) {
         c <- colorRampPalette(c)(n)
     }
+    c <- scales::alpha(c, alpha)
     a <- matrix(c(NA, c)[b], nrow(a), ncol(a))
-    w <- c(0, dim(ia)[3])
-    h <- c(0, dim(ia)[2])
-    # lgd <- if (!is.null(pal)) list(
-    #     guides(col=guide_legend(override.aes=list(alpha=1, size=2))),
-    #     scale_color_identity(NULL, guide="legend", labels=names(pal)),
-    #     geom_point(aes(col=.data$foo), data.frame(foo=pal), x=0, y=0, alpha=0))
+    w <- c(0, dim(la)[2])
+    h <- c(0, dim(la)[1])
     list(
         scale_x_continuous(limits=w), scale_y_reverse(limits=rev(h)),
         annotation_raster(a, w[2],w[1], h[1],h[2], interpolate=FALSE))

R/plot.R

@@ -1,7 +1,5 @@
 #' @name sd_plot
 #' @title Plotting `SpatialData`
-#' 
-#' @aliases sd_plot sd_plot_image
 #'
 #' @return \code{ggplot}
 #'

R/read.R

@@ -41,7 +41,6 @@ NULL
     return(ps)
 }
 
-#' @noRd
 .validate_multiscales_datasets_path <- \(md) {
     ms <- md$multiscales
     if (!is.null(ms)) {