Merge pull request #120 from Artur-man/multiscale_subset

fixing multiscale/check bugs

Author: Artur-man

DESCRIPTION

@@ -65,7 +65,6 @@ Suggests:
     testthat,
     DT
 Enhances:
-    patchwork,
     anndataR,
     pizzarr
 Remotes:

R/ImageArray.R

@@ -16,7 +16,7 @@
 #' @examples
 #' library(SpatialData.data)
 #' dir.create(td <- tempfile())
-#' pa <- unzip_merfish_demo(td)
+#' pa <- SpatialData.data:::.unzip_merfish_demo(td)
 #' pa <- file.path(pa, "images", "rasterized")
 #' (ia <- readImage(pa))
 #'
@@ -128,8 +128,8 @@ setMethod("[", "ImageArray", \(x, i, j, k, ..., drop=FALSE) {
     if (missing(k)) k <- TRUE else if (isFALSE(k)) k <- 0 else .check_jk(k, "k")
     ijk <- list(i, j, k)
     n <- length(data(x, NULL))
+    d <- dim(data(x))
     x@data <- lapply(seq_len(n), \(.) {
-        d <- dim(data(x, .))
         j <- if (isTRUE(j)) seq_len(d[2]) else j
         k <- if (isTRUE(k)) seq_len(d[3]) else k
         jk <- lapply(list(j, k), \(jk) {

R/PointFrame.R

@@ -33,7 +33,7 @@
 #' @examples
 #' library(SpatialData.data)
 #' dir.create(tf <- tempfile())
-#' base <- unzip_merfish_demo(tf)
+#' base <- SpatialData.data:::.unzip_merfish_demo(tf)
 #' x <- file.path(base, "points", "single_molecule")
 #' (p <- readPoint(x))
 #' 

R/ShapeFrame.R

@@ -17,7 +17,7 @@
 #' @examples
 #' library(SpatialData.data)
 #' dir.create(tf <- tempfile())
-#' base <- unzip_merfish_demo(tf)
+#' base <- SpatialData.data:::.unzip_merfish_demo(tf)
 #' y <- file.path(base, "shapes", "cells")
 #' (s <- readShape(y))
 #' plot(sf::st_as_sf(data(s)), cex=0.2)

R/read.R

@@ -63,7 +63,7 @@ allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7",
 #' @examples
 #' library(SpatialData.data)
 #' dir.create(tf <- tempfile())
-#' base <- unzip_merfish_demo(tf)
+#' base <- SpatialData.data:::.unzip_merfish_demo(tf)
 #' (x <- readSpatialData(base))
 NULL