r cmd check cleaning

Author: HelenaLC

.Rbuildignore

@@ -1,6 +1,6 @@
+^\.github$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.github$
 vignettes/*html
 vignettes/*cache
 vignettes/*files

DESCRIPTION

@@ -5,8 +5,8 @@ Version: 0.99.24
 Description: Interface to Python's 'SpatialData', currently including:
     reticulate-based use of 'spatialdata-io' for reading of manufracturer
     data and writing to .zarr, on-disk representation of images/labels as
-    'ZarrArray's ('Rarr') and shapes/points as 'arrow' objects, and method 
-    drafts for visualization and coordinate system handling.
+    'ZarrArray's ('Rarr') and shapes/points as 'arrow' objects, as well 
+    as method drafts for visualization and coordinate system handling.
 Authors@R: c(
 	person("Helena L.", "Crowell", 
 	    role=c("aut", "cre"),
@@ -33,22 +33,19 @@ Authors@R: c(
         email="louise.deconinck@gmail.com",
         comment=c(ORCID="0000-0001-8100-6823")))
 Imports:
+    anndataR,
     arrow,
     basilisk,
-    BiocGenerics,
+    BiocFileCache,
     DelayedArray,
-    dplyr,
     geoarrow,
-    graph,
-    jsonlite,
+    ggplot2,
     Matrix,
     methods,
     Rarr,
-    RBGL,
+    rlang,
     reticulate,
-    sf,
     sfarrow,
-    S4Arrays,
     S4Vectors,
     SingleCellExperiment,
     SummarizedExperiment
@@ -62,8 +59,6 @@ Suggests:
     Rgraphviz,
     testthat,
     DT
-Enhances:
-    anndataR
 Remotes:
     keller-mark/anndataR@keller-mark/zarr
 biocViews: 

NAMESPACE

@@ -25,6 +25,11 @@ export(sdio_list)
 export(zattrs)
 import(geoarrow)
 import(ggplot2)
+importFrom(BiocFileCache,BiocFileCache)
+importFrom(BiocFileCache,bfcadd)
+importFrom(BiocFileCache,bfcneedsupdate)
+importFrom(BiocFileCache,bfcquery)
+importFrom(BiocFileCache,bfcupdate)
 importFrom(DelayedArray,realize)
 importFrom(Rarr,ZarrArray)
 importFrom(Rarr,read_zarr_attributes)
@@ -62,3 +67,4 @@ importFrom(methods,is)
 importFrom(rlang,.data)
 importFrom(sfarrow,read_sf_dataset)
 importFrom(utils,.DollarNames)
+importFrom(utils,unzip)

R/data.R

@@ -47,6 +47,9 @@ sd_osn_list <- \() {
 }
 
 #' @rdname sd_data
+#' @importFrom utils unzip
+#' @importFrom BiocFileCache BiocFileCache 
+#'   bfcquery bfcadd bfcupdate bfcneedsupdate
 #' @export
 sd_osn_load <- \(patt, 
     target=tempfile(),

R/misc.R

@@ -2,31 +2,31 @@
 S4_register(SpatialData)
 
 #' @export
-method(print, SpatialData) <- \(object) { 
+method(print, SpatialData) <- \(x, ...) { 
     cat("class: SpatialData\n")
     l <- list()
     # images
-    i <- names(x <- object@images)
-    d <- lapply(x, \(.) paste(dim(.), collapse=","))
+    i <- names(y <- x@images)
+    d <- lapply(y, \(.) paste(dim(.), collapse=","))
     l <- c(l, list(images=list(i, d)))
     # labels
-    i <- names(x <- object@labels)
-    d <- lapply(x, \(.) paste(dim(.), collapse=","))
+    i <- names(y <- x@labels)
+    d <- lapply(y, \(.) paste(dim(.), collapse=","))
     l <- c(l, list(labels=list(i, d)))
     # points
-    i <- names(x <- object@points)
-    d <- vapply(x, length, integer(1))
+    i <- names(y <- x@points)
+    d <- vapply(y, length, integer(1))
     l <- c(l, list(points=list(i, d)))
     # shapes
-    i <- names(x <- object@shapes)
-    d <- vapply(x, length, integer(1))
-    n <- vapply(x, ncol, integer(1))
+    i <- names(y <- x@shapes)
+    d <- vapply(y, length, integer(1))
+    n <- vapply(y, ncol, integer(1))
     geom <- ifelse(n == 1, "polygon", "circle")
     d <- paste(d, geom, sep=",")
     l <- c(l, list(shapes=list(i, d)))
     # tables
-    i <- names(x <- object@tables)
-    d <- lapply(x, \(.) paste(dim(.), collapse=","))
+    i <- names(y <- x@tables)
+    d <- lapply(y, \(.) paste(dim(.), collapse=","))
     l <- c(l, list(tables=list(i, d)))
     # render
     for (. in names(l)) {
@@ -46,24 +46,23 @@ method(print, SpatialData) <- \(object) {
 }
 
 #' @export
-method(print, ImageArray) <- \(object) .show_ms_array(object)
+method(print, ImageArray) <- \(x, ...) .show_ms_array(x)
 
 #' @export
-method(print, LabelArray) <- \(object) .show_ms_array(object)
+method(print, LabelArray) <- \(x, ...) .show_ms_array(x)
 
-#' @export
-method(print, ShapeFrame) <- \(object) {
-    cat("class: ShapeFrame\n")
-    cat("count:", length(object), "\n")
-    coolcat("data(%d): %s\n", names(object))
+.show_sd_frame <- \(x) {
+    . <- attr(x, "S7_class")@name
+    cat(sprintf("class: %s\n", .))
+    cat("count:", length(x), "\n")
+    coolcat("data(%d): %s\n", names(x))
 }
 
 #' @export
-method(print, PointFrame) <- \(object) {
-    cat("class: PointFrame\n")
-    cat("count:", length(object), "\n")
-    coolcat("data(%d): %s\n", names(object))
-}
+method(print, ShapeFrame) <- \(x, ...) .show_sd_frame(x)
+
+#' @export
+method(print, PointFrame) <- \(x, ...) .show_sd_frame(x)
 
 #' @export
-method(print, Zattrs) <- \(object) cat(class(object))
+method(print, Zattrs) <- \(x, ...) cat(class(x))

R/plot-image.R

@@ -52,7 +52,7 @@ sd_plot_image <- \(x, i=1, c=NULL, ch=NULL, cl=NULL, k=NULL, w=800, h=800) {
     pal <- if (!.is_rgb(ia) && dim(ia)[1] > 1) {
         nms <- channels(ia)[ch]
         pal <- if (is.null(c)) .DEFAULT_COLORS else c
-        setNames(pal[seq_along(ch)], nms)
+        `names<-`(pal[seq_along(ch)], nms)
     }
     lgd <- if (!is.null(pal)) list(
         guides(col=guide_legend(override.aes=list(alpha=1, size=2))),

R/read.R

@@ -8,6 +8,10 @@
 #'   path to a \code{SpatialData}.zarr store.
 #'   For \code{readImage/Label/Point/Shape/Table}, 
 #'   path to a \code{SpatialData} element.
+#' @param images,labels,points,shapes,tables
+#'   control which layers and elements to read;
+#'   FALSE to skip a layer, integer or character 
+#'   vector to read some element(s).
 #' 
 #' @return \code{\link{SpatialData}} object, or one of its elements.
 #' 
@@ -25,7 +29,7 @@
 NULL
 
 #' @importFrom S4Vectors isSequence
-.get_multiscales_datasets_path <- function(md) {
+.get_multiscales_datasets_path <- \(md) {
     .validate_multiscales_datasets_path(md)
     ps <- md$multiscales[[1]]$datasets[[1]]$path
     ps <- suppressWarnings(as.numeric(ps))
@@ -38,7 +42,7 @@ NULL
 }
 
 #' @noRd
-.validate_multiscales_datasets_path <- function(md) {
+.validate_multiscales_datasets_path <- \(md) {
     ms <- md$multiscales
     if (!is.null(ms)) {
         ds <- ms[[1]]$datasets
@@ -60,7 +64,7 @@ NULL
 }
 
 #' @importFrom Rarr read_zarr_attributes
-.read_za <- function(x, ...) {
+.read_za <- \(x) {
     md <- read_zarr_attributes(x)
     ps <- .get_multiscales_datasets_path(md)
     as <- lapply(ps, \(.) ZarrArray(file.path(x, .)))
@@ -70,24 +74,24 @@ NULL
 #' @rdname readSpatialData
 #' @importFrom Rarr ZarrArray
 #' @export
-readImage <- function(x, ...) {
-    za <- .read_za(x, ...)
-    ImageArray(data=za$array, zattrs=Zattrs(za$md), ...)
+readImage <- \(x) {
+    za <- .read_za(x)
+    ImageArray(data=za$array, zattrs=Zattrs(za$md))
 }
 
 #' @rdname readSpatialData
 #' @importFrom Rarr ZarrArray
 #' @export
-readLabel <- function(x, ...) {
-    za <- .read_za(x, ...)
-    LabelArray(data=za$array, zattrs=Zattrs(za$md), ...)
+readLabel <- \(x) {
+    za <- .read_za(x)
+    LabelArray(data=za$array, zattrs=Zattrs(za$md))
 }
 
 #' @rdname readSpatialData
 #' @importFrom arrow open_dataset
 #' @importFrom Rarr read_zarr_attributes
 #' @export
-readPoint <- function(x, ...) {
+readPoint <- \(x) {
     md <- read_zarr_attributes(x)
     pq <- list.files(x, "\\.parquet$", full.names=TRUE)
     PointFrame(data=open_dataset(pq), zattrs=Zattrs(md))
@@ -98,7 +102,7 @@ readPoint <- function(x, ...) {
 #' @importFrom Rarr read_zarr_attributes
 #' @import geoarrow   
 #' @export
-readShape <- function(x, ...) {
+readShape <- \(x) {
     requireNamespace("geoarrow", quietly=TRUE)
     md <- read_zarr_attributes(x)
     # TODO: previously had read_parquet(),