fix R CMD check notes/warnings

DESCRIPTION

@@ -51,7 +51,6 @@ Imports:
     sf,
     S4Arrays,
     S4Vectors,
-    SparseArray,
     SingleCellExperiment,
     SummarizedExperiment
 Suggests:
@@ -63,8 +62,7 @@ Suggests:
     Rgraphviz,
     SpatialData.data,
     SpatialData.plot,
-    testthat,
-    DT
+    testthat
 Remotes:
     keller-mark/anndataR@spatialdata,
     HelenaLC/SpatialData.data,

R/ShapeFrame.R

@@ -55,9 +55,7 @@ setMethod("names", "ShapeFrame", \(x) names(data(x)))
 #' @export
 #' @rdname ShapeFrame
 #' @importFrom utils .DollarNames
-.DollarNames.ShapeFrame <- \(x, pattern="") {
-    grep(pattern, names(x), value=TRUE)
-}
+.DollarNames.ShapeFrame <- \(x) grep("", names(x), value=TRUE)
 
 #' @rdname ShapeFrame
 #' @exportMethod $

R/SpatialData.R

@@ -8,6 +8,8 @@
 #' image images image<- images<- imageNames 
 #' shape shapes shape<- shapes<- shapeNames 
 #' table tables table<- tables<- tableNames 
+#' [[<-,SpatialData,character,ANY-method
+#' [[<-,SpatialData,numeric,ANY-method
 #' 
 #' @description ...
 #' 

R/Zattrs.R

@@ -1,8 +1,6 @@
 #' @name Zattrs
 #' @title The `Zattrs` class
 #' 
-#' @aliases feature_key
-#' 
 #' @param x list extracted from a OME-NGFF compliant .zattrs file.
 #' @param name character string for extraction (see ?base::`$`).
 #' 
@@ -80,22 +78,56 @@ setMethod("$", "Zattrs", \(x, name) x[[name]])
 }
 setMethod("show", "Zattrs", .showZattrs)
 
+#' @name SDattrs
+#' @title \code{SpatialData} attributes
+#' 
+#' @aliases
+#' region
+#' region_key
+#' feature_key
+#' instance_key
+#' 
+#' @param x depends on which attributes are available; 
+#'   specifically, \code{PointFrame} (\code{feature/instance_key}), or
+#'   \code{SingleCellExperiment} (\code{region}, \code{region/instance_key}),
+#' 
+#' @return character string
+#'
+#' @examples
+#' x <- file.path("extdata", "blobs.zarr")
+#' x <- system.file(x, package="SpatialData")
+#' x <- readSpatialData(x, anndataR=TRUE)
+#' 
+#' region(table(x))
+#' region_key(table(x))
+#' 
+#' instance_key(point(x))
+#' fk <- feature_key(point(x))
+#' base::table(point(x)[[fk]])
+NULL
+
 # TODO: only points can have this?
 #' @export
+#' @rdname SDattrs
 setMethod("feature_key", "list", \(x) x$spatialdata_attrs$feature_key)
 #' @export
 setMethod("feature_key", "PointFrame", \(x) feature_key(meta(x)))
 
 # TODO: only tables can have this?
 #' @export
+#' @rdname SDattrs
 setMethod("region_key", "SingleCellExperiment", \(x) meta(x)$region_key)
 #' @export
+#' @rdname SDattrs
 setMethod("region", "SingleCellExperiment", \(x) meta(x)[[region_key(x)]])
 
 # TODO: only tables and points can have this?
 #' @export
+#' @rdname SDattrs
 setMethod("instance_key", "list", \(x) x$instance_key)
 #' @export
+#' @rdname SDattrs
 setMethod("instance_key", "PointFrame", \(x) instance_key(meta(x)$spatialdata_attrs))
 #' @export
+#' @rdname SDattrs
 setMethod("instance_key", "SingleCellExperiment", \(x) instance_key(meta(x)))

R/query.R

@@ -10,8 +10,8 @@
 #'
 #' @param x \code{SpatialData} element.
 #' @param y query specification; 
-#' bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax' 
-#' (order is irrelevant); polygon: numeric matrix with ≥ 3 rows and 2 columns.
+#' bounding box: length-4 numeric list with names 'xmin/xmax/ymin/ymax';
+#' polygon: numeric matrix with at least 3 rows and exactly 2 columns.
 #' @param i for \code{SpatialData}, index or name of table to query.
 #' @param ... optional arguments passed to and from other methods.
 #'

R/sdArray.R

@@ -1,15 +1,14 @@
-#' @name Array-methods
+#' @name sdArray
 #' @title Methods for `ImageArray` and `LabelArray` class
 #' 
 #' @aliases 
+#' data_type
 #' data,ImageArray-method
 #' data,LabelArray-method
 #' dim,ImageArray-method
 #' dim,LabelArray-method
 #' length,ImageArray-method
 #' length,LabelArray-method
-#' data_type,ImageArray-method
-#' data_type,LabelArray-method
 #' 
 #' @param x \code{ImageArray} or  \code{LabelArray}
 #' @param k scalar index specifying which scale to extract.
@@ -30,7 +29,7 @@
 #' @importFrom methods new
 NULL
 
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @export
 setMethod("data", "sdArray", \(x, k=1) {
   if (is.null(k)) return(x@data)
@@ -41,25 +40,25 @@ setMethod("data", "sdArray", \(x, k=1) {
   stop("'k=", k, "' but only ", n, " resolution(s) available")
 })
 
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @export
 setMethod("dim", "sdArray", \(x) dim(data(x)))
 
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @export
 setMethod("length", "sdArray", \(x) length(data(x, NULL)))
 
 #' @export
-#' @rdname Array-methods
+#' @rdname sdArray
 #' @importFrom S4Vectors metadata
 setMethod("data_type", "sdArray", \(x) {
     if (is(y <- data(x), "DelayedArray")) 
         data_type(y) else metadata(x)$data_type
 })
 
-#' @rdname Array-methods
+#' @export
+#' @rdname sdArray
 #' @importFrom DelayedArray DelayedArray
 #' @importFrom Rarr zarr_overview
 #' @importFrom ZarrArray path
-#' @export
 setMethod("data_type", "DelayedArray", \(x) zarr_overview(path(x), as_data_frame=TRUE)$data_type)

R/trans.R

@@ -3,9 +3,7 @@
 #' @title Transformations
 #' @aliases scale rotate translation flip flop mirror
 #' 
-#' @param x \code{SpatialData} element
-#' @param j scalar character or numeric; 
-#'   name or index of coordinate space.
+#' @param x \code{SpatialData} element.
 #' @param t transformation data; exceptions: for \code{mirror}, controls
 #'   whether to perform \bold{v}ertical or \bold{h}orizontal reflection;
 #'   no data is needed for \code{flip} (\bold{v}) and \code{flop} (\bold{h}).
@@ -106,6 +104,8 @@ setMethod("rotate", c("sdArray", "numeric"), \(x, t, k=1,...) {
     .trans_a(x, f, k)
 })
 
+#' @export
+#' @rdname trans
 #' @importFrom EBImage translate
 setMethod("translation", c("sdArray", "numeric"), \(x, t, k=1, ...) {
     stopifnot(length(t) == length(dim(x)), is.finite(t))

R/utils.R

@@ -3,8 +3,9 @@
 #' @title Utilities
 #' @aliases centroids extent
 #' 
-#' @param x a \code{SpatialData} element (any but image)
-#' @param as determines how results will be returned
+#' @param x a \code{SpatialData} element (any but image).
+#' @param as character string; how results should be returned.
+#' @param ... optional arguments passed to and from other methods.
 #' 
 #' @examples
 #' x <- file.path("extdata", "blobs.zarr")

README.md

@@ -1,7 +1,5 @@
 # `SpatialData`
 
-[![x](https://github.com/HelenaLC/SpatialData/actions/workflows/check-bioc.yml/badge.svg?branch=main)](https://github.com/HelenaLC/SpatialData/actions/workflows/check-bioc.yml)
-
 [![x](https://github.com/HelenaLC/SpatialData/actions/workflows/check-bioc.yml/badge.svg?branch=main&event=push)](https://github.com/HelenaLC/SpatialData/actions/workflows/check-bioc.yml)
 
 > for a demo of the class, see the [vignette](https://htmlpreview.github.io/?https://github.com/HelenaLC/SpatialData/blob/main/vignettes/SpatialData.html)