near-clean check

Author: HelenaLC

R/SDattrs.R

@@ -1,6 +1,13 @@
 #' @name SpatialDataAttrs
 #' @title The `SpatialDataAttrs` class
 #' 
+#' @aliases region region<- 
+#' @aliases regions regions<- 
+#' @aliases instances instances<- 
+#' @aliases region_key region_key<- 
+#' @aliases feature_key feature_key<- 
+#' @aliases instance_key instance_key<- 
+#' 
 #' @param x element or list extracted from a OME-NGFF compliant .zattrs file.
 #' @param name character string for extraction (see ?base::`$`).
 #' @param type character string; either "array" (image/label) or "frame" (point/shape).

R/SpatialData.R

@@ -1,7 +1,24 @@
 #' @name SpatialData
 #' @title The `SpatialData` class
 #' 
-#' @description ...
+#' @aliases data meta layer element
+#' @aliases image label point shape table
+#' @aliases images labels points shapes tables
+#' @aliases image<- label<- point<- shape<- table<-
+#' @aliases images<- labels<- points<- shapes<- tables<-
+#' @aliases imageNames labelNames pointNames shapeNames tableNames
+#' @aliases imageNames<- labelNames<- pointNames<- shapeNames<- tableNames<-
+#' @aliases [[,SpatialData,character,ANY
+#' @aliases [[,SpatialData,numeric,ANY
+#' 
+#' @description 
+#' \code{SpatialData} provides an R interface to Python's \code{spatialdata},
+#' which enables the representation of diverse spatial omics datasets using 
+#' the OME-NGFF (Next Generation File Format) standard. In R, 
+#' \itemize{
+#' \item images and labels are \code{ZarrArray}s (\code{Rarr} package).
+#' \item points and shapes are managed using \code{duckspatial} tables.
+#' \item tables are \code{SingleCellExperiment}s (read with \code{anndataR}).}
 #' 
 #' @param images list of \code{\link{SpatialDataImage}}s
 #' @param labels list of \code{\link{SpatialDataLabel}}s

R/methods.R

@@ -1,14 +1,14 @@
-#' @importFrom utils .DollarNames
 #' @export
+#' @importFrom utils .DollarNames
 .DollarNames.SpatialData <- \(x, pattern="") grep(pattern, .LAYERS, value=TRUE)
 
-#' @rdname SpatialData
 #' @exportMethod $
+#' @rdname SpatialData
 setMethod("$", "SpatialData", \(x, name) attr(x, name))
 
+#' @export
 #' @rdname SpatialData
 #' @importFrom methods callNextMethod
-#' @export
 setMethod("[[", c("SpatialData", "numeric"), \(x, i, ...) {
     i <- .LAYERS[i]
     callNextMethod(x, i)

R/sdArray.R

@@ -1,5 +1,6 @@
 #' @name SpatialDataArray
 #' @title Methods for `SpatialDataArray`s
+#' @aliases data_type
 #' 
 #' @param x \code{SpatialDataImage} or \code{SpatialDataLabel}.
 #' @param k scalar index specifying which scale to extract.

R/sdFrame.R

@@ -1,13 +1,13 @@
 #' @name SpatialDataFrame
 #' @title The `SpatialDataFrame` class
-#' @aliases SpatialDataPoint SpatialDataShape
+#' @aliases SpatialDataPoint SpatialDataShape geom_type
 #'
-#' @description
-#' The \code{SpatialDataPoint} and \code{SpatialDataShape} classes store 
-#' \code{SpatialData} elements from its \code{"points"} and 
-#' \code{"shapes"} layers, respectively. These are represented 
-#' as \code{duckspatial_df} (\code{data} slot) associated with 
-#' .zattrs stored as \code{\link{SpatialDataAttrs}} (\code{meta} slot); 
+#' @description 
+#' The \code{SpatialDataPoint} and \code{-Shape} classes represent 
+#' elements from a \code{SpatialData}'s \code{points/} and \code{shapes/} 
+#' layers, respectively. In both cases, these  are represented as a 
+#' \code{duckspatial_df} (\code{data} slot), and associated with .zattrs 
+#' represented as \code{\link{SpatialDataAttrs}} (\code{meta} slot); 
 #' a list of \code{metadata} stores other arbitrary info.
 #'
 #' Currently defined methods (here, \code{x} is an \code{SpatialDataFrame}):