clean R CMD check

Author: HelenaLC

R/CTutils.R

@@ -103,11 +103,21 @@ setMethod("CTname", "SpatialDataAttrs", \(x, ...) {
 
 # SpatialDataElement ----
 
-.SDE_METS <- c("axes", "CTlist", "CTtype", "CTname")
-for (. in .SDE_METS) {
-    setMethod(., "SpatialDataElement", 
-        eval(parse(text=sprintf("\\(x, ...) %s(meta(x), ...)", .))))
-}
+#' @rdname CTutils
+#' @export
+setMethod("axes", "SpatialDataElement", \(x, ...) axes(meta(x), ...))
+
+#' @rdname CTutils
+#' @export
+setMethod("CTlist", "SpatialDataElement", \(x, ...) CTlist(meta(x), ...))
+
+#' @rdname CTutils
+#' @export
+setMethod("CTtype", "SpatialDataElement", \(x, ...) CTtype(meta(x), ...))
+
+#' @rdname CTutils
+#' @export
+setMethod("CTname", "SpatialDataElement", \(x, ...) CTname(meta(x), ...))
 
 #' @rdname CTutils
 #' @export
@@ -185,7 +195,6 @@ setMethod("addCT", "SpatialDataElement",
 #' @rdname CTutils
 #' @export
 setMethod("addCT", "SpatialDataAttrs", \(x, name, type="identity", data=NULL) {
-    #x <- meta(image(sd, 2)); name <- "lowres"; type="identity"; data=NULL
     stopifnot(
         is.character(name), length(name) == 1,
         is.character(type), length(type) == 1)

R/SDattrs.R

@@ -1,11 +1,23 @@
 #' @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).
-#' @param axes list of axes; if NULL, defaults to cyx (array) or xy (frame).
-#' @param transformations list of transformations; if NULL, defaults to global identity.
+#' @param label flag; when \code{type="frame"}, should attributes be for a label?
+#' @param trans list of coordinate transformations; defaults to identity only.
+#' @param value character string (for one \code{region} and \code{_key}s), 
+#'   or vector (for many \code{region}s, \code{instances} and \code{regions}).
+#' @param ver character string; specified the .zarr version to comply with.
+#' @param nch scalar integer; how many channels should there be?
+#'   (ignored unless \code{type="frame"} and \code{label=FALSE}). 
 #' @param ... additional attributes (e.g., version, feature_key).
 #' 
 #' @details 
@@ -42,12 +54,12 @@
 #' # constructor
 #' SpatialDataAttrs(type="frame")
 #' SpatialDataAttrs(type="array")
-#' SpatialDataAttrs(type="array", n=7)
+#' SpatialDataAttrs(type="array", nch=7)
 #' SpatialDataAttrs(type="array", label=TRUE)
 #' 
 #' @export
 SpatialDataAttrs <- \(x, type=c("array", "frame"), 
-    label=FALSE, trans=NULL, ver="0.4", n=3, ...) 
+    label=FALSE, trans=NULL, ver="0.4", nch=3, ...) 
 {
     if (!missing(x)) return(.SpatialDataAttrs(x))
     type <- match.arg(type)
@@ -68,7 +80,7 @@ SpatialDataAttrs <- \(x, type=c("array", "frame"),
     if (type == "array") {
         # default structure
         res <- list(
-            omero=list(channels=list(label=letters[seq_len(n)])),
+            omero=list(channels=list(label=letters[seq_len(nch)])),
             multiscales=list(list(
                 axes=ax,
                 version="0.4",
@@ -126,20 +138,10 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
 #' @noRd 
 .ms <- \(x) switch(.zv(x), "0.3"=x$ome$multiscales, x$multiscales)
 
-# internal use only!
-#' @noRd 
-.ch <- \(x) {
-    if (.zv(x) == "0.3") x <- x$ome
-    unlist(x$omero$channels)
-}
-
 # internal use only!
 #' @noRd 
 setMethod("multiscales", "list", .ms)
 
-#' @export
-setMethod("channels", "SpatialDataAttrs", \(x, ...) .ch(x))
-
 # features ----
 
 #' @export

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-method
+#' @aliases [[<-,SpatialData,numeric,ANY-method
+#' 
+#' @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/combine.R

@@ -17,42 +17,42 @@
 #' imageNames(y)
 #' region(table(y, 1))
 #' region(table(y, 2))
-#' 
-#' @importFrom BiocGenerics combine
+NULL
+
 #' @export
-setMethod("combine", 
-    c("SpatialData", "SpatialData"), 
-    \(x, y, ...) {
-        # ensure element names are unique across objects
-        old <- list(unlist(colnames(x)), unlist(colnames(y)))
-        idx <- rep.int(c(1, 2), vapply(old, length, integer(1)))
-        new <- split(make.unique(unlist(old)), idx)
-        for (i in c(1, 2)) {
-            z <- get(c("x", "y")[i])
-            layer_nms <- setdiff(rownames(z), "tables")
-            old_nms <- unlist(colnames(z)[layer_nms])
-            # find new names for these elements
-            j <- match(old_nms, old[[i]])
-            new_nms <- new[[i]][j]
-            
-            # rename elements
-            for (l in layer_nms) {
-                j <- match(names(z[[l]]), old[[i]])
-                names(z[[l]]) <- new[[i]][j]
-            }
-            # sync tables
-            z <- .sync_tables(z, old_nms, new_nms)
-            
-            # rename tables themselves
-            j <- match(tableNames(z), old[[i]])
-            tableNames(z) <- new[[i]][j]
-            
-            assign(c("x", "y")[i], z)
+#' @rdname combine
+#' @importFrom BiocGenerics combine
+setMethod("combine", c("SpatialData", "SpatialData"), \(x, y, ...) {
+    # ensure element names are unique across objects
+    old <- list(unlist(colnames(x)), unlist(colnames(y)))
+    idx <- rep.int(c(1, 2), vapply(old, length, integer(1)))
+    new <- split(make.unique(unlist(old)), idx)
+    for (i in c(1, 2)) {
+        z <- get(c("x", "y")[i])
+        layer_nms <- setdiff(rownames(z), "tables")
+        old_nms <- unlist(colnames(z)[layer_nms])
+        # find new names for these elements
+        j <- match(old_nms, old[[i]])
+        new_nms <- new[[i]][j]
+        
+        # rename elements
+        for (l in layer_nms) {
+            j <- match(names(z[[l]]), old[[i]])
+            names(z[[l]]) <- new[[i]][j]
         }
-        SpatialData(
-            images=c(x$images, y$images),
-            labels=c(x$labels, y$labels),
-            points=c(x$points, y$points),
-            shapes=c(x$shapes, y$shapes),
-            tables=c(x$tables, y$tables))
-    })
+        # sync tables
+        z <- .sync_tables(z, old_nms, new_nms)
+        
+        # rename tables themselves
+        j <- match(tableNames(z), old[[i]])
+        tableNames(z) <- new[[i]][j]
+        
+        assign(c("x", "y")[i], z)
+    }
+    SpatialData(
+        images=c(x$images, y$images),
+        labels=c(x$labels, y$labels),
+        points=c(x$points, y$points),
+        shapes=c(x$shapes, y$shapes),
+        tables=c(x$tables, y$tables))
+})

R/mask.R

@@ -163,6 +163,7 @@ setMethod(".mask", c("SpatialDataShape", "SpatialDataShape"), \(i, j, how=NULL,
     if (nrow(collect(head(ij, 1))) == 0)
         stop("found no intersections",
             " between shapes 'i' and 'j'")
+    id_x <- id_y <- NULL # R CMD check
     is <- pull(ij, id_y) # elements in i
     js <- pull(ij, id_x) # masks in j
     na <- setdiff(seq_len(nrow(i)), is)

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)
@@ -144,12 +144,24 @@ setMethod("element", c("SpatialData", "ANY"), \(x, i)
 
 # get all ----
 
-#' @name SpatialData
-#' @exportMethod images labels points shapes tables
+#' @export
+#' @rdname SpatialData
 setMethod("images", "SpatialData", \(x) x$images)
+
+#' @export
+#' @rdname SpatialData
 setMethod("labels", "SpatialData", \(x) x$labels)
+
+#' @export
+#' @rdname SpatialData
 setMethod("points", "SpatialData", \(x) x$points)
+
+#' @export
+#' @rdname SpatialData
 setMethod("shapes", "SpatialData", \(x) x$shapes)
+
+#' @export
+#' @rdname SpatialData
 setMethod("tables", "SpatialData", \(x) x$tables)
 
 # get nms ----

R/read.R

@@ -12,10 +12,6 @@
 #'   Control which elements should be read for each layer.
 #'   The default, NULL, reads all elements; alternatively, may be FALSE
 #'   to skip a layer, or a integer vector specifying which elements to read.
-#' @param anndataR logical specifying whether
-#'   to use \code{anndataR} to read tables;
-#'   defaults to FALSE in `readSpatialData`, and `readTable`,
-#'   so that pythonic \code{anndata} are used.
 #' @param ... option arguments passed to and from other methods.
 #'
 #' @return
@@ -146,6 +142,7 @@ readSpatialData <- function(x,
         lapply(j, \(.) do.call(f, list(.)))
     }
 
-    sd <- lapply(setNames(nm=.LAYERS[!skip]), .readLayer)
+    names(ls) <- ls <- .LAYERS[!skip]
+    sd <- lapply(ls, .readLayer)
     do.call(SpatialData, sd)
 }