R CMD check notes on documentation links

Author: lambdamoses

NAMESPACE

@@ -274,6 +274,7 @@ importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SingleCellExperiment,reducedDims)
 importFrom(SpatialExperiment,"imgData<-")
 importFrom(SpatialExperiment,"spatialCoords<-")
+importFrom(SpatialExperiment,"spatialCoordsNames<-")
 importFrom(SpatialExperiment,SpatialExperiment)
 importFrom(SpatialExperiment,addImg)
 importFrom(SpatialExperiment,getImg)
@@ -293,6 +294,7 @@ importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
+importFrom(data.table,":=")
 importFrom(data.table,as.data.table)
 importFrom(data.table,fread)
 importFrom(data.table,is.data.table)
@@ -399,4 +401,5 @@ importFrom(utils,getFromNamespace)
 importFrom(utils,head)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
+importFrom(utils,tail)
 importFrom(zeallot,"%<-%")

R/SFE-class.R

@@ -1,7 +1,7 @@
 #' The SpatialFeatureExperiment class
 #'
-#' This class inherits from the \code{\link{SpatialExperiment}} (SPE) class,
-#' which in turn inherits from \code{\link{SingleCellExperiment}} (SCE).
+#' This class inherits from the \code{\link[SpatialExperiment]{SpatialExperiment}} (SPE) class,
+#' which in turn inherits from \code{\link[SingleCellExperiment]{SingleCellExperiment}} (SCE).
 #' \code{SpatialFeatureExperiment} stores geometries of spots or cells in
 #' \code{sf} objects which form columns of a \code{DataFrame} which is in turn a
 #' column of the \code{int_colData} \code{DataFrame} of the underlying SCE
@@ -72,10 +72,10 @@ setClass("SpatialFeatureExperiment", contains = "SpatialExperiment")
 #'   \code{*Geometries} arguments have ordinary data frames, to identify the
 #'   columns in the ordinary data frames that specify the spatial coordinates.
 #'   If \code{colGeometries} is not specified, then this argument will behave as
-#'   in \code{\link{SpatialExperiment}}, but \code{colGeometries} will be given
+#'   in \code{\link[SpatialExperiment]{SpatialExperiment}}, but \code{colGeometries} will be given
 #'   precedence if provided.
 #' @param spatialCoords A numeric matrix containing columns of spatial
-#'   coordinates, as in \code{\link{SpatialExperiment}}. The coordinates are
+#'   coordinates, as in \code{\link[SpatialExperiment]{SpatialExperiment}}. The coordinates are
 #'   centroids of the entities represented by the columns of the gene count
 #'   matrix. If \code{colGeometries} is also specified, then it will be given
 #'   priority and a warning is issued. Otherwise, the \code{sf} representation
@@ -87,8 +87,8 @@ setClass("SpatialFeatureExperiment", contains = "SpatialExperiment")
 #'   arguments. Ignored for geometries that are not POINT or MULTIPOINT.
 #' @param unit Unit the coordinates are in, either microns or pixels in full
 #'   resolution image.
-#' @param ... Additional arguments passed to the \code{\link{SpatialExperiment}}
-#'   and \code{\link{SingleCellExperiment}} constructors.
+#' @param ... Additional arguments passed to the \code{\link[SpatialExperiment]{SpatialExperiment}}
+#'   and \code{\link[SingleCellExperiment]{SingleCellExperiment}} constructors.
 #' @return A SFE object. If neither \code{colGeometries} nor \code{spotDiameter}
 #'   is specified, then a \code{colGeometry} called "centroids" will be made,
 #'   which is essentially the spatial coordinates as sf POINTs. If

R/aggregate.R

@@ -42,6 +42,7 @@
 #' @importFrom data.table as.data.table
 #' @importFrom sf st_make_grid
 #' @importFrom rlang %||%
+#' @importFrom utils tail
 #' @concept Geometric operations
 #' @export
 aggregateTx <- function(file, df = NULL, by = NULL, sample_id = "sample01",
@@ -399,7 +400,7 @@ aggregateTxTech <- function(data_dir, df = NULL, by = NULL,
 #' @param rowGeometryName Which \code{rowGeometry} to spatially aggregate
 #' @param new_geometry_name Name to give to the new \code{colGeometry} in the
 #'   output. Defaults to "bins".
-#' @param BPPARAM A \code{\link{BiocParallelParam}} object specifying parallel
+#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} object specifying parallel
 #'   computing when aggregating data with functions other than sum and mean when
 #'   aggregating cells. When aggregating transcript spots, this specifies
 #'   parallel computing over genes. Defaults to \code{SerialParam()}.

R/featureData.R

@@ -20,7 +20,7 @@
 #' @param MARGIN Integer, 1 means rowGeometry, 2 means colGeometry, and 3 means
 #'   annotGeometry. Defaults to 2, colGeometry.
 #' @param dimred Name of a dimension reduction, can be seen in
-#'   \code{\link{reducedDimNames}}.
+#'   \code{\link{[SingleCellExperiment]reducedDimNames}}.
 #' @concept Getters and setters
 #' @return A \code{DataFrame}.
 #' @seealso getParams
@@ -95,7 +95,7 @@ reducedDimFeatureData <- function(sfe, dimred) {
 #'   \code{colGeometry} has precedence so this argument is ignored if
 #'   \code{colGeometryName} is specified.
 #' @param reducedDimName Name of a dimension reduction, can be seen in
-#'   \code{\link{reducedDimNames}}. \code{colGeometryName} and
+#'   \code{\link[SingleCellExperiment]{reducedDimNames}}. \code{colGeometryName} and
 #'   \code{annotGeometryName} have precedence over \code{reducedDimName}.
 #' @return A named list showing the parameters
 #' @concept Getters and setters

R/formatTxSpots.R

@@ -265,7 +265,7 @@ addSelectTx <- function(sfe, file, gene_select, sample_id = 1L,
 #'   3D geometries will always be constructed since there are no z-planes to
 #'   speak of. This argument does not apply when `spatialCoordsNames` has length
 #'   2.
-#' @param BPPARAM \code{\link{BiocParallelParam}} object to specify
+#' @param BPPARAM \code{\link[BiocParallel]{BiocParallelParam}} object to specify
 #'   multithreading to convert raw char in some parquet files to R objects. Not
 #'   used otherwise.
 #' @param sample_id Which sample in the SFE object the transcript spots should

R/geometry_operation.R

@@ -11,7 +11,7 @@
 #' @param x An object of class \code{sf}, \code{sfc}, or \code{sfg}.
 #' @param y Another object of class \code{sf}, \code{sfc}, or \code{sfg}.
 #' @param pred A geometric binary predicate function, such as
-#'   \code{\link{st_intersects}}. It should return an object of class
+#'   \code{\link[sf]{st_intersects}}. It should return an object of class
 #'   \code{sgbp}, for sparse predicates.
 #' @param yx Whether to do \code{pred(y, x)} instead of \code{pred(x, y)}. For
 #'   symmetric predicates, the results should be the same. When x has a large
@@ -172,7 +172,7 @@ st_n_intersects <- function(x, y) st_n_pred(x, y, st_intersects)
 #' @param sample_id Which sample(s) to operate on. Can be "all" to indicate all
 #'   samples.
 #' @param pred Predicate function to use, defaults to
-#'   \code{\link{st_intersects}}.
+#'   \code{\link[sf]{st_intersects}}.
 #' @return For \code{annotPred}, a logical vector of the same length as the
 #'   number of columns in the sample(s) of interest, with barcodes (or
 #'   corresponding column names of sfe) as names. For \code{annotNPred}, a
@@ -224,7 +224,7 @@ annotNPred <- function(sfe, colGeometryName = 1L, annotGeometryName = 1L,
 #'
 #' @inheritParams annotPred
 #' @param op A binary operation function for the geometries. Defaults to
-#' \code{\link{st_intersection}}.
+#' \code{\link[sf]{st_intersection}}.
 #' @return A \code{sf} data frame with \code{geometry} column containing the
 #' geometries and corresponding column names of sfe as row names. There is no
 #' guarantee that the returned geometries are valid or preserve the geometry
@@ -386,7 +386,7 @@ annotSummary <- function(sfe, colGeometryName = 1L, annotGeometryName = 1L,
 #'   indicated in \code{y}, then the same geometry or bounding box is used to
 #'   subset all samples specified in the \code{sample_id} argument.
 #' @param op A geometric operation function to crop the geometries in the SFE
-#'   object. Only \code{\link{st_intersection}} and \code{\link{st_difference}}
+#'   object. Only \code{\link[sf]{st_intersection}} and \code{\link[sf]{st_difference}}
 #'   are allowed. If "intersection", then only things inside \code{y} is kept
 #'   after cropping. If "difference", then only things outside \code{y} is kept.
 #' @param keep_whole Character vector, can be one or more of "col" and "annot"

R/graph_wrappers.R

@@ -422,7 +422,7 @@
 #' \code{listw} is used in many methods that facilitate the spatial neighborhood
 #' graph in the \code{spdep}, \code{spatialreg}, and \code{adespatial}. The edge
 #' weights of the graph in the \code{listw} object are by default style W (see
-#' \code{\link{nb2listw}}) and the unweighted neighbor list is in the
+#' \code{\link[spdep]{nb2listw}}) and the unweighted neighbor list is in the
 #' \code{neighbours} field of the \code{listw} object.
 #'
 #' @inheritParams spdep::nb2listw
@@ -448,13 +448,13 @@
 #' \code{BiocNeighbors} are used. For "spdep", methods from the \code{spdep}
 #' package are used. The "bioc" option is more scalable to larger datasets and
 #' supports multithreading.
-#' @param BPPARAM A \code{\link{BiocParallelParam}} object for multithreading.
+#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} object for multithreading.
 #' Only used for k nearest neighbor and distance based neighbor with
 #' \code{nn_method = "bioc"}.
-#' @param BNPARAM A \code{\link{BiocNeighborParam}} object specifying the
+#' @param BNPARAM A \code{\link[BiocNeighbors]{BiocNeighborParam}} object specifying the
 #' algorithm to find k nearest neighbors and distance based neighbors with
 #' \code{nn_method = "bioc"}. For distance based neighbors, only
-#' \code{\link{KmknnParam}} and \code{\link{VptreeParam}} are applicable.
+#' \code{\link[BiocNeighbors]{KmknnParam}} and \code{\link[BiocNeighbors]{VptreeParam}} are applicable.
 #' @param alpha Only relevant when \code{dist_type = "dpd"}.
 #' @param dmax Only relevant when \code{dist_type = "dpd"}.
 #' @param ... Extra arguments passed to the \code{spdep} function stated in the

R/image.R

@@ -11,15 +11,15 @@ setMethod("NCOL", "AlignedSpatialImage", function(x) 1L)
 #' \code{SpatialFeatureExperiment} and the \code{Voyager} package work with
 #' images differently from \code{SpatialExperiment}. In SFE and
 #' \code{Voyager}'s, plotting functions for SFE objects, the images can be read
-#' with \code{\link{rast}} and represented as \code{SpatRaster}, so the image is
+#' with \code{\link[terra]{rast}} and represented as \code{SpatRaster}, so the image is
 #' not entirely loaded into memory unless necessary. Plotting will not load a
 #' large image into memory; rather the image will be downsampled and the
 #' downsampled version is plotted. A \code{SpatRasterImage} object (as of Bioc
 #' 3.19 or SFE version 1.6 and above) is a \code{SpatRaster} object but also
 #' inheriting from \code{VirtualSpatialImage} as required by
 #' \code{SpatialExperiment}.
 #'
-#' @param img A \code{\link{SpatRaster}} or \code{PackedSpatRaster} object.
+#' @param img A \code{\link[terra]{SpatRaster}} or \code{PackedSpatRaster} object.
 #' @param object A \code{SpatRasterImage} object.
 #' @return A \code{SpatRasterImage} object.
 #' @importClassesFrom SpatialExperiment VirtualSpatialImage
@@ -87,7 +87,7 @@ setMethod("showAsCell", "SpatRasterImage", function(object) {
 #' that can be read with \code{BioFormats}. The image is not loaded into memory,
 #' and when it is, the the \code{BioFormatsImage} object is converted into
 #' \code{\link{ExtImage}} because the loaded image is of a class that inherits
-#' from \code{\link{Image}}. The \code{\link{ExtImage}} class is a thin wrapper
+#' from \code{\link[EBImage]{Image}}. The \code{\link{ExtImage}} class is a thin wrapper
 #' inheriting from \code{VirtualSpatialImage} so it's compatible with
 #' \code{SpatialExperiment} from which SFE is derived. This class might
 #' drastically change as it matures, say to accommodate other formats supported
@@ -308,7 +308,7 @@ setReplaceMethod("transformation", "BioFormatsImage", function(x, value) {
 
 #' Use the EBImage \code{Image} class in SFE objects
 #'
-#' This is a thin wrapper around the \code{\link{Image}} class in the
+#' This is a thin wrapper around the \code{\link[EBImage]{Image}} class in the
 #' \code{EBImage} package so it inherits from \code{VirtualSpatialImage} to be
 #' compatible with \code{SpatialExperiment} from which SFE inherits. An
 #' \code{ext} field is added to specify the spatial extent of the image in
@@ -701,7 +701,7 @@ setMethod("dim", "ExtImage", function(x) {
 #' Image setter
 #'
 #' Modify or replace images stored in a \code{SpatialExperiment} object. This is
-#' different from \code{\link{addImg}} which adds the image from files and can't
+#' different from \code{\link[SpatialExperiment]{addImg}} which adds the image from files and can't
 #' replace existing images, which is there to be consistent with
 #' \code{SpatialExperiment}. This setter here can replace existing images with
 #' another object that inherits from \code{VirtualSpatialImage}, including

R/read.R

@@ -38,6 +38,7 @@
 #' @importFrom rjson fromJSON
 #' @importFrom SummarizedExperiment rowData<-
 #' @importFrom utils read.csv
+#' @importFrom SpatialExperiment spatialCoordsNames<-
 #' @concept Read data into SFE
 #' @importFrom DropletUtils read10xCounts
 #' @note It is assumed that the images have not been cropped. Otherwise the
@@ -418,6 +419,7 @@ readVisiumHD <- function(data_dir, bin_size = c(2L, 8L, 16L),
 #' @importFrom sf st_is_empty st_drop_geometry
 #' @importFrom BiocParallel bplapply
 #' @importFrom utils head
+#' @importFrom data.table :=
 .filter_polygons <- function(polys, min_area,
                              is_Xenium = FALSE, # indicate if input tech is Xenium or not
                              BPPARAM = SerialParam()) {
@@ -651,7 +653,7 @@ readVisiumHD <- function(data_dir, bin_size = c(2L, 8L, 16L),
 #' The coordinates are in microns. Cell centroids are read into
 #' \code{\link{colGeometry}} "centroids", and cell segmentations are read into
 #' \code{colGeometry} "cellSeg". The image(s) (polyT, DAPI, and cell boundaries)
-#' are also read as \code{\link{SpatRaster}} objects so they are not loaded into
+#' are also read as \code{\link[terra]{SpatRaster}} objects so they are not loaded into
 #' memory unless necessary. Because the image's origin is the top left while the
 #' geometry's origin is bottom left, either the image or the geometry needs to
 #' be flipped. Because the image accompanying MERFISH datasets are usually very
@@ -688,11 +690,11 @@ readVisiumHD <- function(data_dir, bin_size = c(2L, 8L, 16L),
 #' @param use_cellpose Whether to read the parquet files from CellPose cell
 #'   segmentation. If \code{FALSE}, cell segmentation will be read from the HDF5
 #'   files. Note that reading HDF5 files for numerous FOVs is very slow.
-#' @param BPPARAM A \code{\link{BiocParallelParam}} object specifying parallel
+#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} object specifying parallel
 #'   processing backend and number of threads to use for parallelizable tasks:
 #'   \enumerate{ \item To load cell segmentation from HDF5 files from different
 #'   fields of view (FOVs) with multiple cores. A progress bar can be configured
-#'   in the \code{\link{BiocParallelParam}} object. When there are numerous
+#'   in the \code{\link[BiocParallel]{BiocParallelParam}} object. When there are numerous
 #'   FOVs, reading in the geometries can be time consuming, so we recommend
 #'   using a server and larger number of threads. This argument is not used if
 #'   \code{use_cellpose = TRUE} and the parquet file is present.

R/saveRDS.R

@@ -1,7 +1,7 @@
 #' Save SpatialFeatureExperiment as RDS file
 #'
 #' Saving SFE objects as RDS files is complicated by the \code{SpatRaster} class
-#' of the images. If present, the images need to be wrapped with the \code{\link{wrap}}
+#' of the images. If present, the images need to be wrapped with the \code{\link[terra]{wrap}}
 #' function in \code{terra} before serializing the SFE object. Otherwise the
 #' images will be invalid pointers when the RDS is reloaded. If the image does
 #' not fit in memory and its file source is unknown, then it will be written to