Get rid of R CMD check errors and warnings

Author: lambdamoses

DESCRIPTION

@@ -46,7 +46,7 @@ Imports:
     zeallot
 License: Artistic-2.0
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate: 
     'AllGenerics.R'
     'utils.R'
@@ -98,6 +98,7 @@ Suggests:
     sparseMatrixStats,
     testthat (>= 3.0.0),
     tidyr,
+    VisiumIO,
     Voyager (>= 1.7.2),
     withr,
     xml2

R/aggregate.R

@@ -32,7 +32,7 @@
 #'   be loaded into memory. \code{\link[arrow]{open_dataset}} is used to open a
 #'   link to the data and then transcript spots of one gene is loaded into
 #'   memory at a time.
-#' @param pregressbar Logical, whether to show progress bar. This argument is
+#' @param progressbar Logical, whether to show progress bar. This argument is
 #'   only used when \code{save_memory = TRUE} because otherwise the
 #'   \code{progressbar} argument can be specified in \code{BPPARAM}.
 #' @param .orig_nrows Only used internally in the SFE method of \code{aggregate}

R/coerce.R

@@ -111,8 +111,17 @@
 #' @aliases toSpatialFeatureExperiment
 #' @concept SpatialFeatureExperiment class
 #' @examples
-#' library(SpatialExperiment)
-#' example(read10xVisium)
+#' library(VisiumIO)
+#' # From examples of TENxVisium()
+#' sample_dir <- system.file(
+#' file.path("extdata", "10xVisium", "section1"),
+#' package = "VisiumIO"
+#' )
+#' ## using spacerangerOut folder
+#' tv <- TENxVisium(
+#'     spacerangerOut = sample_dir, processing = "raw", images = "lowres"
+#' )
+#' spe <- import(tv)
 #' # There can't be duplicate barcodes
 #' colnames(spe) <- make.unique(colnames(spe), sep = "-")
 #' rownames(spatialCoords(spe)) <- colnames(spe)

R/dimGeometries.R

@@ -617,8 +617,17 @@ txSpots <- function(x, sample_id = 1L, withDimnames = TRUE) {
 #' @concept Geometric operations
 #' @export
 #' @examples
-#' library(SpatialExperiment)
-#' example(read10xVisium)
+#' library(VisiumIO)
+#' # From examples of TENxVisium()
+#' sample_dir <- system.file(
+#' file.path("extdata", "10xVisium", "section1"),
+#' package = "VisiumIO"
+#' )
+#' ## using spacerangerOut folder
+#' tv <- TENxVisium(
+#'     spacerangerOut = sample_dir, processing = "raw", images = "lowres"
+#' )
+#' spe <- import(tv)
 #' # There can't be suplicate barcodes
 #' colnames(spe) <- make.unique(colnames(spe), sep = "-")
 #' rownames(spatialCoords(spe)) <- colnames(spe)

R/graph_wrappers.R

@@ -483,6 +483,7 @@
 #' @concept Spatial neighborhood graph
 #' @export
 #' @name findSpatialNeighbors
+#' @aliases findSpatialNeighbors,SpatialFeatureExperiment-method
 #' @examples
 #' library(SFEData)
 #' sfe <- McKellarMuscleData(dataset = "small")

R/read.R

@@ -22,7 +22,6 @@
 #'   unit. If using microns, then spacing between spots in pixels will be used
 #'   to convert the coordinates into microns, as the spacing is known to be 100
 #'   microns. This is used to plot scale bar.
-#' @param load Deprecated. Not used, kept for backward compatibility for now.
 #' @param flip Whether to flip the geometries or the images, because in
 #'   \code{sf} and \code{terra}, the geometries use the Cartesian coordinates
 #'   greater y coordinates going up, while in images, greater y values go down.
@@ -53,8 +52,7 @@
 #' list.files(samples[1])
 #' list.files(file.path(samples[1], "spatial"))
 #' (sfe <- read10xVisiumSFE(dirs = samples, sample_id = sample_ids,
-#'     type = "sparse", data = "filtered",
-#'     load = FALSE
+#'     type = "sparse", data = "filtered"
 #' ))
 #' 
 read10xVisiumSFE <- function(samples = deprecated(),

R/saveRDS.R

@@ -30,21 +30,17 @@ setMethod("saveRDS", "SpatialFeatureExperiment",
                   warning("This object contains out of memory data that may
                           break when the RDS file is moved.")
               }
-              if (!nrow(imgData(object)))
-                  base::saveRDS(object, file = file, ascii = ascii,
-                                version = version, compress = compress,
-                                refhook = refhook)
-              else {
+              if (nrow(imgData(object))) {
                   for (i in seq_len(nrow(imgData(object)))) {
                       img <- int_metadata(object)$imgData$data[[i]]
                       if (inherits(img, "SpatRasterImage"))
                           img <- new("PackedRasterImage", wrap(img))
                       int_metadata(object)$imgData$data[[i]] <- img
                   }
-                  base::saveRDS(object, file = file, ascii = ascii,
-                                version = version, compress = compress,
-                                refhook = refhook)
               }
+              base::saveRDS(object, file = file, ascii = ascii,
+                            version = version, compress = compress,
+                            refhook = refhook)
           })
 # From terra
 setMethod("readRDS", signature(file="character"),

R/tissue_boundary.R

@@ -56,6 +56,7 @@
 #'
 #' @param sfe An SFE object with images
 #' @param sample_id Sample id(s) whose tissue boundaries are to be found.
+#' @param image_id ID of image to use to get boundary.
 #' @param image_type Character, either "brightfield" or "fluorescent"
 #' @param channel Channel to use for tissue segmentation. If \code{NULL} use
 #'   average of all channels.
@@ -124,6 +125,8 @@ getTissueBoundaryImg <- function(sfe, sample_id = NULL, image_id = NULL,
 #' 
 #' @inheritParams getTissueBoundaryImg
 #' @inheritParams sf::st_concave_hull
+#' @param colGeometryName Name of the \code{colGeometry} to use to infer the
+#' concave hull.
 #' @return A \code{sf} data frame with columns \code{sample_id} and
 #'   \code{geometry}.
 #' @export