Added examples

R/formatTxSpots.R

@@ -118,6 +118,18 @@
 #'   the transcript spots of the selected genes added.
 #' @name readSelectTx
 #' @export
+#' @examples
+#' library(SFEData)
+#' fp <- tempdir()
+#' dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' fn_tx <- formatTxTech(dir_use, tech = "Xenium", flip = TRUE, return = FALSE,
+#'                       file_out = file.path(dir_use, "tx_spots.parquet"))
+#' gene_select <- c("ACE2", "BMX")
+#' df <- readSelectTx(fn_tx, gene_select)
+#'
+#' sfe <- readXenium(dir_use)
+#' sfe <- addSelectTx(sfe, fn_tx, head(rownames(sfe), 5), swap_rownames = "Symbol")
+#' unlink(dir_use, recursive = TRUE)
 readSelectTx <- function(file, gene_select, z = "all",
                          z_option = c("3d", "split")) {
     if (!gdalParquetAvailable()) {
@@ -504,6 +516,13 @@ addTxSpots <- function(sfe, file, sample_id = 1L,
 #'   `return = FALSE`.
 #' @name formatTxTech
 #' @export
+#' @examples
+#' library(SFEData)
+#' fp <- tempdir()
+#' dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' fn_tx <- formatTxTech(dir_use, tech = "Xenium", flip = TRUE, return = FALSE,
+#'                       file_out = file.path(dir_use, "tx_spots.parquet"))
+#'
 formatTxTech <- function(data_dir, tech = c("Vizgen", "Xenium", "CosMX"),
                          dest = c("rowGeometry", "colGeometry"),
                          z = "all", min_phred = 20,

R/read.R

@@ -832,20 +832,15 @@ readCosMX <- function(data_dir,
 #' @importFrom DropletUtils read10xCounts
 #' @importFrom zeallot %<-%
 #' @examples
-#' # TODO: Example code for Xenium toy data
-#'
-#' # custom example run:
-#' if (FALSE)
-#' sfe <-
-#'  readXenium(data_dir = data_dir,
-#'  sample_id = "test_xenium",
-#'  image = c("morphology_focus", "morphology_mip"),
-#'  segmentations = c("cell", "nucleus"),
-#'  flip = "geometry",
-#'  filter_counts = TRUE,
-#'  add_molecules = TRUE,
-#'  file_out = NULL)
-#'
+#' library(SFEData)
+#' library(RBioFormats)
+#' fp <- tempdir()
+#' dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' # RBioFormats issue
+#' try(sfe <- readXenium(dir_use, add_molecules = TRUE))
+#' sfe <- readXenium(dir_use, add_molecules = TRUE)
+#' unlink(dir_use, recursive = TRUE)
+
 readXenium <- function(data_dir,
                        sample_id = "sample01",
                        image = c("morphology_focus", "morphology_mip"),

R/utils.R

@@ -169,6 +169,12 @@ bbox_center <- function(bbox) {
 #' @return Numeric vector of length 2 of pixel size in x and y. Usually they're
 #' the same.
 #' @export
+#' @examples
+#' library(SFEData)
+#' fp <- tempdir()
+#' dir_use <- XeniumOutput("v1", file_path = file.path(fp, "xenium_test"))
+#' getPixelSize(file.path(dir_use, "morphology_focus.ome.tif"))
+#' unlink(dir_use, recursive = TRUE)
 getPixelSize <- function(file, resolution = 1L) {
     check_installed(c("xml2", "RBioFormats"))
     xml_meta <- RBioFormats::read.omexml(file) |>
@@ -206,6 +212,10 @@ getPixelSize <- function(file, resolution = 1L) {
 #' or a list of bounding boxes which are named numeric vectors.
 #' @return A named numeric vector for the total bounding box.
 #' @export
+#' @examples
+#' bboxes <- list(c(xmin = 5, xmax = 10, ymin = 2, ymax = 20),
+#' c(xmin = 8, xmax = 18, ymin = 0, ymax = 15))
+#' bbox_all <- aggBboxes(bboxes)
 aggBboxes <- function(bboxes) {
     if (is.list(bboxes)) {
         bboxes <- lapply(bboxes, function(x) x[c("xmin", "ymin", "xmax", "ymax")])
@@ -227,6 +237,11 @@ aggBboxes <- function(bboxes) {
 #' @inheritParams sampleIDs
 #' @return A character vector of \code{image_ids}.
 #' @export
+#' @examples
+#' fp <- system.file(file.path("extdata", "sample01"),
+#' package = "SpatialFeatureExperiment")
+#' sfe <- read10xVisiumSFE(fp, type = "sparse")
+#' imageIDs(sfe)
 imageIDs <- function(sfe) imgData(sfe)$image_id
 
 #' Check if Parquet GDAL driver is available
@@ -248,6 +263,9 @@ imageIDs <- function(sfe) imgData(sfe)$image_id
 #'
 #' @return Logical, indicating whether the Parquet driver is present.
 #' @export
+#' @examples
+#' gdalParquetAvailable()
+#'
 gdalParquetAvailable <- function() {
     "Parquet" %in% rownames(sf::st_drivers())
 }