Add some examples to avoid BiocCheck ERROR https://github.com/LieberI…

…nstitute/visiumStitched/actions/runs/9197197064/job/25297069045#step:23:88 for now.

R/add_array_coords.R

@@ -49,6 +49,9 @@
 #' coords_dir <- "dev/test_data"
 #' spe_new <- add_array_coords(spe, sample_info, coords_dir, overwrite = TRUE)
 #' }
+#'
+#' ## TODO: add working examples
+#' args(add_array_coords)
 add_array_coords <- function(spe, sample_info, coords_dir, overwrite = TRUE) {
     #   55-micrometer diameter for Visium spot; 100 micrometers between spots;
     #   65-micrometer spot diameter used in 'spot_diameter_fullres' calculation

R/add_overlap_info.R

@@ -44,6 +44,9 @@
 #' print(p_old)
 #' print(p_new)
 #' }
+#'
+#' ## TODO: add working examples
+#' args(add_overlap_info)
 add_overlap_info <- function(spe, metric_name) {
     #   State assumptions about columns expected to be in the colData
     expected_cols <- c(

R/build_spe.R

@@ -31,6 +31,9 @@
 #' metric_name <- "sum_umi"
 #' spe <- build_spe(sample_info, coords_dir, metric_name)
 #' }
+#'
+#' ## TODO: add working examples
+#' args(build_spe)
 build_spe <- function(sample_info, coords_dir, metric_name, count_type = "sparse") {
     message("Building SpatialExperiment using capture area as sample ID")
     spe <- read10xVisium(