Edit the R docs a bit

LieberInstitute · May 22, 2024 · 460558b · 460558b
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Showing 6 changed files with 12 additions and 10 deletions.
diff --git a/R/add_array_coords.R b/R/add_array_coords.R
@@ -43,7 +43,7 @@
 #' @examples
 #' #   For internal testing
 #' \dontrun{
-#' library(HDF5Array)
+#' library("HDF5Array")
 #' spe <- loadHDF5SummarizedExperiment("dev/test_data/spe_filtered")
 #' sample_info <- readr::read_csv("dev/test_data/sample_info.csv")
 #' coords_dir <- "dev/test_data"

diff --git a/R/add_overlap_info.R b/R/add_overlap_info.R
@@ -28,7 +28,7 @@
 #' @examples
 #' #   For internal testing
 #' \dontrun{
-#' library(HDF5Array)
+#' library("HDF5Array")
 #' spe <- loadHDF5SummarizedExperiment("dev/test_data/spe_filtered")
 #' spe_new <- add_overlap_info(spe, metric_name = "sum_umi")
 #' p_old <- spot_plot(

diff --git a/R/spe_to_seurat.R b/R/spe_to_seurat.R
@@ -21,8 +21,8 @@
 #'
 #' @examples
 #'
-#' #   Grab an example SpatialExperiment and add dummy "transformed" versions of
-#' #   spatial coordinates, which are to be converted
+#' ## Grab an example SpatialExperiment and add dummy "transformed" versions of
+#' ## spatial coordinates, which are to be converted
 #' spe <- if (!exists("spe")) {
 #'     spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
 #' }
@@ -32,8 +32,9 @@
 #' spe$pxl_col_in_fullres_transformed <- SpatialExperiment::spatialCoords(spe)[, "pxl_col_in_fullres"]
 #' colnames(spe) <- spe$key
 #'
-#' #   Convert
+#' ## Convert from a SpatialExperiment to a Seurat object
 #' seur <- spe_to_seurat(spe)
+#' seur
 spe_to_seurat <- function(spe, verbose = TRUE) {
     SPOT_DIAMETER <- 55e-6
 

diff --git a/man/add_array_coords.Rd b/man/add_array_coords.Rd
diff --git a/man/add_overlap_info.Rd b/man/add_overlap_info.Rd
diff --git a/man/spe_to_seurat.Rd b/man/spe_to_seurat.Rd