Try using BiocFileCache instead of RDS files for persistence of sampl…

…e info across examples (not tests yet)

R/add_array_coords.R

@@ -63,10 +63,13 @@
 #' ########################################################################
 #' #   Prepare sample_info
 #' ########################################################################
-#'
-#' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS("sample_info.rds")
-#' } else {
+#' 
+#' #    Cache sample_info across examples
+#' bfc <- BiocFileCache::BiocFileCache()
+#' cached_file <- BiocFileCache::bfcquery(bfc, 'visiumStitched_sample_info')
+#' 
+#' if (nrow(cached_file) == 0) {
+#'     #    Then we need to construct the table of sample information
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
 #'         capture_area = c("V13B23-283_A1", "V13B23-283_C1", "V13B23-283_D1")
@@ -92,8 +95,18 @@
 #'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#'
-#'     saveRDS(sample_info, "sample_info.rds")
+#'     
+#'     #    Cache sample info for later
+#'     sample_info_path <- BiocFileCache::bfcnew(
+#'         bfc, "visiumStitched_sample_info", ext = "csv"
+#'     )
+#'     readr::write_csv(sample_info, sample_info_path)
+#' } else {
+#'     #    Pull sample info from the cache
+#'     sample_info_path <- BiocFileCache::bfcquery(
+#'         bfc, 'visiumStitched_sample_info'
+#'     )$rpath
+#'     sample_info = readr::read_csv(sample_info_path)
 #' }
 #'
 #' ## Preparing Fiji coordinates and images for build_SpatialExperiment()

R/build_SpatialExperiment.R

@@ -39,9 +39,12 @@
 #' #   Prepare sample_info
 #' ########################################################################
 #'
-#' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS("sample_info.rds")
-#' } else {
+#' #    Cache sample_info across examples
+#' bfc <- BiocFileCache::BiocFileCache()
+#' cached_file <- BiocFileCache::bfcquery(bfc, 'visiumStitched_sample_info')
+#' 
+#' if (nrow(cached_file) == 0) {
+#'     #    Then we need to construct the table of sample information
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
 #'         capture_area = c("V13B23-283_A1", "V13B23-283_C1", "V13B23-283_D1")
@@ -67,8 +70,18 @@
 #'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#'
-#'     saveRDS(sample_info, "sample_info.rds")
+#'     
+#'     #    Cache sample info for later
+#'     sample_info_path <- BiocFileCache::bfcnew(
+#'         bfc, "visiumStitched_sample_info", ext = "csv"
+#'     )
+#'     readr::write_csv(sample_info, sample_info_path)
+#' } else {
+#'     #    Pull sample info from the cache
+#'     sample_info_path <- BiocFileCache::bfcquery(
+#'         bfc, 'visiumStitched_sample_info'
+#'     )$rpath
+#'     sample_info = readr::read_csv(sample_info_path)
 #' }
 #'
 #' ## Preparing Fiji coordinates and images for build_SpatialExperiment()

R/prep_fiji.R

@@ -39,9 +39,12 @@
 #' @author Nicholas J. Eagles
 #'
 #' @examples
-#' if (file.exists("sample_info.rds")) {
-#'     sample_info <- readRDS("sample_info.rds")
-#' } else {
+#' #    Cache sample_info across examples
+#' bfc <- BiocFileCache::BiocFileCache()
+#' cached_file <- BiocFileCache::bfcquery(bfc, 'visiumStitched_sample_info')
+#' 
+#' if (nrow(cached_file) == 0) {
+#'     #    Then we need to construct the table of sample information
 #'     sample_info <- dplyr::tibble(
 #'         group = "Br2719",
 #'         capture_area = c("V13B23-283_A1", "V13B23-283_C1", "V13B23-283_D1")
@@ -67,8 +70,18 @@
 #'
 #'     ## Re-size images and add more information to the sample_info
 #'     sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
-#'
-#'     saveRDS(sample_info, "sample_info.rds")
+#'     
+#'     #    Cache sample info for later
+#'     sample_info_path <- BiocFileCache::bfcnew(
+#'         bfc, "visiumStitched_sample_info", ext = "csv"
+#'     )
+#'     readr::write_csv(sample_info, sample_info_path)
+#' } else {
+#'     #    Pull sample info from the cache
+#'     sample_info_path <- BiocFileCache::bfcquery(
+#'         bfc, 'visiumStitched_sample_info'
+#'     )$rpath
+#'     sample_info = readr::read_csv(sample_info_path)
 #' }
 #'
 #' spe_input_dir <- tempdir()