Update docs after having updated the LS data on Dropbox. Aka, the sti…

…tched LS object is now compatible out of the box with spatialLIBD::run_app()

DESCRIPTION

@@ -79,7 +79,7 @@ Imports:
     statmod,
     MatrixGenerics,
     rlang
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/LieberInstitute/spatialLIBD
 BugReports: https://support.bioconductor.org/tag/spatialLIBD

R/run_app.R

@@ -198,22 +198,6 @@
 #' ## Notice the use of "exclude_overlapping"
 #' table(spe_stitched$exclude_overlapping, useNA = "ifany")
 #'
-#' ## Drop NAs
-#' spe_stitched <- spe_stitched[, !is.na(spe_stitched$exclude_overlapping)]
-#'
-#' ## Make it compatible with spatialLIBD::run_app()
-#' spe_stitched <- add_key(spe_stitched)
-#' spe_stitched$sum_umi <- colSums(logcounts(spe_stitched))
-#' spe_stitched$sum_gene <- colSums(logcounts(spe_stitched) > 0)
-#' rowData(spe_stitched)$gene_name <- rowData(spe_stitched)$symbol
-#' rowData(spe_stitched)$gene_id <- rownames(spe_stitched)
-#' rowData(spe_stitched)$gene_search <- paste0(rowData(spe_stitched)$gene_name, "; ", rowData(spe_stitched)$gene_id)
-#' is_mito <- seq_len(1000)
-#' spe_stitched$expr_chrM <- colSums(logcounts(spe_stitched)[is_mito, , drop = FALSE])
-#' spe_stitched$expr_chrM_ratio <- spe_stitched$expr_chrM / spe_stitched$sum_umi
-#' ## Add a variable for saving the manual annotations
-#' spe_stitched$ManualAnnotation <- "NA"
-#'
 #' ## Run the app with this stitched data
 #' run_app(
 #'     spe = spe_stitched,