From 3b78be48940b3a58791d2c07684a331607b25d3f Mon Sep 17 00:00:00 2001
From: lcolladotor <lcolladotor@gmail.com>
Date: Wed, 3 Jul 2024 16:45:45 -0400
Subject: [PATCH] Update docs after having updated the LS data on Dropbox. Aka,
 the stitched LS object is now compatible out of the box with
 spatialLIBD::run_app()

---
 DESCRIPTION    |  2 +-
 R/run_app.R    | 16 ----------------
 man/run_app.Rd | 16 ----------------
 3 files changed, 1 insertion(+), 33 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c8db0a99..55eed6e3 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/R/run_app.R b/R/run_app.R
index 4352ce03..851045a3 100644
--- a/R/run_app.R
+++ b/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$ManualAnnotation <- "NA"
-#'
 #' ## Run the app with this stitched data
 #' run_app(
 #'     spe = spe_stitched,
diff --git a/man/run_app.Rd b/man/run_app.Rd
index 5c8f19f0..0eb0295d 100644
--- a/man/run_app.Rd
+++ b/man/run_app.Rd
@@ -253,22 +253,6 @@ spe_stitched
 ## Notice the use of "exclude_overlapping"
 table(spe_stitched$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,