make names unique, otherwise it becomes an issue for the ExperimentHu…

…b submission
LieberInstitute · Mar 17, 2023 · 23ce3a3 · 23ce3a3
1 parent 4336985
commit 23ce3a3
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 6 deletions.
diff --git a/code/98_prepare_to_share/01_prepare_to_share.R b/code/98_prepare_to_share/01_prepare_to_share.R
@@ -12,9 +12,6 @@ dir.create(dir_rdata, showWarnings = FALSE)
 suffix <-
     ifelse(as.numeric(Sys.getenv("SGE_TASK_ID")) == 1, "wholegenome", "targeted")
 
-## Create output directory
-dir.create(file.path(dir_rdata, suffix), showWarnings = FALSE)
-
 ## Load the data
 spe <- readRDS(here::here(
     "processed-data",
@@ -101,7 +98,7 @@ source(here("code", "colors_pathology.R"), echo = TRUE, max.deparse.length = 500
 spe$path_groups_colors <- colors_pathology[as.character(spe$path_groups)]
 
 ## Save the final object that we can share through spatialLIBD
-save(spe, file = file.path(dir_rdata, suffix, "spe.Rdata"))
+save(spe, file = file.path(dir_rdata, paste0("Visium_SPG_AD_spe_", suffix, ".Rdata")))
 
 ## Reproducibility information
 print("Reproducibility information:")

diff --git a/code/99_prepare_for_shiny/01_prepare_shiny.R b/code/99_prepare_for_shiny/01_prepare_shiny.R
@@ -11,8 +11,7 @@ suffix <-
 load(here::here(
     "processed-data",
     "98_prepare_to_share",
-    suffix,
-    "spe.Rdata"
+    paste0("Visium_SPG_AD_spe_", suffix, ".Rdata")
 ), verbose = TRUE)
 
 ## Drop images we don't really use in the app