change the variable name from downstream

openproblems-bio · Aug 27, 2024 · 956ca12 · 956ca12
1 parent 7f3a5fb
commit 956ca12
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Showing 2 changed files with 15 additions and 4 deletions.
diff --git a/src/metrics/downstream/script.R b/src/metrics/downstream/script.R
@@ -1,3 +1,14 @@
+requireNamespace("anndata", quietly = TRUE)
+requireNamespace("edgeR", quietly = TRUE)
+requireNamespace("ks", quietly = TRUE)
+requireNamespace("resample", quietly = TRUE)
+requireNamespace("reshape2", quietly = TRUE)
+requireNamespace("MuSiC", quietly = TRUE)
+requireNamespace("CARD", quietly = TRUE)
+requireNamespace("SingleCellExperiment", quietly = TRUE)
+requireNamespace("SummarizedExperiment", quietly = TRUE)
+
+
 ## VIASH START
 par <- list(
   input_spatial_dataset = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",

diff --git a/src/process_datasets/generate_sim_spatialcluster/script.R b/src/process_datasets/generate_sim_spatialcluster/script.R
@@ -3,8 +3,8 @@
 ## VIASH START
 par <- list(
   # inputs
-  input_spatial_dataset = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",
-  input_simulated_dataset = "resources_test/datasets/MOBNEW/simulated_dataset.h5ad",
+  input_sp = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",
+  input_sp_sim = "resources_test/datasets/MOBNEW/simulated_dataset.h5ad",
   # outputs
   output_sp = "resources_test/datasets/MOBNEW/simulated_dataset.h5ad"
 )
@@ -15,8 +15,8 @@ meta <- list(
 source(file.path(meta$resources_dir, "utils.R"))
 
 cat("Read input files\n")
-input_real_sp <- anndata::read_h5ad(par$input_spatial_dataset)
-input_simulated_sp <- anndata::read_h5ad(par$input_simulated_dataset)
+input_real_sp <- anndata::read_h5ad(par$input_sp)
+input_simulated_sp <- anndata::read_h5ad(par$input_sp_sim)
 
 sim_sce <- scater::logNormCounts(SingleCellExperiment::SingleCellExperiment(
   list(counts = Matrix::t(input_simulated_sp$layers[["counts"]])),