update negative method

src/control_methods/negative/script.R

@@ -1,6 +1,6 @@
 ## VIASH START
 par <- list(
-  input = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",
+  input = "resources_test/spatialsimbench_mobnew/dataset_sp.h5ad",
   output = "simulated_dataset.h5ad"
 )
 meta <- list(
@@ -13,17 +13,15 @@ input <- anndata::read_h5ad(par$input)
 
 count_matrix <- as.matrix(input$layers[['counts']])
 
+shuffled_values <- sample(as.vector(count_matrix))
 
-n_rows <- nrow(count_matrix)
-n_cols <- ncol(count_matrix)
+shuffled_matrix <- matrix(shuffled_values, nrow = nrow(count_matrix), ncol = ncol(count_matrix))
 
-random_matrix_uniform <- matrix(runif(n_rows * n_cols), nrow = n_rows, ncol = n_cols)
-rownames(random_matrix_uniform) <- rownames(count_matrix)
 
 cat("Generate outoput file\n")
 output <- anndata::AnnData(
   layers = list(
-    counts = random_matrix_uniform
+    counts = shuffled_matrix
   ),
   obs = input$obs[c("row", "col")],
   var = input$var,