updated SRTsim

still testing
openproblems-bio · Jul 10, 2024 · 02a0b05 · 02a0b05
1 parent 5366822
commit 02a0b05
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/src/methods/SRTsim/script.R b/src/methods/SRTsim/script.R
@@ -20,9 +20,8 @@ sce <- SingleCellExperiment(
   colData = input$obs
 )
 
-real_count <- counts(sce)
-real_loc <- data.frame(x = colData(sce)$row,y = colData(sce)$col, region = colData(sce)$spatial.cluster)
-rownames(real_loc) <- rownames(colData(sce))
+real_count <- as.matrix(Matrix::t(input$layers[["counts"]]))
+real_loc <- data.frame(x = adata$obs$row,y = adata$obs$col, region = adata$obs$spatial_cluster)
 
 simSRT<- createSRT(count_in=real_count,loc_in =real_loc)
 

diff --git a/src/methods/splatter/script.R b/src/methods/splatter/script.R
@@ -21,7 +21,6 @@ sce <- SingleCellExperiment(
 
 cat("Splatter simulation start\n")
 
-set.seed(1)
 if (par$base != "domain") {
   stop("ONLY domain base")
 }