add scFeatures result in the real dataset

openproblems-bio · Aug 14, 2024 · a8d6718 · a8d6718
1 parent ebfc830
commit a8d6718
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Showing 2 changed files with 5 additions and 11 deletions.
diff --git a/src/process_datasets/downstream/config.vsh.yaml b/src/process_datasets/downstream/config.vsh.yaml
@@ -22,6 +22,7 @@ argument_groups:
 resources:
   - type: r_script
     path: script.R
+  - path: /src/helpers/utils.R
 
 test_resources:
   - path: /resources_test/datasets/MOBNEW

diff --git a/src/process_datasets/scFeatures/script.R b/src/process_datasets/scFeatures/script.R
@@ -44,28 +44,21 @@ cat("Transforming spatial into AnnData\n")
 
 output_sp <- anndata::AnnData(
   layers = list(
-    counts = Matrix::t(assay(input_sp, "counts")),
-    logcounts = Matrix::t(assay(input_sp, "logcounts"))
-  ),
-  obs = data.frame(
-    row.names = colnames(input_sp),
-    col = colData(input_sp)$col,
-    row = colData(input_sp)$row,
-    sizeFactor = colData(input_sp)$sizeFactor,
-    spatial_cluster = colData(input_sp)$spatial.cluster
+    counts =input_sp$layers[['counts']],
+    logcounts = input_sp$layers[['logcounts']]
   ),
+  obs = input_sp$obs,
   var = data.frame(
     row.names = rownames(input_sp),
     feature_id = rownames(input_sp),
     feature_name = rownames(input_sp)
   ),
   obsm = list(
-    celltype_proportions = celltype_proportions,
+    celltype_proportions = input_sp$obsm[['celltype_proportions']],
     L_stats = scfeatures_result$L_stats,
     celltype_interaction = scfeatures_result$celltype_interaction,
     nn_correlation = scfeatures_result$nn_correlation,
     morans_I = scfeatures_result$morans_I
-
   ),
   uns = list(
     dataset_id = par$dataset_id,