add model reactives to workflow

Author: serareif

app.py

@@ -38,7 +38,7 @@ def server(input, output, session):
     _model = reactive.value(model_path)
     composition_server("composition", _dataframe)
     export_server("export")
-    dgea_server("dgea", _adata)
+    dgea_server("dgea", _adata, _model)
     tree_server("tree", _tree)
 
 app = App(app_ui, server)

dgea/dgea_scvi.py

@@ -17,7 +17,7 @@ def dgea_ui():
                     )
 
 @module.server
-def dgea_server(input, output, session, _adata: reactive.Value[ad.AnnData]):
+def dgea_server(input, output, session, _adata: reactive.Value[ad.AnnData], _model: reactive.Value[str]):
     _counts = reactive.value(None)
     _uniques = reactive.value([])
 
@@ -32,9 +32,9 @@ def dgea_server(input, output, session, _adata: reactive.Value[ad.AnnData]):
     _filtered_genes = reactive.value(None)
     _filtered_counts = reactive.value(None)
 
-    run_dgea_server("run_dgea", _adata, _result, _counts, _reference, _alternative, _uniques, _contrast)
+    run_dgea_server("run_dgea", _adata, _result, _counts, _reference, _alternative, _model, _uniques, _contrast)
     filter_dgea_server("filter_dgea", _adata, _counts, _uniques,
                        _result, _filtered_result, _filtered_genes,
-                       _filtered_counts, _reference, _alternative, _contrast, _log10_p, _lfc)
+                       _filtered_counts, _reference, _alternative, _contrast, _model, _log10_p, _lfc)
     plot_dgea_server("plot_dgea", _filtered_counts, _contrast, _reference, _alternative,
                      _result, _log10_p, _lfc)

dgea/filter_dgea_scvi.py

@@ -17,7 +17,7 @@ def filter_dgea_ui():
 def filter_dgea_server(input, output, session, 
                        _adata, _counts, _uniques,
                        _result, _filtered_result, _filtered_genes, _filtered_counts,
-                       _reference, _alternative, _contrast,
+                       _reference, _alternative, _contrast, _model,
                        _log10_p, _lfc
                        ):
 
@@ -57,11 +57,12 @@ def update_result():
         reference = _reference.get()
         alternative = _alternative.get()
         contrast = _contrast.get()
+        model = _model.get()
 
         if None in (reference, alternative, contrast):
             return
 
-        res_df = scanvi_dgea(adata, contrast, reference, alternative)
+        res_df = scanvi_dgea(adata, contrast, reference, alternative, model)
         res_counts = get_normalized_counts(adata)
         _result.set(res_df)
         _counts.set(res_counts)