Fix AnnData tmap parameter if layers already exist

tissuumaps/read_h5ad.py

@@ -284,8 +284,6 @@ def h5ad_to_tmap(basedir, path, library_id=None):
     obsList = getObsList(adata)
     new_tmap_project = copy.deepcopy(tmap_template)
 
-    new_tmap_project["layers"] = layers
-    new_tmap_project["plugins"] = plugins
     if "tmap" in list(adata.get("uns", [])):
         new_tmap_project = json.loads(
             adata.get(
@@ -295,6 +293,14 @@ def h5ad_to_tmap(basedir, path, library_id=None):
         )
         if "markerFiles" not in new_tmap_project.keys():
             new_tmap_project["markerFiles"] = []
+    if "layers" in new_tmap_project.keys():
+        new_tmap_project["layers"] += layers
+    else:
+        new_tmap_project["layers"] = layers
+    if "plugins" in new_tmap_project.keys():
+        new_tmap_project["plugins"] += plugins
+    else:
+        new_tmap_project["plugins"] = plugins
     obsListCategorical = []
     obsListNumerical = []
     palette = {}