Sort markers in numerical observations of AnnData objects

cavenel · Feb 17, 2023 · fe6d558 · fe6d558
1 parent 1e853ef
commit fe6d558
Showing 1 changed file with 9 additions and 1 deletion.
diff --git a/tissuumaps/read_h5ad.py b/tissuumaps/read_h5ad.py
@@ -309,6 +309,7 @@ def h5ad_to_tmap(basedir, path, library_id=None):
                 "cb_gr_rand": False,
                 "pie_check": False,
                 "scale_check": False,
+                "sortby_check": True,
                 "shape_col": False,
                 "shape_fixed": True,
                 "shape_gr": False,
@@ -321,7 +322,12 @@ def h5ad_to_tmap(basedir, path, library_id=None):
             "name": "Numerical observations",
             "path": os.path.basename(path),
             "dropdownOptions": [
-                {"optionName": obs, "name": obs, "expectedHeader.cb_col": f"/obs/{obs}"}
+                {
+                    "optionName": obs,
+                    "name": obs,
+                    "expectedHeader.cb_col": f"/obs/{obs}",
+                    "expectedHeader.sortby_col": f"/obs/{obs}",
+                }
                 for obs in obsList
                 if adata.get(f"/obs/{obs}/categories") is None
                 and adata.get(f"/obs/__categories/{obs}") is None
@@ -398,6 +404,7 @@ def h5ad_to_tmap(basedir, path, library_id=None):
                 "scale_check": False,
                 "shape_col": False,
                 "shape_fixed": True,
+                "sortby_check": True,
                 "shape_gr": False,
                 "shape_gr_dict": False,
                 "shape_gr_rand": True,
@@ -412,6 +419,7 @@ def h5ad_to_tmap(basedir, path, library_id=None):
                     "optionName": gene,
                     "name": "Gene expression: " + gene,
                     "expectedHeader.cb_col": f"/X;{index}",
+                    "expectedHeader.sortby_col": f"/X;{index}",
                 }
                 for index, gene in enumerate(varList)
             ],