put coordinates into ad.obsm

scelvis/callbacks.py

@@ -661,8 +661,8 @@ def update_filter_cells_controls(
                     + hidden_rangeslider
                 )
             else:
-                range_min = values.min()
-                range_max = values.max()
+                range_min = values.dropna().min()
+                range_max = values.dropna().max()
                 if attribute in filters:
                     val_min = filters[attribute][0]
                     val_max = filters[attribute][1]

scelvis/convert.py

@@ -11,6 +11,7 @@
 import attr
 import scanpy as sc
 import scipy.sparse
+import re
 import scipy.io
 import pandas as pd
 from logzero import logger
@@ -321,9 +322,13 @@ def _load_expression(self, coords, annotation, markers):
         logger.info("Combining data")
         ad = sc.AnnData(
             X=X,
-            obs=pd.concat([coords.loc[cells], annotation.loc[cells]], axis=1),
+            obs=annotation.loc[cells],
             var=pd.DataFrame([], index=genes),
         )
+        coords_types = set([re.sub('[-_][0-9]*$','',c).upper() for c in coords.columns])
+        for ct in coords_types:
+            ct_cols = [c for c in coords.columns if ct in c.upper()]
+            ad.obsm['X_'+ct] = coords.loc[cells, ct_cols].values
         for col in markers.columns:
             ad.uns["marker_" + col] = markers[col].values
 

tox.ini

@@ -8,13 +8,19 @@ passenv =
     CI
     TRAVIS*
     py36: CODACY_PROJECT_TOKEN
+    py37: CODACY_PROJECT_TOKEN
 deps =
     -r{toxinidir}/requirements/test.txt
     py36: -r{toxinidir}/requirements/test_black.txt
+    py37: -r{toxinidir}/requirements/test_black.txt
 commands =
     pip install -U pip
     xvfb-run pytest
     py36: flake8 .
     py36: black -l 100 --check .
     py36: python setup.py check -r -s
     py36: python-codacy-coverage -r coverage.xml
+    py37: flake8 .
+    py37: black -l 100 --check .
+    py37: python setup.py check -r -s
+    py37: python-codacy-coverage -r coverage.xml