Merge branch 'master' into dev

scripts/cluster_diffex.py

@@ -203,6 +203,17 @@ def main():
         print('Exiting because received flag --markers-only')
         return
 
+    # check that all cells have some marker expression
+    marker_per_cell = redux.astype(bool).sum()
+    if np.any(marker_per_cell == 0):
+        ncells_nomark = np.sum(marker_per_cell == 0)
+        msg = '{} of {} cells'.format(ncells_nomark, redux.shape[1])
+        msg += ' do not express any  of the {}'.format(len(marker_ix))
+        msg += ' marker genes. Either remove these cells or alter thresholds'
+        msg += ' to increase the number of molecules.'
+        raise ValueError(msg)
+
+
     # get distance
     metric_label = _get_distance_label(args.distance)
     running_prefix.append(metric_label)