Fix #44.

Quick & dirty fix by setting the default target_col to `has_tcr`. Can be improved in a later stage.
scverse · Mar 30, 2020 · d0ce730 · d0ce730
1 parent 8ce1265
commit d0ce730
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/scirpy/_plotting/_group_abundance.py b/scirpy/_plotting/_group_abundance.py
@@ -12,7 +12,7 @@
 def group_abundance(
     adata: Union[dict, AnnData],
     groupby: str,
-    target_col: str,
+    target_col: str = "has_tcr",
     *,
     fraction: Union[None, str, bool] = None,
     max_cols: Union[None, int] = None,
@@ -30,6 +30,8 @@ def group_abundance(
         Group by this column from `obs`. Samples or diagnosis for example.
     target_col
         Column on which to compute the abundance. 
+        Defaults to `has_tcr` which computes the number of all cells
+        that have a T-cell receptor. 
     fraction
         If True, compute fractions of abundances relative to the `groupby` column
         rather than reporting abosolute numbers. Alternatively, a column 

diff --git a/scirpy/_tools/_group_abundance.py b/scirpy/_tools/_group_abundance.py
@@ -54,7 +54,7 @@ def _group_abundance(
 def group_abundance(
     adata: AnnData,
     groupby: str,
-    target_col: str,
+    target_col: str = "has_tcr",
     *,
     fraction: Union[None, str, bool] = None,
 ) -> pd.DataFrame: