Merge pull request #969 from AswaniSahoo/feat/fst-lower-triangle-820

feat: add "lower triangle" annotation option to plot_pairwise_average_fst (#820)

Author: jonbrenas

malariagen_data/anoph/fst.py

@@ -536,7 +536,7 @@ def plot_pairwise_average_fst(
 
         # Set up plot title.
         title = "<i>F</i><sub>ST</sub>"
-        if annotation is not None:
+        if annotation is not None and annotation != "lower triangle":
             title += " ⧅ " + annotation
 
         # Fill the figure dataframe from the Fst dataframe.
@@ -549,12 +549,15 @@ def plot_pairwise_average_fst(
                     fig_df.loc[cohort1, cohort2] = np.nan
                 else:
                     fig_df.loc[cohort1, cohort2] = fst / se
+            elif annotation == "lower triangle":
+                # Leave the upper triangle as NaN (empty).
+                pass
             else:
                 fig_df.loc[cohort1, cohort2] = fst
 
         # Don't colour the plot if the upper triangle is SE or Z score,
         # as the colouring doesn't really make sense.
-        if annotation is not None and zmax is None:
+        if annotation is not None and annotation != "lower triangle" and zmax is None:
             zmax = 1e9
 
         # Dynamically size the figure based on number of cohorts.

malariagen_data/anoph/fst_params.py

@@ -35,10 +35,12 @@
 ]
 
 annotation: TypeAlias = Annotated[
-    Optional[Literal["standard error", "Z score"]],
+    Optional[Literal["standard error", "Z score", "lower triangle"]],
     """
-    How to annotate the upper-right corner of the plot. Default behaviour (None) is using Fst, other options
-    are using the standard error (if annotation is 'standard error') or the Z score of the two
-    cohorts being the same (if annotation is 'Z score').
+    How to annotate the upper-right corner of the plot. Default behaviour (None)
+    is using Fst, other options are using the standard error (if annotation is
+    'standard error'), the Z score of the two cohorts being the same (if
+    annotation is 'Z score'), or leaving the upper triangle empty (if annotation
+    is 'lower triangle').
     """,
 ]

tests/anoph/test_fst.py

@@ -257,6 +257,10 @@ def check_pairwise_average_fst(api: AnophelesFstAnalysis, fst_params):
         assert isinstance(fig, go.Figure)
         fig = api.plot_pairwise_average_fst(fst_df, annotation="Z score", show=False)
         assert isinstance(fig, go.Figure)
+        fig = api.plot_pairwise_average_fst(
+            fst_df, annotation="lower triangle", show=False
+        )
+        assert isinstance(fig, go.Figure)
 
 
 @pytest.mark.parametrize("cohorts", ["country", "admin1_year", "cohort_admin2_month"])