fix: document metric parameter and add unique/absolute test coverage

Author: 31puneet

malariagen_data/anoph/hapclust.py

@@ -881,6 +881,14 @@ def _compute_haplotype_sharing(
         summary="""
             Plot an arc diagram showing haplotype sharing between cohorts.
         """,
+        parameters=dict(
+            metric="""
+                The metric to use for measuring haplotype sharing. If 'unique'
+                (default), counts the number of highly identical distinct shared
+                haplotypes. If 'absolute', counts the absolute number of original
+                haplotypes shared between the cohorts.
+            """,
+        ),
     )
     def plot_haplotype_sharing_arc(
         self,
@@ -1018,6 +1026,14 @@ def plot_haplotype_sharing_arc(
         summary="""
             Plot a chord diagram showing haplotype sharing between cohorts.
         """,
+        parameters=dict(
+            metric="""
+                The metric to use for measuring haplotype sharing. If 'unique'
+                (default), counts the number of highly identical distinct shared
+                haplotypes. If 'absolute', counts the absolute number of original
+                haplotypes shared between the cohorts.
+            """,
+        ),
     )
     def plot_haplotype_sharing_chord(
         self,

tests/anoph/test_hapclust.py

@@ -101,22 +101,26 @@ def test_plot_haplotype_clustering(fixture, api: AnophelesHapClustAnalysis):
 @parametrize_with_cases("fixture,api", cases=".")
 def test_plot_haplotype_sharing_arc(fixture, api: AnophelesHapClustAnalysis):
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    fig = api.plot_haplotype_sharing_arc(
-        region=fixture.random_region_str(region_size=5000),
-        cohort_col="country",
-        sample_sets=[random.choice(all_sample_sets)],
-        show=False,
-    )
-    assert fig is not None
+    for metric in ["unique", "absolute"]:
+        fig = api.plot_haplotype_sharing_arc(
+            region=fixture.random_region_str(region_size=5000),
+            cohort_col="country",
+            sample_sets=[random.choice(all_sample_sets)],
+            metric=metric,
+            show=False,
+        )
+        assert fig is not None
 
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_plot_haplotype_sharing_chord(fixture, api: AnophelesHapClustAnalysis):
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    fig = api.plot_haplotype_sharing_chord(
-        region=fixture.random_region_str(region_size=5000),
-        cohort_col="country",
-        sample_sets=[random.choice(all_sample_sets)],
-        show=False,
-    )
-    assert fig is not None
+    for metric in ["unique", "absolute"]:
+        fig = api.plot_haplotype_sharing_chord(
+            region=fixture.random_region_str(region_size=5000),
+            cohort_col="country",
+            sample_sets=[random.choice(all_sample_sets)],
+            metric=metric,
+            show=False,
+        )
+        assert fig is not None