Extended the tests to CNVs and HAPs

malariagen · Dec 12, 2024 · 86e7e02 · 86e7e02
1 parent 48d0274
commit 86e7e02
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Showing 2 changed files with 44 additions and 8 deletions.
diff --git a/tests/anoph/test_cnv_frq.py b/tests/anoph/test_cnv_frq.py
@@ -11,6 +11,13 @@
 from malariagen_data import ag3 as _ag3
 from malariagen_data.anoph.cnv_frq import AnophelesCnvFrequencyAnalysis
 from malariagen_data.util import compare_series_like
+from .test_frq import (
+    test_plot_frequencies_heatmap,
+    test_plot_frequencies_time_series,
+    test_plot_frequencies_time_series_with_taxa,
+    test_plot_frequencies_time_series_with_areas,
+    test_plot_frequencies_interactive_map,
+)
 
 
 @pytest.fixture
@@ -109,6 +116,8 @@ def test_gene_cnv_frequencies_with_str_cohorts(
     # Run the function under test.
     df_cnv = api.gene_cnv_frequencies(**params)
 
+    test_plot_frequencies_heatmap(api, df_cnv)
+
     # Figure out expected cohort labels.
     df_samples = api.sample_metadata(sample_sets=sample_sets)
     if "cohort_" + cohorts in df_samples:
@@ -166,12 +175,14 @@ def test_gene_cnv_frequencies_with_min_cohort_size(
         return
 
         # Run the function under test.
-    df_snp = api.gene_cnv_frequencies(**params)
+    df_cnv = api.gene_cnv_frequencies(**params)
+
+    test_plot_frequencies_heatmap(api, df_cnv)
 
     # Standard checks.
     check_gene_cnv_frequencies(
         api=api,
-        df=df_snp,
+        df=df_cnv,
         cohort_labels=cohort_labels,
         region=region,
     )
@@ -212,12 +223,14 @@ def test_gene_cnv_frequencies_with_str_cohorts_and_sample_query(
     )
 
     # Run the function under test.
-    df_snp = api.gene_cnv_frequencies(**params)
+    df_cnv = api.gene_cnv_frequencies(**params)
+
+    test_plot_frequencies_heatmap(api, df_cnv)
 
     # Standard checks.
     check_gene_cnv_frequencies(
         api=api,
-        df=df_snp,
+        df=df_cnv,
         cohort_labels=cohort_labels,
         region=region,
     )
@@ -268,12 +281,14 @@ def test_gene_cnv_frequencies_with_str_cohorts_and_sample_query_options(
     )
 
     # Run the function under test.
-    df_snp = api.gene_cnv_frequencies(**params)
+    df_cnv = api.gene_cnv_frequencies(**params)
+
+    test_plot_frequencies_heatmap(api, df_cnv)
 
     # Standard checks.
     check_gene_cnv_frequencies(
         api=api,
-        df=df_snp,
+        df=df_cnv,
         cohort_labels=cohort_labels,
         region=region,
     )
@@ -305,12 +320,14 @@ def test_gene_cnv_frequencies_with_dict_cohorts(
     )
 
     # Run the function under test.
-    df_snp = api.gene_cnv_frequencies(**params)
+    df_cnv = api.gene_cnv_frequencies(**params)
+
+    test_plot_frequencies_heatmap(api, df_cnv)
 
     # Standard checks.
     check_gene_cnv_frequencies(
         api=api,
-        df=df_snp,
+        df=df_cnv,
         cohort_labels=cohort_labels,
         region=region,
     )
@@ -350,6 +367,9 @@ def test_gene_cnv_frequencies_without_drop_invariant(
     df_cnv_a = api.gene_cnv_frequencies(drop_invariant=True, **params)
     df_cnv_b = api.gene_cnv_frequencies(drop_invariant=False, **params)
 
+    test_plot_frequencies_heatmap(api, df_cnv_a)
+    test_plot_frequencies_heatmap(api, df_cnv_b)
+
     # Standard checks.
     check_gene_cnv_frequencies(
         api=api,
@@ -418,6 +438,8 @@ def test_gene_cnv_frequencies_with_max_coverage_variance(
         # checks.
         df_cnv = api.gene_cnv_frequencies(**params)
 
+        test_plot_frequencies_heatmap(api, df_cnv)
+
         # Figure out expected cohort labels.
         df_samples = api.sample_metadata(sample_sets=sample_sets)
         if "cohort_" + cohorts in df_samples:
@@ -711,6 +733,10 @@ def check_gene_cnv_frequencies_advanced(
 
     # Check the result.
     assert isinstance(ds, xr.Dataset)
+    test_plot_frequencies_time_series(api, ds)
+    test_plot_frequencies_time_series_with_taxa(api, ds)
+    test_plot_frequencies_time_series_with_areas(api, ds)
+    test_plot_frequencies_interactive_map(api, ds)
     assert set(ds.dims) == {"cohorts", "variants"}
 
     # Check variant variables.

diff --git a/tests/anoph/test_hap_frq.py b/tests/anoph/test_hap_frq.py
@@ -8,6 +8,12 @@
 
 from malariagen_data import ag3 as _ag3
 from malariagen_data.anoph.hap_frq import AnophelesHapFrequencyAnalysis
+from .test_frq import (
+    test_plot_frequencies_time_series,
+    test_plot_frequencies_time_series_with_taxa,
+    test_plot_frequencies_time_series_with_areas,
+    test_plot_frequencies_interactive_map,
+)
 
 
 @pytest.fixture
@@ -82,6 +88,10 @@ def check_hap_frequencies_advanced(
     ds,
 ):
     assert isinstance(ds, xr.Dataset)
+    test_plot_frequencies_time_series(api, ds)
+    test_plot_frequencies_time_series_with_taxa(api, ds)
+    test_plot_frequencies_time_series_with_areas(api, ds)
+    test_plot_frequencies_interactive_map(api, ds)
     assert set(ds.dims) == {"cohorts", "variants"}
 
     expected_cohort_vars = [