DOC/TST: add working usage example for mann-whitney-u (#8)

q2_fmt/_examples.py

@@ -37,6 +37,11 @@ def faithpd_timedist_factory():
         'GroupDist[Ordered, Matched]', _get_data_from_tests('faithpd_timedist')
     )
 
+def faithpd_refdist_factory():
+    return qiime2.Artifact.import_data(
+        'GroupDist[Unordered, Independent]', _get_data_from_tests('faithpd_refdist')
+    )
+
 def faithpd_md_factory():
     return qiime2.Metadata.load(
         _get_data_from_tests('metadata-faithpd.tsv')
@@ -110,9 +115,24 @@ def wilcoxon_baseline0(use):
 
     stats_table.assert_output_type('StatsTable[Pairwise]')
 
-#TODO: usage example for mann-whitney
-def mann_whitney_u(use):
-    pass
+def mann_whitney_pairwise(use):
+    timedist = use.init_artifact('timedist', faithpd_timedist_factory)
+    refdist = use.init_artifact('refdist', faithpd_refdist_factory)
+
+    stats_table, = use.action(
+        use.UsageAction('fmt', 'mann_whitney_u'),
+        use.UsageInputs(
+            distribution=refdist,
+            hypothesis='all-pairwise',
+            against_each=timedist,
+            p_val_approx='asymptotic',
+        ),
+        use.UsageOutputNames(
+            stats='stats'
+        )
+    )
+
+    stats_table.assert_output_type('StatsTable[Pairwise]')
 
 # Engraftment example using faith PD, baseline0 hypothesis
 def engraftment_baseline(use):

q2_fmt/plugin_setup.py

@@ -148,7 +148,10 @@
         'stats': 'The Mann-Whitney U distribution for either the `reference` or `all-pairwise` hypothesis.',
     },
     name='Mann-Whitney U Test',
-    description=''
+    description='',
+    examples={
+        'mann_whitney_pairwise': ex.mann_whitney_pairwise
+    }
 )
 
 plugin.methods.register_function(

q2_fmt/tests/data/faithpd_refdist/data.tsv

@@ -0,0 +1,29 @@
+id	measure	group
+S879369	10.248839183	reference
+S435802	10.379970859	reference
+S409550	8.379513518	reference
+S916057	10.551980282	reference
+S405044	9.263042352	reference
+S953010	12.138687523999998	control
+S358668	12.402660535	control
+S842739	12.771875893	control
+S691441	8.145593314	control
+S427307	12.967708926	control
+S238639	11.649627363	control
+S611569	7.989246995999999	control
+S298842	9.500026592	control
+S160074	14.460895127	control
+S211105	11.767674432	control
+S460372	9.547484785000002	control
+S728037	9.597018329	control
+S282059	9.282152505	control
+S388055	10.279025972	control
+S630647	12.086278795	control
+S59807	11.167537754	control
+S255688	10.029524157	control
+S889561	4.4655846960000005	control
+S990074	5.138442046	control
+S269036	13.110583296	control
+S684586	12.705425981	control
+S696581	15.902021065	control
+S322808	13.960754461	control

q2_fmt/tests/data/faithpd_refdist/metadata.tsv

@@ -0,0 +1,4 @@
+column	unit	description
+id	id	...
+measure	faith_pd	faith_pd
+group	InitialDonorSampleID or IsControl	...

q2_fmt/tests/data/faithpd_timedist/data.tsv

@@ -1,88 +1,88 @@
 id	measure	group	subject
-340445	7.662921088	0	141
-892825	8.431734297	0	33
-460691	8.513263823	0	407
-33196	11.47176562	0	68
-676122	9.914657833	0	404
-64538	12.62560928	0	354
-820102	9.453417415	0	799
-19325	9.646052305	0	40
-677034	7.778748399	0	745
-45687	12.68877984	0	959
-634737	11.79632603	0	491
-42188	7.386190882	0	604
-733472	11.19719621	0	327
-660492	10.18787122	0	17
-728527	8.448317067	0	555
-101304	11.3228199	0	648
-352530	7.314753809	0	423
-49899	8.27086375	0	704
-179157	10.83320209	3	141
-932597	9.8956928	3	33
-593887	11.86970243	3	407
-804240	10.12497616	3	68
-823495	9.478838334	3	404
-515494	8.502002897	3	354
-38418	9.246871802	3	799
-656022	12.62000749	3	40
-568016	10.50579797	3	959
-604276	7.830091789	3	491
-376907	6.725748683	3	604
-268616	11.98183356	3	327
-158516	12.43679596	3	17
-311633	9.592979726	3	555
-740172	8.880897012	3	648
-119473	9.092078686	3	423
-257623	8.522314493	3	704
-265	10.83670704	10	141
-669048	9.172597583	10	33
-95356	11.60664407	10	407
-40277	10.78345691	10	68
-459758	11.48168273	10	404
-564018	17.43370405	10	354
-936973	15.2623358	10	799
-291167	13.53128149	10	40
-41971	15.96814451	10	745
-681493	13.61043486	10	959
-824846	10.62683459	10	491
-285186	7.444009936	10	604
-773741	9.728676749	10	327
-163514	12.77874569	10	17
-297641	10.65211873	10	555
-794108	11.12683676	10	648
-96318	9.027651356	10	423
-920509	9.059711997	10	704
-683282	11.68795212	18	141
-263946	10.65262785	18	33
-513816	10.94184424	18	407
-456128	13.26471277	18	68
-454628	11.69071803	18	404
-316090	14.96844078	18	354
-318234	10.49866422	18	799
-204144	11.09989491	18	40
-334403	10.31360211	18	745
-743943	11.76570288	18	959
-662822	13.66553354	18	491
-387858	8.598030851	18	604
-131881	11.78182748	18	327
-236141	12.20070358	18	17
-462162	9.750043462	18	555
-784577	10.8908099	18	648
-103872	8.990062701	18	423
-159294	14.73197158	18	704
-466166	14.95236844	100	141
-763905	10.26127503	100	33
-734500	12.24557912	100	407
-599248	19.96358026	100	68
-209330	10.82326355	100	404
-934977	12.95731892	100	354
-540115	14.46464274	100	799
-301520	14.68263437	100	40
-351280	15.48569583	100	959
-726967	16.0492848	100	491
-340645	10.87510264	100	604
-754317	8.866448342	100	327
-91814	13.57054725	100	555
-984262	12.36040446	100	648
-623940	11.07684349	100	423
-476406	12.98841452	100	704
+S340445	7.662921088	0	141
+S892825	8.431734297	0	33
+S460691	8.513263823	0	407
+S33196	11.47176562	0	68
+S676122	9.914657833	0	404
+S64538	12.62560928	0	354
+S820102	9.453417415	0	799
+S19325	9.646052305	0	40
+S677034	7.778748399	0	745
+S45687	12.68877984	0	959
+S634737	11.79632603	0	491
+S42188	7.386190882	0	604
+S733472	11.19719621	0	327
+S660492	10.18787122	0	17
+S728527	8.448317067	0	555
+S101304	11.3228199	0	648
+S352530	7.314753809	0	423
+S49899	8.27086375	0	704
+S179157	10.83320209	3	141
+S932597	9.8956928	3	33
+S593887	11.86970243	3	407
+S804240	10.12497616	3	68
+S823495	9.478838334	3	404
+S515494	8.502002897	3	354
+S38418	9.246871802	3	799
+S656022	12.62000749	3	40
+S568016	10.50579797	3	959
+S604276	7.830091789	3	491
+S376907	6.725748683	3	604
+S268616	11.98183356	3	327
+S158516	12.43679596	3	17
+S311633	9.592979726	3	555
+S740172	8.880897012	3	648
+S119473	9.092078686	3	423
+S257623	8.522314493	3	704
+S265	10.83670704	10	141
+S669048	9.172597583	10	33
+S95356	11.60664407	10	407
+S40277	10.78345691	10	68
+S459758	11.48168273	10	404
+S564018	17.43370405	10	354
+S936973	15.2623358	10	799
+S291167	13.53128149	10	40
+S41971	15.96814451	10	745
+S681493	13.61043486	10	959
+S824846	10.62683459	10	491
+S285186	7.444009936	10	604
+S773741	9.728676749	10	327
+S163514	12.77874569	10	17
+S297641	10.65211873	10	555
+S794108	11.12683676	10	648
+S96318	9.027651356	10	423
+S920509	9.059711997	10	704
+S683282	11.68795212	18	141
+S263946	10.65262785	18	33
+S513816	10.94184424	18	407
+S456128	13.26471277	18	68
+S454628	11.69071803	18	404
+S316090	14.96844078	18	354
+S318234	10.49866422	18	799
+S204144	11.09989491	18	40
+S334403	10.31360211	18	745
+S743943	11.76570288	18	959
+S662822	13.66553354	18	491
+S387858	8.598030851	18	604
+S131881	11.78182748	18	327
+S236141	12.20070358	18	17
+S462162	9.750043462	18	555
+S784577	10.8908099	18	648
+S103872	8.990062701	18	423
+S159294	14.73197158	18	704
+S466166	14.95236844	100	141
+S763905	10.26127503	100	33
+S734500	12.24557912	100	407
+S599248	19.96358026	100	68
+S209330	10.82326355	100	404
+S934977	12.95731892	100	354
+S540115	14.46464274	100	799
+S301520	14.68263437	100	40
+S351280	15.48569583	100	959
+S726967	16.0492848	100	491
+S340645	10.87510264	100	604
+S754317	8.866448342	100	327
+S91814	13.57054725	100	555
+S984262	12.36040446	100	648
+S623940	11.07684349	100	423
+S476406	12.98841452	100	704

q2_fmt/tests/test_engraftment.py

@@ -14,6 +14,7 @@
 
 from q2_fmt._engraftment import group_timepoints
 from q2_fmt._stats import wilcoxon_srt, mann_whitney_u
+from q2_fmt._examples import faithpd_timedist_factory
 
 class TestBase(TestPluginBase):
     package='q2_fmt.tests'
@@ -27,8 +28,7 @@ def setUp(self):
         self.dm = DistanceMatrix.read(self.get_data_path('dist_matrix_donors.tsv')).to_series()
         self.alpha = pd.read_csv(self.get_data_path('alpha_div.tsv'), sep='\t', index_col=0, squeeze=True)
 
-        self.faithpd_timedist = pd.read_csv(self.get_data_path('faithpd_timedist/data.tsv'),
-                                            sep='\t', index_col=0, squeeze=True)
+        self.faithpd_timedist = faithpd_timedist_factory().view(pd.DataFrame)
 
 class ErrorMixins:
     def test_with_time_column_input_not_in_metadata(self):

setup.py

@@ -16,7 +16,8 @@
     packages=find_packages(),
     package_data={
         'q2_fmt': ['assets/*'],
-        'q2_fmt.tests': ['data/*', 'data/faithpd_timedist/*'],
+        'q2_fmt.tests': ['data/*', 'data/faithpd_timedist/*',
+                         'data/faithpd_refdist/*'],
     },
     author='Liz Gehret',
     author_email='[email protected]',