add tools test

scimap/tests/test_tl.py

@@ -0,0 +1,111 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 23 10:51:50 2024
+@author: aj
+Test for tools
+"""
+
+import pytest
+import os
+import anndata as ad
+import pandas as pd
+
+# load data
+@pytest.fixture
+def adata():
+    image_path = os.getcwd() + '/scimap/tests/scimapExampleData/scimapExampleData.h5ad'
+    adata = ad.read_h5ad(image_path)
+    return adata
+
+
+#phenotype_cells
+def test_phenotype (adata):
+    from scimap.tools.phenotype_cells import phenotype_cells
+    # Load phenotype and test phenotyping
+    phenotype = pd.read_csv(os. getcwd() + '/scimap/tests/scimapExampleData/phenotype_workflow.csv')
+    adata = phenotype_cells (adata, phenotype=phenotype, gate = 0.5, label="phenotype")
+    assert adata.obs['phenotype'].iloc[0] == 'Immune'
+
+#cluster
+def test_cluster (adata):
+    from scimap.tools.cluster import cluster
+    adata = cluster (adata,  method = 'kmeans', k= 5, use_raw = True)
+    assert adata.obs['kmeans'].value_counts().iloc[4] == 81
+
+
+#umap
+def test_umap (adata):
+    from scimap.tools.umap import umap
+    adata = umap(adata, label='umap_test')
+    assert adata.obsm['umap_test'].shape == (11201, 2)
+
+
+#foldchange
+def test_foldchange (adata):
+    from scimap.tools.foldchange import foldchange
+    adata = foldchange(adata, from_group = 'ROI1', imageid='ROI')
+    assert round(adata.uns['foldchange_fc']['Immune'], 2).values[0] == 1.87
+
+
+#spatial_distance
+def test_spatial_distance (adata):
+    from scimap.tools.spatial_distance import spatial_distance
+    adata = spatial_distance (adata)
+    assert round(adata.uns['spatial_distance']['Immune'].iloc[0], 2) == 521.27
+
+
+#spatial_interaction
+def test_spatial_interaction (adata):
+    from scimap.tools.spatial_interaction import spatial_interaction
+    adata = spatial_interaction (adata,  method = 'knn', knn= 5, permutation = 10)
+    assert adata.uns['spatial_interaction'] is not None
+
+
+#spatial_count &
+#spatial_cluster
+def test_spatial_count (adata):
+    from scimap.tools.spatial_count import spatial_count
+    adata = spatial_count (adata, phenotype='phenotype',method='knn',radius=5)
+    assert adata.uns['spatial_count'] is not None
+
+    # test spatial cluster
+    from scimap.tools.spatial_cluster import spatial_cluster
+    adata = spatial_cluster(adata, df_name='spatial_count')
+    assert adata.obs['spatial_kmeans'].value_counts().iloc[3] == 1213
+
+
+#spatial_lda
+def test_spatial_lda (adata):
+    from scimap.tools.spatial_lda import spatial_lda
+    adata = spatial_lda (adata, num_motifs=10, radius=30)
+    assert round(adata.uns['spatial_lda']['Motif_0'].iloc[0], 3) == 0.05
+
+
+#spatial_expression
+def test_spatial_expression (adata):
+    from scimap.tools.spatial_expression import spatial_expression
+    adata = spatial_expression (adata, method='radius', radius=30, use_raw=True, label='spatial_expression')
+    assert round(adata.uns['spatial_expression']['ECAD'].sum(),0) == 81404.0
+
+
+#spatial_pscore
+def test_spatial_pscore (adata):
+    from scimap.tools.spatial_pscore import spatial_pscore
+    adata = spatial_pscore (adata,  proximity= ['Immune', 'ECAD+'])
+    assert adata.uns['spatial_pscore']['Immune_ECAD+'].values[0] == 2095
+
+
+#spatial_aggregate
+def test_spatial_aggregate (adata):
+    from scimap.tools.spatial_aggregate import spatial_aggregate
+    adata = spatial_aggregate (adata, purity = 60, phenotype='phenotype', method='knn', radius=10)
+    assert adata.obs['spatial_aggregate'].value_counts()['Immune'] == 3439
+
+
+#spatial_similarity_search
+def test_spatial_similarity_search (adata):
+    from scimap.tools.spatial_similarity_search import spatial_similarity_search
+    adata = spatial_similarity_search (adata, ROI_column='ROI', similarity_threshold=0.6,  method='knn', radius=10)
+    assert adata.obs['spatial_similarity_search_ROI2'].value_counts()['similar_to_ROI'] == 4786
+