check if plotting tests is compatable with github actions

scimap/helpers/downloadDemoData.py

@@ -9,7 +9,7 @@
 from tqdm import tqdm
 import os
 
-def downloadDemoData(directory):
+def downloadDemoData(directory, api_url=None):
     """
     Downloads all files from a Zenodo record into the specified directory,
     showing a progress bar for each file.
@@ -27,7 +27,9 @@ def downloadDemoData(directory):
         print(f"Created directory: {directory}")
 
     # Get record details from Zenodo API
-    api_url = "https://zenodo.org/api/records/10845625"
+    if api_url is None:
+        api_url = "https://zenodo.org/api/records/10845625"
+
     response = requests.get(api_url)
     if response.status_code != 200:
         print(f"Failed to retrieve record details. HTTP status code: {response.status_code}")

scimap/helpers/merge_adata_obs.py

@@ -92,7 +92,7 @@ def merge_adata_obs (adata,
         df = pd.DataFrame()
         uns_count = []
         for i in adata:
-            tmp = ad.read(i)
+            tmp = ad.read_h5ad(i)
             # OBS
             tmp_df = tmp.obs
             df = pd.concat([df, tmp_df], axis=1)
@@ -120,7 +120,7 @@ def merge_adata_obs (adata,
     # create the final anndata object
     # Load the data 
     if isinstance(adata[0], str):
-        final_adata = ad.read(adata[uns_index])
+        final_adata = ad.read_h5ad(adata[uns_index])
     else:
         final_adata = adata[uns_index]
 
@@ -129,15 +129,13 @@ def merge_adata_obs (adata,
 
     # replace obs
     final_adata.obs = df
-
-    # Find name of file
-    image_path = pathlib.Path(adata[0])    
+
 
     # Save data if requested
     if output_dir is not None:
         output_dir = pathlib.Path(output_dir)
         output_dir.mkdir(exist_ok=True, parents=True)
-        final_adata.write(output_dir / image_path.name)
+        final_adata.write(output_dir / 'combined_adata.h5ad')
     else:    
         # Return data
         return final_adata

scimap/tests/scimapExampleData/manual_gates.csv

@@ -0,0 +1,10 @@
+marker,exemplar-001--unmicst_cell
+ELANE,7.8
+CD57,8.9
+CD45,6.4
+CD11B,7.6
+SMA,7.5
+CD16,6.5
+ECAD,7.35
+FOXP3,7.4
+NCAM,7

scimap/tests/scimapExampleData/markers.csv

@@ -0,0 +1,13 @@
+channel_number,cycle_number,marker_name,Filter,excitation_wavelength,emission_wavelength,background,exposure,remove
+21,6,DNA_6,DAPI,395,431,,100,
+22,6,ELANE,FITC,485,525,,100,
+23,6,CD57,Sytox,555,590,,100,
+24,6,CD45,Cy5,640,690,,100,
+25,7,DNA_7,DAPI,395,431,,100,
+26,7,CD11B,FITC,485,525,,100,
+27,7,SMA,Sytox,555,590,,100,
+28,7,CD16,Cy5,640,690,,100,
+29,8,DNA_8,DAPI,395,431,,100,
+30,8,ECAD,FITC,485,525,,100,
+31,8,FOXP3,Sytox,555,590,,100,
+32,8,NCAM,Cy5,640,690,,100,

scimap/tests/scimapExampleData/phenotype_workflow.csv

@@ -0,0 +1,8 @@
+,,ELANE,CD57,CD45,CD11B,SMA,CD16,ECAD,FOXP3,NCAM
+all,ECAD+,,,,,,,pos,,
+all,Immune,,,pos,,,,,,
+all,SMA+,,,,,pos,,,,
+Immune,NK cells,,allpos,,neg,,allpos,,,
+Immune,Other myeloid cells,,,,pos,,,,,
+Immune,Treg,,,,,,,,pos,
+Other myeloid cells,Dendritic cells,,allneg,,,,allneg,,,

scimap/tests/test_hl.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 23 20:14:55 2024
+@author: aj
+Test helper function
+"""
+
+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
+
+
+# classify
+def test_classify (adata):
+    from scimap.helpers.classify import classify
+    adata = classify(adata, pos=['FOXP3'], neg=['ECAD'], phenotype='phenotype')
+    assert adata.obs['classify'].value_counts()['passed_classify'] == 228
+
+# rename
+def test_rename (adata):
+    from scimap.helpers.rename import rename
+    name= {'renamed': ['Dendritic cells', 'NK cells']}
+    adata = rename (adata, name, from_column='phenotype', to_column='phenotype_renamed')
+    assert adata.obs['phenotype_renamed'].value_counts()['renamed'] == 85
+
+# dropFeatures
+def test_dropFeatures (adata):
+    from scimap.helpers.dropFeatures import dropFeatures
+    adata = dropFeatures(adata, drop_markers=['ELANE', 'NCAM'])
+    assert len(adata.var.index) == 7
+
+# merge_adata_obs
+def test_merge_adata_obs (adata):
+    from scimap.helpers.merge_adata_obs import merge_adata_obs
+    bdata = adata.copy()
+    bdata.obs['new_col'] = bdata.obs['imageid']
+    combined_adata = merge_adata_obs(adata=[adata, bdata])
+    assert len(combined_adata.obs.columns) == 14
+
+# scimap_to_csv
+def test_scimap_to_csv (adata):
+    from scimap.helpers.scimap_to_csv import scimap_to_csv
+    data = scimap_to_csv(adata)
+    assert data.shape == (11201, 22)
+
+# downloadDemoData
+def downloadDemoData ():
+    from scimap.helpers.downloadDemoData import downloadDemoData
+    download_directory = os.getcwd() + '/demodata'
+    downloadDemoData (download_directory, api_url="https://zenodo.org/api/records/11054442")
+    downloaded_data = pd.read_csv(os.getcwd() + '/demodata/manual_gates.csv')
+    assert downloaded_data.shape == (9, 2)
+
+# addROI_omero
+
+# animate

scimap/tests/test_pl.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 23 21:22:21 2024
+@author: aj
+Test plotting functions
+"""
+
+import pytest
+import os
+import anndata as ad
+import matplotlib.pyplot as plt
+
+# load data
+@pytest.fixture
+def adata():
+    image_path = os.getcwd() + '/scimap/tests/scimapExampleData/scimapExampleData.h5ad'
+    adata = ad.read_h5ad(image_path)
+    return adata
+
+
+# heatmap
+def test_heatmap (adata):
+    from scimap.plotting.heatmap import heatmap
+    heatmap(adata, groupBy='phenotype', standardScale='column')
+
+
+
+
+# markerCorrelation
+# groupCorrelation
+# distPlot
+# densityPlot2D
+# cluster_plots
+# umap
+# foldchange
+# spatial_scatterPlot
+# spatial_distance
+# spatial_interaction
+# spatialInteractionNetwork
+# spatial_pscore
+# stacked_barplot
+# pie
+# voronoi
+
+
+# image_viewer
+# addROI_image
+# gate_finder

scimap/tests/test_pp.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Apr 22 22:16:06 2024
+@author: aj
+Pre processing tools tests
+"""
+
+import pytest
+import os
+import anndata as ad
+import pandas as pd
+
+
+#os.chdir ('/Users/aj/Dropbox (Partners HealthCare)/nirmal lab/softwares/scimap')
+
+# loading via mcmicro
+def test_mcmicro_to_scimap():
+    from scimap.preprocessing.mcmicro_to_scimap import mcmicro_to_scimap
+    feature_table_path = [os.getcwd() + '/scimap/tests/scimapExampleData/exemplar-001--unmicst_cell.csv']
+    adata = mcmicro_to_scimap (feature_table_path)
+    assert adata.shape == (11201, 9)
+
+
+@pytest.fixture
+def adata():
+    image_path = os.getcwd() + '/scimap/tests/scimapExampleData/scimapExampleData.h5ad'
+    adata = ad.read_h5ad(image_path)
+    return adata
+
+
+# log1p
+def test_log1p (adata):
+    from scimap.preprocessing.log1p import log1p
+    adata = log1p (adata, layer='log_test')
+    assert adata.layers['log_test'].shape == (11201, 9)
+
+
+# rescale
+def test_rescale (adata):
+    from scimap.preprocessing.rescale import rescale
+    manual_gate = pd.read_csv(os.getcwd() + '/scimap/tests/scimapExampleData/manual_gates.csv')
+    adata = rescale (adata, gate=manual_gate)
+    assert round(adata.X[0][0], 2) == 0.12
+
+
+# combat
+def test_combat (adata):
+    from scimap.preprocessing.combat import combat   
+    adata = combat (adata, batch='ROI')
+    assert adata.layers['combat'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', layer='raw', label='combat_raw')
+    assert adata.layers['combat_raw'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', log=True, label='combat_log')
+    assert adata.layers['combat_log'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', layer='log', label='combat_log_layer')
+    assert adata.layers['combat_log_layer'].shape == (11201, 9)
+    adata = combat (adata, batch='ROI', replaceOriginal=True)
+    assert round(adata.X[0][0], 2) == 0.12