Address code review comments (part 1)

ark/phenotyping/consensus_cluster.R

@@ -12,8 +12,6 @@ library(arrow)
 library(data.table)
 library(ConsensusClusterPlus)
 
-set.seed(59)
-
 # get the command line arguments
 args <- commandArgs(trailingOnly=TRUE)
 

ark/phenotyping/create_som_matrix.R

@@ -13,8 +13,6 @@ library(arrow)
 library(data.table)
 library(FlowSOM)
 
-set.seed(59)
-
 # get the command line arguments
 args <- commandArgs(trailingOnly=TRUE)
 

ark/phenotyping/som_utils.py

@@ -17,7 +17,7 @@
 
 def compute_cluster_avg(fovs, channels, base_dir, cluster_col,
                         cluster_dir='pixel_mat_clustered'):
-    """Averages channel values across all fovs in pixel_mat_clustered
+    """For each fov, compute the average channel values across each SOM cluster
 
     Args:
         fovs (list):
@@ -130,7 +130,7 @@ def create_pixel_matrix(fovs, base_dir, tiff_dir, seg_dir,
                         pre_dir='pixel_mat_preprocessed',
                         sub_dir='pixel_mat_subsetted', is_mibitiff=False,
                         blur_factor=2, subset_proportion=0.1, seed=None):
-    """Preprocess the images for FlowSOM clustering and creates a pixel-level matrix
+    """For each fov, add a Gaussian blur to each channel and normalize channel sums for each pixel
 
     Saves preprocessed data to pre_dir and subsetted data to sub_dir
 

ark/phenotyping/som_utils_test.py

@@ -150,12 +150,6 @@ def test_compute_cluster_avg():
         # compute cluster average matrix
         cluster_avg = som_utils.compute_cluster_avg(fovs, chans, temp_dir, 'cluster')
 
-        # assert that pixel_cluster_avg.feather was actually created
-        # assert os.path.exists(os.path.join(temp_dir, 'pixel_cluster_avg.feather'))
-
-        # read the averaged results
-        # cluster_avg = feather.read_dataframe(os.path.join(temp_dir, 'pixel_cluster_avg.feather'))
-
         # verify the provided channels and the channels in cluster_avg are exactly the same
         misc_utils.verify_same_elements(
             cluster_avg_chans=cluster_avg[chans].columns.values,

ark/utils/notebooks_test.py

@@ -25,17 +25,17 @@ def _exec_notebook(nb_filename):
         subprocess.check_call(args)
 
 
-# # test runs with default inputs
-# def test_segment_image_data():
-#     _exec_notebook('Segment_Image_Data.ipynb')
+# test runs with default inputs
+def test_segment_image_data():
+    _exec_notebook('Segment_Image_Data.ipynb')
 
 
-# def test_example_spatial_analysis():
-#     _exec_notebook('example_spatial_analysis_script.ipynb')
+def test_example_spatial_analysis():
+    _exec_notebook('example_spatial_analysis_script.ipynb')
 
 
-# def test_example_neighborhood_analysis():
-#     _exec_notebook('example_neighborhood_analysis_script.ipynb')
+def test_example_neighborhood_analysis():
+    _exec_notebook('example_neighborhood_analysis_script.ipynb')
 
 
 # test mibitiff segmentation