Merge pull request #183 from gwaygenomics/single-cell-docs

Fix dataframe reference in SingleCells function

pycytominer/cyto_utils/cells.py

@@ -28,8 +28,9 @@ class SingleCells(object):
 
     Attributes
     ----------
-    file_or_conn : str or pandas.core.frame.DataFrame
-        A file string or database connection storing the location of single cell profiles.
+    sql_file : str
+        SQLite connection pointing to the single cell database.
+        The string prefix must be "sqlite:///".
     strata : list of str, default ["Metadata_Plate", "Metadata_Well"]
         The columns to groupby and aggregate single cells.
     aggregation_operation : str, default "median"
@@ -81,7 +82,7 @@ class SingleCells(object):
 
     def __init__(
         self,
-        file_or_conn,
+        sql_file,
         strata=["Metadata_Plate", "Metadata_Well"],
         aggregation_operation="median",
         output_file="none",
@@ -112,7 +113,7 @@ def __init__(
             0 < subsample_frac and 1 >= subsample_frac
         ), "subsample_frac must be between 0 and 1"
 
-        self.file_or_conn = file_or_conn
+        self.sql_file = sql_file
         self.strata = strata
         self.load_image_data = load_image_data
         self.aggregation_operation = aggregation_operation.lower()
@@ -147,7 +148,7 @@ def __init__(
             self.set_subsample_n(self.subsample_n)
 
         # Connect to sqlite engine
-        self.engine = create_engine(self.file_or_conn)
+        self.engine = create_engine(self.sql_file)
         self.conn = self.engine.connect()
 
         # Throw an error if both subsample_frac and subsample_n is set

pycytominer/tests/test_cyto_utils/test_cells.py

@@ -129,41 +129,41 @@ def build_random_data(
 nuclei_df.to_sql("nuclei", con=test_engine_image, index=False, if_exists="replace")
 
 # Setup SingleCells Class
-ap = SingleCells(file_or_conn=file)
+ap = SingleCells(sql_file=file)
 ap_subsample = SingleCells(
-    file_or_conn=file,
+    sql_file=file,
     subsample_n=2,
     subsampling_random_state=123,
 )
 ap_new = SingleCells(
-    file_or_conn=new_file,
+    sql_file=new_file,
     load_image_data=False,
     compartments=new_compartments,
     compartment_linking_cols=new_linking_cols,
 )
 
 ap_image_all_features = SingleCells(
-    file_or_conn=image_file,
+    sql_file=image_file,
     add_image_features=True,
     image_feature_categories=["Count", "Granularity", "Texture"],
 )
 
 ap_image_subset_features = SingleCells(
-    file_or_conn=image_file,
+    sql_file=image_file,
     add_image_features=True,
     image_feature_categories=["Count", "Texture"],
 )
 
 ap_image_count = SingleCells(
-    file_or_conn=image_file, add_image_features=True, image_feature_categories=["Count"]
+    sql_file=image_file, add_image_features=True, image_feature_categories=["Count"]
 )
 
 
 def test_SingleCells_init():
     """
     Testing initialization of SingleCells
     """
-    assert ap.file_or_conn == file
+    assert ap.sql_file == file
     assert ap.strata == ["Metadata_Plate", "Metadata_Well"]
     assert ap.merge_cols == ["TableNumber", "ImageNumber"]
     assert ap.image_cols == ["TableNumber", "ImageNumber", "Metadata_Site"]
@@ -192,7 +192,7 @@ def test_SingleCells_reset_variables():
     """
     Testing initialization of SingleCells
     """
-    ap_switch = SingleCells(file_or_conn=file)
+    ap_switch = SingleCells(sql_file=file)
     assert ap_switch.subsample_frac == 1
     assert ap_switch.subsample_n == "all"
     assert ap_switch.subsampling_random_state == "none"
@@ -357,7 +357,7 @@ def test_merge_single_cells():
 def test_merge_single_cells_subsample():
 
     for subsample_frac in [0.1, 0.5, 0.9]:
-        ap_subsample = SingleCells(file_or_conn=file, subsample_frac=subsample_frac)
+        ap_subsample = SingleCells(sql_file=file, subsample_frac=subsample_frac)
 
         sc_merged_df = ap_subsample.merge_single_cells(
             sc_output_file="none",
@@ -383,7 +383,7 @@ def test_merge_single_cells_subsample():
         assert sc_merged_df.shape[0] == cells_df.shape[0] * subsample_frac
 
     for subsample_n in [2, 5, 10]:
-        ap_subsample = SingleCells(file_or_conn=file, subsample_n=subsample_n)
+        ap_subsample = SingleCells(sql_file=file, subsample_n=subsample_n)
 
         sc_merged_df = ap_subsample.merge_single_cells(
             sc_output_file="none",
@@ -668,7 +668,7 @@ def test_aggregate_count_cells_multiple_strata():
 
     # Setup SingleCells Class
     ap_strata = SingleCells(
-        file_or_conn=file,
+        sql_file=file,
         subsample_n="4",
         strata=["Metadata_Plate", "Metadata_Well", "Metadata_Site"],
     )