Merge pull request #4 from czbiohub-sf/v0.0.5-metrics

v0.0.7 update
czbiohub-sf · Mar 7, 2024 · 92745ca · 92745ca
2 parents 17a866a + a72a342
commit 92745ca
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Showing 2 changed files with 35 additions and 19 deletions.
diff --git a/setup.py b/setup.py
@@ -33,7 +33,7 @@ def get_data_files(parent_dir):
 
 setup(
     name="stats_utils",
-    version="0.0.5",
+    version="0.0.7",
     description="Statistics utilities for remoscope and corresponding paper",
     long_description=readme(),
     url="https://github.com/czbiohub-sf/remo-stats-utils",

diff --git a/stats_utils/compensator.py b/stats_utils/compensator.py
@@ -26,7 +26,13 @@
 
 
 class CountCompensator(CountCorrector):
-    def __init__(self, model_name: str, clinical=True, heatmaps=False):
+    def __init__(
+        self,
+        model_name: str,
+        clinical: bool = True,
+        heatmaps: bool = False,
+        skip: bool = False,
+    ):
         """
         Initialize count compensator
 
@@ -39,28 +45,38 @@ def __init__(self, model_name: str, clinical=True, heatmaps=False):
         - heatmaps (optional):
             True for heatmap nuked data
             False otherwise (default)
+        - skip (optional):
+            True to skip compensation (will ignore previous clinical and heatmap args in)
+            False to proceed with normal compensation, according to other args in(default)
         """
 
-        # Generate directory for compensation metrics csv
-        if clinical:
-            suffix1 = CLINICAL_COMPENSATION_SUFFIX1
-        else:
-            suffix1 = CULTURED_COMPENSATION_SUFFIX1
-        if heatmaps:
-            suffix2 = W_HEATMAPS_SUFFIX2
+        if skip:
+            m = 1.0
+            b = 0.0
+            cov_m = 0.0
+            cov_b = 0.0
         else:
-            suffix2 = NO_HEATMAPS_SUFFIX2
-        compensation_csv_dir = str(
-            DATA_DIR / model_name / (model_name + suffix1 + suffix2)
-        )
-
-        # Check that compensation metrics csv exists
-        if not Path(compensation_csv_dir).is_file():
-            raise FileNotFoundError(
-                f"Could not find compensation metrics for {model_name} ({compensation_csv_dir})"
+            # Generate directory for compensation metrics csv
+            if clinical:
+                suffix1 = CLINICAL_COMPENSATION_SUFFIX1
+            else:
+                suffix1 = CULTURED_COMPENSATION_SUFFIX1
+            if heatmaps:
+                suffix2 = W_HEATMAPS_SUFFIX2
+            else:
+                suffix2 = NO_HEATMAPS_SUFFIX2
+            compensation_csv_dir = str(
+                DATA_DIR / model_name / (model_name + suffix1 + suffix2)
             )
 
-        m, b, cov_m, cov_b = self._get_fit_metrics(compensation_csv_dir)
+            # Check that compensation metrics csv exists
+            if not Path(compensation_csv_dir).is_file():
+                raise FileNotFoundError(
+                    f"Could not find compensation metrics for {model_name} ({compensation_csv_dir})"
+                )
+
+            m, b, cov_m, cov_b = self._get_fit_metrics(compensation_csv_dir)
+
         inv_cmatrix = self._get_matrix(m, b)
         inv_cmatrix_std = self._get_matrix_std(cov_m, cov_b)