rectanglepy 0.1.6__tar.gz → 0.1.7__tar.gz

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.6
+current_version = 0.1.7
 tag = True
 commit = True
 

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/CHANGELOG.md

@@ -10,6 +10,12 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+## [0.1.7] - 2024-07-25
+
+### Fixed
+
+-   Fixed bug in the consensus method.
+
 ## [0.1.6] - 2024-05-07
 
 ### Added

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: rectanglepy
-Version: 0.1.6
+Version: 0.1.7
 Summary: Hierarchical deconvolution of bulk  transcriptomics
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
@@ -31,6 +31,7 @@ License: MIT License
 License-File: LICENSE
 Requires-Python: >=3.10
 Requires-Dist: loguru
+Requires-Dist: numpy<2.0.0,>=1.0.0
 Requires-Dist: pydeseq2==0.4.1
 Requires-Dist: quadprog==0.1.11
 Provides-Extra: dev

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "rectanglepy"
-version = "0.1.6"
+version = "0.1.7"
 description = "Hierarchical deconvolution of bulk  transcriptomics"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -22,6 +22,7 @@ dependencies = [
     "pydeseq2==0.4.1",
     "quadprog==0.1.11",
     "loguru",
+    "numpy>=1.0.0,<2.0.0",
 ]
 
 [project.optional-dependencies]

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/src/rectanglepy/pp/create_signature.py

@@ -245,6 +245,7 @@ def build_rectangle_signatures(
     subsample: bool = False,
     sample_size: int = 1500,
     n_cpus: int = None,
+    run: int = 0,
 ) -> RectangleSignatureResult:
     r"""Builds rectangle signatures based on single-cell  count data and annotations.
 
@@ -272,6 +273,8 @@ def build_rectangle_signatures(
         The log fold change threshold for the DE analysis (only used if optimize_cutoffs is False).
     n_cpus
         The number of cpus to use for the DE analysis. Defaults to the number of cpus available.
+    run
+        The consensus run number for the analysis. Defaults to 0.
 
     Returns
     -------
@@ -286,7 +289,7 @@ def build_rectangle_signatures(
 
     annotations = adata.obs[cell_type_col]
     if subsample:
-        annotations = _even(annotations, sample_size)
+        annotations = _even(annotations, sample_size, run)
         adata = adata[annotations.index]
 
     if layer is not None:
@@ -448,7 +451,8 @@ def _reduce_to_common_genes(bulks: pd.DataFrame, sc_data: pd.DataFrame):
     return bulks, sc_data
 
 
-def _even(annotations: pd.Series, number: int) -> pd.Series:
+def _even(annotations: pd.Series, number: int, run=0) -> pd.Series:
+    np.random.seed(run)
     assert number > 0, "Number of cells must be greater than 0"
     annotation_counts = annotations.value_counts()
     selected_cells = []

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/src/rectanglepy/rectangle.py

@@ -94,8 +94,8 @@ def rectangle_consens(
     rectangle_signature_results = []
     most_recent_signatures = None
 
-    for _i in range(consensus_runs):
-        logger.info(f"Running consensus run {_i + 1} of {consensus_runs}")
+    for i in range(consensus_runs):
+        logger.info(f"Running consensus run {i + 1} of {consensus_runs}")
         signatures = build_rectangle_signatures(
             adata,
             cell_type_col,
@@ -108,6 +108,7 @@ def rectangle_consens(
             n_cpus=n_cpus,
             subsample=subsample,
             sample_size=sample_size,
+            run=i,
         )
         rectangle_signature_results.append(signatures)
         most_recent_signatures = signatures

{rectanglepy-0.1.6 → rectanglepy-0.1.7}/tests/test_rectangle.py

@@ -25,12 +25,21 @@ def test_rectangle():
 
 def test_rectangle_consensus():
     sc_data, annotations, bulks = rectanglepy.load_tutorial_data()
+    sc_data = sc_data.iloc[:, :500]
     sc_data_adata = AnnData(sc_data, obs=annotations.to_frame(name="cell_type"))
 
     result = rectanglepy.rectangle_consens(
-        sc_data_adata, bulks, optimize_cutoffs=False, p=0.5, lfc=0.0, consensus_runs=2, sample_size=50
+        sc_data_adata, bulks, optimize_cutoffs=False, p=0.5, lfc=0.0, consensus_runs=3, sample_size=50
     )
 
     assert isinstance(result[0], pd.DataFrame)
     assert isinstance(result[1], RectangleSignatureResult)
     assert isinstance(result[2], ConsensusResult)
+
+    # all bias factors should differ, else there is a problem with the random sampling
+    consensus_results = result[2]
+    signature_results = consensus_results.rectangle_signature_results
+    bias_factors = [result.bias_factors for result in signature_results]
+    assert bias_factors[0]["Monocytes"] != bias_factors[1]["Monocytes"]
+    assert bias_factors[0]["Monocytes"] != bias_factors[2]["Monocytes"]
+    assert bias_factors[1]["Monocytes"] != bias_factors[2]["Monocytes"]