CostaLab · Copilot · Apr 1, 2026 · Apr 1, 2026 · Apr 1, 2026
diff --git a/.coverage b/.coverage
diff --git a/pycrosstalker/__pycache__/__init__.cpython-312.pyc b/pycrosstalker/__pycache__/__init__.cpython-312.pyc
diff --git a/pycrosstalker/plots/__pycache__/__init__.cpython-312.pyc b/pycrosstalker/plots/__pycache__/__init__.cpython-312.pyc
diff --git a/pycrosstalker/plots/__pycache__/plot.cpython-312.pyc b/pycrosstalker/plots/__pycache__/plot.cpython-312.pyc
diff --git a/pycrosstalker/plots/plot.py b/pycrosstalker/plots/plot.py
@@ -192,7 +192,7 @@ def plot_pca_LR_comparative(lrobj_tblPCA, pca_table, dims=(1, 2), ret=False, ggi
 
         # Mapping Table
         if include_tf:
-            map_df = pd.DataFrame(pca_df.index, columns=["gene"])
+            map_df = pd.DataFrame({"gene": pca_df.index})
             map_df["mapping"] = map_df["gene"].apply(lambda gene: "Receptor" if "|R" in gene else ("Ligand" if "|L" in gene else "Transcription Factor"))
             color_groups = ["#f8756b", "#00b835", "#619cff"]
         else:
@@ -334,9 +334,9 @@ def plot_bar_rankings(annData, table_name, ranking, type = None, filter_sign = N
             pass
 
         if filter_sign == 'pos':
-            rankings_table = rankings_table[rankings_table['ranking'] > 0]
+            rankings_table = rankings_table[rankings_table[ranking] > 0]
         elif filter_sign == 'neg':
-            rankings_table = rankings_table[rankings_table['ranking'] < 0]
+            rankings_table = rankings_table[rankings_table[ranking] < 0]
 
 
         if rankings_table.empty:

diff --git a/pycrosstalker/tools/__pycache__/Comparative_condition.cpython-312.pyc b/pycrosstalker/tools/__pycache__/Comparative_condition.cpython-312.pyc
diff --git a/pycrosstalker/tools/__pycache__/Single_Condition.cpython-312.pyc b/pycrosstalker/tools/__pycache__/Single_Condition.cpython-312.pyc
diff --git a/pycrosstalker/tools/__pycache__/__init__.cpython-312.pyc b/pycrosstalker/tools/__pycache__/__init__.cpython-312.pyc
diff --git a/pycrosstalker/tools/__pycache__/generate_report.cpython-312.pyc b/pycrosstalker/tools/__pycache__/generate_report.cpython-312.pyc
diff --git a/pycrosstalker/tools/__pycache__/lrobject.cpython-312.pyc b/pycrosstalker/tools/__pycache__/lrobject.cpython-312.pyc
diff --git a/pycrosstalker/tools/__pycache__/utils.cpython-312.pyc b/pycrosstalker/tools/__pycache__/utils.cpython-312.pyc
diff --git a/test/__init__.py b/test/__init__.py
diff --git a/test/__pycache__/__init__.cpython-312.pyc b/test/__pycache__/__init__.cpython-312.pyc
diff --git a/test/__pycache__/conftest.cpython-312-pytest-9.0.2.pyc b/test/__pycache__/conftest.cpython-312-pytest-9.0.2.pyc
diff --git a/test/__pycache__/helpers.cpython-312.pyc b/test/__pycache__/helpers.cpython-312.pyc
diff --git a/test/__pycache__/test_basic.cpython-312-pytest-9.0.2.pyc b/test/__pycache__/test_basic.cpython-312-pytest-9.0.2.pyc
diff --git a/test/__pycache__/test_check_with_R_data.cpython-312-pytest-9.0.2.pyc b/test/__pycache__/test_check_with_R_data.cpython-312-pytest-9.0.2.pyc
diff --git a/test/__pycache__/test_coverage.cpython-312-pytest-9.0.2.pyc b/test/__pycache__/test_coverage.cpython-312-pytest-9.0.2.pyc
diff --git a/test/__pycache__/test_mpl.cpython-312-pytest-9.0.2.pyc b/test/__pycache__/test_mpl.cpython-312-pytest-9.0.2.pyc
diff --git a/test/conftest.py b/test/conftest.py
@@ -0,0 +1,22 @@
+"""
+Shared pytest fixtures for pyCrossTalkeR tests.
+"""
+import pytest
+from anndata import AnnData
+from pycrosstalker import tools as cttl
+from test.helpers import SEL_COLUMNS, make_lr_df  # noqa: F401 – re-exported for tests
+
+__all__ = ["SEL_COLUMNS", "make_lr_df"]
+
+
+@pytest.fixture(scope="session")
+def analysed_adata():
+    """Fully analysed AnnData built from synthetic data (runs once per session)."""
+    adata = AnnData()
+    adata.uns['pycrosstalker'] = {
+        'path': {
+            'CTR': make_lr_df(0),
+            'EXP': make_lr_df(1),
+        }
+    }
+    return cttl.analise_LR(adata, save=False)
diff --git a/test/helpers.py b/test/helpers.py
@@ -0,0 +1,32 @@
+"""
+Shared test helpers for pyCrossTalkeR tests.
+"""
+import numpy as np
+import pandas as pd
+
+SEL_COLUMNS = ['source', 'target', 'gene_A', 'gene_B', 'type_gene_A', 'type_gene_B', 'MeanLR']
+
+
+def make_lr_df(seed=0):
+    """Create a minimal synthetic LR interaction DataFrame.
+
+    Uses 3 cell types and 3 LR pairs so that PCA(n_components=2) always has
+    enough samples (3 nodes) and features (Listener, Influencer, Mediator).
+    """
+    np.random.seed(seed)
+    cell_types = ['CellA', 'CellB', 'CellC']
+    lr_pairs = [('GENE_L1', 'GENE_R1'), ('GENE_L2', 'GENE_R2'), ('GENE_L3', 'GENE_R3')]
+    rows = []
+    for src in cell_types:
+        for tgt in cell_types:
+            for gl, gr in lr_pairs:
+                rows.append({
+                    'source': src,
+                    'target': tgt,
+                    'gene_A': gl,
+                    'gene_B': gr,
+                    'type_gene_A': 'Ligand',
+                    'type_gene_B': 'Receptor',
+                    'MeanLR': abs(float(np.random.normal(1.5, 0.5))) + 0.1,
+                })
+    return pd.DataFrame(rows)