combatlearn 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

combatlearn/__init__.py

@@ -1,4 +1,4 @@
 from .combat import ComBatModel, ComBat
 
 __all__ = ["ComBatModel", "ComBat"]
-__version__ = "0.2.0"
+__version__ = "0.2.2"

combatlearn/combat.py

@@ -18,6 +18,7 @@ from sklearn.utils.validation import check_is_fitted
 from sklearn.decomposition import PCA
 from sklearn.manifold import TSNE
 import matplotlib.pyplot as plt
+import matplotlib.colors as mcolors
 from typing import Literal, Optional, Union, Dict, Tuple, Any, cast
 import numpy.typing as npt
 import warnings
@@ -811,7 +812,7 @@ class ComBat(BaseEstimator, TransformerMixin):
         else:
             fig = self._create_interactive_plot(
                 X_embedded_orig, X_embedded_trans, batch_vec,
-                reduction_method, n_components, title, show_legend
+                reduction_method, n_components, cmap, title, show_legend
             )
 
         if return_embeddings:
@@ -930,6 +931,7 @@ class ComBat(BaseEstimator, TransformerMixin):
             batch_labels: pd.Series,
             method: str,
             n_components: int,
+            cmap: str,
             title: Optional[str],
             show_legend: bool) -> Any:
         """Create interactive plots using plotly."""
@@ -953,43 +955,69 @@ class ComBat(BaseEstimator, TransformerMixin):
 
         unique_batches = batch_labels.drop_duplicates()
 
+        n_batches = len(unique_batches)
+        cmap_func = plt.cm.get_cmap(cmap)
+        color_list = [mcolors.to_hex(cmap_func(i / max(n_batches - 1, 1))) for i in range(n_batches)]
+
+        batch_to_color = dict(zip(unique_batches, color_list))
+
         for batch in unique_batches:
             mask = batch_labels == batch
 
             if n_components == 2:
                 fig.add_trace(
-                    go.Scatter(x=X_orig[mask, 0], y=X_orig[mask, 1],
-                              mode='markers',
-                              name=f'Batch {batch}',
-                              marker=dict(size=8, line=dict(width=1, color='black')),
-                              showlegend=False),
+                    go.Scatter(
+                        x=X_orig[mask, 0], y=X_orig[mask, 1],
+                        mode='markers',
+                        name=f'Batch {batch}',
+                        marker=dict(
+                            size=8,
+                            color=batch_to_color[batch],
+                            line=dict(width=1, color='black')
+                        ),
+                        showlegend=False),
                     row=1, col=1
                 )
 
                 fig.add_trace(
-                    go.Scatter(x=X_trans[mask, 0], y=X_trans[mask, 1],
-                              mode='markers',
-                              name=f'Batch {batch}',
-                              marker=dict(size=8, line=dict(width=1, color='black')),
-                              showlegend=show_legend),
+                    go.Scatter(
+                        x=X_trans[mask, 0], y=X_trans[mask, 1],
+                        mode='markers',
+                        name=f'Batch {batch}',
+                        marker=dict(
+                            size=8,
+                            color=batch_to_color[batch],
+                            line=dict(width=1, color='black')
+                        ),
+                        showlegend=show_legend),
                     row=1, col=2
                 )
             else:
                 fig.add_trace(
-                    go.Scatter3d(x=X_orig[mask, 0], y=X_orig[mask, 1], z=X_orig[mask, 2],
-                                mode='markers',
-                                name=f'Batch {batch}',
-                                marker=dict(size=5, line=dict(width=0.5, color='black')),
-                                showlegend=False),
+                    go.Scatter3d(
+                        x=X_orig[mask, 0], y=X_orig[mask, 1], z=X_orig[mask, 2],
+                        mode='markers',
+                        name=f'Batch {batch}',
+                        marker=dict(
+                            size=5,
+                            color=batch_to_color[batch],
+                            line=dict(width=0.5, color='black')
+                        ),
+                        showlegend=False),
                     row=1, col=1
                 )
 
                 fig.add_trace(
-                    go.Scatter3d(x=X_trans[mask, 0], y=X_trans[mask, 1], z=X_trans[mask, 2],
-                                mode='markers',
-                                name=f'Batch {batch}',
-                                marker=dict(size=5, line=dict(width=0.5, color='black')),
-                                showlegend=show_legend),
+                    go.Scatter3d(
+                        x=X_trans[mask, 0], y=X_trans[mask, 1], z=X_trans[mask, 2],
+                        mode='markers',
+                        name=f'Batch {batch}',
+                        marker=dict(
+                            size=5,
+                            color=batch_to_color[batch],
+                            line=dict(width=0.5, color='black')
+                        ),
+                        showlegend=show_legend),
                     row=1, col=2
                 )
 

{combatlearn-0.2.0.dist-info → combatlearn-0.2.2.dist-info}/METADATA

@@ -1,34 +1,12 @@
 Metadata-Version: 2.4
 Name: combatlearn
-Version: 0.2.0
+Version: 0.2.2
 Summary: Batch-effect harmonization for machine learning frameworks.
 Author-email: Ettore Rocchi <ettoreroc@gmail.com>
-License: MIT License
-        
-        Copyright (c) 2025 Ettore Rocchi
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
+License-Expression: MIT
 Keywords: machine-learning,harmonization,combat,preprocessing
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
@@ -37,6 +15,7 @@ License-File: LICENSE
 Requires-Dist: pandas>=1.3
 Requires-Dist: numpy>=1.21
 Requires-Dist: scikit-learn>=1.2
+Requires-Dist: matplotlib>=3.4
 Requires-Dist: plotly>=5.0
 Requires-Dist: nbformat>=4.2
 Requires-Dist: umap-learn>=0.5

combatlearn-0.2.2.dist-info/RECORD

@@ -0,0 +1,7 @@
+combatlearn/__init__.py,sha256=qZK8xAUibzM9TQJ-xho1cjMYmTGkdWvpFRTXOokNvMY,98
+combatlearn/combat.py,sha256=pVauFEgZ7wiYRimGZe7ZhBWZN7sGQ67A3o_SrBUtoJ8,38126
+combatlearn-0.2.2.dist-info/licenses/LICENSE,sha256=O34CBRTmdL59PxDYOa6nq1N0-2A9xyXGkBXKbsL1NeY,1070
+combatlearn-0.2.2.dist-info/METADATA,sha256=CNm0pbXPVVWORk4pI97WS1DohjWOu7fB88JS1JZ-3-A,7491
+combatlearn-0.2.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+combatlearn-0.2.2.dist-info/top_level.txt,sha256=3cFQv4oj2sh_NKra45cPy8Go0v8W9x9-zkkUibqZCMk,12
+combatlearn-0.2.2.dist-info/RECORD,,

combatlearn-0.2.0.dist-info/RECORD

@@ -1,7 +0,0 @@
-combatlearn/__init__.py,sha256=wJ5E-Nrz6s7KLCHDY_p1kpUwMws-Q6Xd_1cK3JksNxU,98
-combatlearn/combat.py,sha256=g6YnCVWq40j_fMU2OcXrJ1O0MCSyt2owCaZ4gfyF-Pw,37268
-combatlearn-0.2.0.dist-info/licenses/LICENSE,sha256=O34CBRTmdL59PxDYOa6nq1N0-2A9xyXGkBXKbsL1NeY,1070
-combatlearn-0.2.0.dist-info/METADATA,sha256=oEL_LK1fJUUeacf0k09I5HlEOVejeUWEGu3i-QJhL3Y,8735
-combatlearn-0.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-combatlearn-0.2.0.dist-info/top_level.txt,sha256=3cFQv4oj2sh_NKra45cPy8Go0v8W9x9-zkkUibqZCMk,12
-combatlearn-0.2.0.dist-info/RECORD,,