sclab 0.1.7__tar.gz

sclab-0.1.7/PKG-INFO

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+Metadata-Version: 2.3
+Name: sclab
+Version: 0.1.7
+Summary: sclab
+Author-email: Argenis Arriojas <ArriojasMaldonado001@umb.edu>
+Requires-Python: >=3.10,<3.13
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: anndata
+Requires-Dist: anywidget
+Requires-Dist: ipywidgets
+Requires-Dist: itables
+Requires-Dist: numpy<2.2
+Requires-Dist: pandas
+Requires-Dist: plotly
+Requires-Dist: scanpy
+Requires-Dist: scikit-learn
+Requires-Dist: scikit-misc
+Requires-Dist: svgpathtools
+Requires-Dist: pytest>=8.3.4 ; extra == "test"
+Project-URL: Bug Tracker, https://github.com/umbibio/sclab/issues
+Project-URL: Changelog, https://github.com/umbibio/sclab/blob/main/CHANGELOG.md
+Project-URL: Documentation, https://github.com/umbibio/sclab/docs
+Project-URL: Homepage, https://github.com/umbibio/sclab
+Project-URL: Repository, https://github.com/umbibio/sclab.git
+Provides-Extra: test
+
+# SCLab
+
+SCLab is an interactive single-cell analysis toolkit that provides a seamless interface for analyzing and visualizing single-cell RNA sequencing data. Built on top of popular tools like scanpy and AnnData, SCLab offers an event-driven architecture for real-time updates and interactive visualizations.
+
+## Features
+
+- **Interactive Data Analysis**: Built-in dashboard with real-time updates
+- **Quality Control**: Comprehensive QC metrics and filtering capabilities
+- **Preprocessing**: Normalization, log transformation, and scaling with progress tracking
+- **Dimensionality Reduction**: PCA with batch effect correction support
+- **Visualization**: Interactive plots and tables using plotly and itables
+- **Event System**: Robust event-driven architecture for real-time updates
+
+## Installation
+
+```bash
+pip install sclab
+```
+
+## Quick Start
+
+Open a Jupyter Notebook and run the following:
+
+```python
+from sclab import SCLabDashboard
+import scanpy as sc
+from IPython.display import display
+
+# Load your data
+adata = sc.read_10x_h5("your_data.h5")
+
+# Create dashboard
+dashboard = SCLabDashboard(adata, name="My Analysis")
+
+# Display dashboard
+display(dashboard)
+
+# The dashboard provides easy access to components:
+dashboard.ds  # Dataset (wrapper for AnnData)
+dashboard.pl  # Plotter
+dashboard.pr  # Processor
+```
+
+## Components
+
+### SCLabDashboard
+
+The main interface that integrates all components with a tabbed layout:
+- Main graph for visualizations
+- Observations table
+- Genes table
+- Event logs
+
+### Dataset
+
+Handles data management with:
+- AnnData integration
+- Interactive tables
+- Row selection and filtering
+- Metadata handling
+
+### Processor
+
+Handles data processing steps. It is configurable with custom steps implementing the `ProcessorStepBase` interface. This package provides multiple examples of steps:
+
+- QC
+- Preprocessing
+- PCA
+- Nearest Neighbors
+- UMAP
+- Clustering
+
+### Plotter
+
+Provides interactive visualizations with:
+- Real-time updates
+- Customizable plots
+- Batch effect visualization
+- Export capabilities
+
+## Requirements
+
+- Python ≥ 3.12
+- anndata ≥ 0.11.3
+- scanpy ≥ 1.10.4
+- Other dependencies listed in pyproject.toml
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+## License
+
+This project is licensed under the BSD 3-Clause License - see the [LICENSE](LICENSE) file for details.
+
+## Citation
+
+If you use SCLab in your research, please cite:
+
+```bibtex
+@software{sclab2024,
+  author = {Arriojas, Argenis},
+  title = {SCLab: Interactive Single-Cell Analysis Toolkit},
+  year = {2024},
+  publisher = {GitHub},
+  url = {https://github.com/umbibio/sclab}
+}
+

sclab-0.1.7/README.md

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+# SCLab
+
+SCLab is an interactive single-cell analysis toolkit that provides a seamless interface for analyzing and visualizing single-cell RNA sequencing data. Built on top of popular tools like scanpy and AnnData, SCLab offers an event-driven architecture for real-time updates and interactive visualizations.
+
+## Features
+
+- **Interactive Data Analysis**: Built-in dashboard with real-time updates
+- **Quality Control**: Comprehensive QC metrics and filtering capabilities
+- **Preprocessing**: Normalization, log transformation, and scaling with progress tracking
+- **Dimensionality Reduction**: PCA with batch effect correction support
+- **Visualization**: Interactive plots and tables using plotly and itables
+- **Event System**: Robust event-driven architecture for real-time updates
+
+## Installation
+
+```bash
+pip install sclab
+```
+
+## Quick Start
+
+Open a Jupyter Notebook and run the following:
+
+```python
+from sclab import SCLabDashboard
+import scanpy as sc
+from IPython.display import display
+
+# Load your data
+adata = sc.read_10x_h5("your_data.h5")
+
+# Create dashboard
+dashboard = SCLabDashboard(adata, name="My Analysis")
+
+# Display dashboard
+display(dashboard)
+
+# The dashboard provides easy access to components:
+dashboard.ds  # Dataset (wrapper for AnnData)
+dashboard.pl  # Plotter
+dashboard.pr  # Processor
+```
+
+## Components
+
+### SCLabDashboard
+
+The main interface that integrates all components with a tabbed layout:
+- Main graph for visualizations
+- Observations table
+- Genes table
+- Event logs
+
+### Dataset
+
+Handles data management with:
+- AnnData integration
+- Interactive tables
+- Row selection and filtering
+- Metadata handling
+
+### Processor
+
+Handles data processing steps. It is configurable with custom steps implementing the `ProcessorStepBase` interface. This package provides multiple examples of steps:
+
+- QC
+- Preprocessing
+- PCA
+- Nearest Neighbors
+- UMAP
+- Clustering
+
+### Plotter
+
+Provides interactive visualizations with:
+- Real-time updates
+- Customizable plots
+- Batch effect visualization
+- Export capabilities
+
+## Requirements
+
+- Python ≥ 3.12
+- anndata ≥ 0.11.3
+- scanpy ≥ 1.10.4
+- Other dependencies listed in pyproject.toml
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.
+
+## License
+
+This project is licensed under the BSD 3-Clause License - see the [LICENSE](LICENSE) file for details.
+
+## Citation
+
+If you use SCLab in your research, please cite:
+
+```bibtex
+@software{sclab2024,
+  author = {Arriojas, Argenis},
+  title = {SCLab: Interactive Single-Cell Analysis Toolkit},
+  year = {2024},
+  publisher = {GitHub},
+  url = {https://github.com/umbibio/sclab}
+}

sclab-0.1.7/pyproject.toml

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+[project]
+name = "sclab"
+version = "0.1.7"
+description = "sclab"
+readme = "README.md"
+authors = [
+    { name = "Argenis Arriojas", email = "ArriojasMaldonado001@umb.edu" },
+]
+requires-python = ">=3.10,<3.13"
+classifiers = [
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "anndata",
+    "anywidget",
+    "ipywidgets",
+    "itables",
+    "numpy<2.2",
+    "pandas",
+    "plotly",
+    "scanpy",
+    "scikit-learn",
+    "scikit-misc",
+    "svgpathtools",
+]
+
+[project.urls]
+"Repository" = "https://github.com/umbibio/sclab.git"
+"Documentation" = "https://github.com/umbibio/sclab/docs"
+"Homepage" = "https://github.com/umbibio/sclab"
+"Bug Tracker" = "https://github.com/umbibio/sclab/issues"
+"Changelog" = "https://github.com/umbibio/sclab/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+test = ["pytest>=8.3.4"]
+
+[build-system]
+requires = ["flit_core>=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[tool.flit.module]
+name = "sclab"
+source = "src/sclab"
+
+[dependency-groups]
+dev = [
+    "bump-my-version>=0.31.1",
+    "pre-commit>=4.1.0",
+    "ruff>=0.9.4",
+    "nox>=2024.1.29",
+    "pytest>=8.3.4",
+]

sclab-0.1.7/src/sclab/__init__.py

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+from ._sclab import SCLabDashboard
+
+__all__ = [
+    "SCLabDashboard",
+]
+
+__version__ = "0.1.7"

sclab-0.1.7/src/sclab/_io.py

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+from pathlib import Path
+
+import anndata as ad
+
+
+def read_adata(path: str | Path, var_names: str = "gene_ids") -> ad.AnnData:
+    path = Path(path)
+
+    match path.suffix:
+        case ".h5" | "":
+            try:
+                import scanpy as sc
+            except ImportError:
+                raise ImportError("Please install scanpy: `pip install scanpy`")
+
+    match path.suffix:
+        case ".h5":
+            adata = sc.read_10x_h5(path)
+        case ".h5ad":
+            adata = ad.read_h5ad(path)
+        case "":
+            assert path.is_dir()
+            adata = sc.read_10x_mtx(path)
+        case _:
+            raise ValueError(
+                "Input file must be a 10x h5, h5ad or a folder of 10x mtx files"
+            )
+
+    if var_names in adata.var:
+        adata.var = adata.var.set_index(var_names)
+
+    return adata

sclab-0.1.7/src/sclab/_sclab.py

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+from pathlib import Path
+
+from anndata import AnnData
+from ipywidgets.widgets import GridBox, Layout, Tab
+
+from ._io import read_adata
+from .dataset import SCLabDataset
+from .dataset.plotter import Plotter
+from .dataset.processor import Processor
+from .event import EventBroker
+
+
+class SCLabDashboard(GridBox):
+    broker: EventBroker
+
+    def __init__(
+        self,
+        adata: AnnData | None = None,
+        filepath: str | Path | None = None,
+        name: str = "SCLab Dashboard",
+        counts_layer: str = "counts",
+        batch_key: str | None = None,
+        copy: bool = True,
+    ):
+        if adata is None and filepath is None:
+            raise ValueError("Either adata or filepath must be provided")
+
+        if adata is None:
+            adata = read_adata(filepath)
+
+        self.broker = EventBroker()
+        self.dataset = SCLabDataset(
+            adata, name=name, counts_layer=counts_layer, copy=copy, broker=self.broker
+        )
+        self.plotter = Plotter(self.dataset)
+        self.processor = Processor(
+            self.dataset,
+            self.plotter,
+            batch_key=batch_key,
+        )
+
+        self.main_content = Tab(
+            children=[
+                self.plotter,
+                self.dataset.obs_table,
+                self.dataset.var_table,
+                self.broker.logs_tab,
+            ],
+            titles=[
+                "Main graph",
+                "Observations",
+                "Genes",
+                "Logs",
+            ],
+        )
+
+        super().__init__(
+            [
+                self.processor.main_accordion,
+                self.main_content,
+            ],
+            layout=Layout(
+                width="100%",
+                grid_template_columns="350px auto",
+                grid_template_areas=""" "processor plotter" """,
+                border="0px solid black",
+            ),
+        )
+
+    @property
+    def ds(self):
+        return self.dataset
+
+    @property
+    def pr(self):
+        return self.processor
+
+    @property
+    def pl(self):
+        return self.plotter

sclab-0.1.7/src/sclab/dataset/__init__.py

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+from . import plotter, processor
+from ._dataset import SCLabDataset
+
+__all__ = [
+    "plotter",
+    "processor",
+    "SCLabDataset",
+]