pysee-bio 0.1.3

Interactive, Reproducible Bioinformatics Visualization for Python

🔬 PySEE — Interactive, Reproducible Bioinformatics Visualization for Python

PySEE is an open-source project bringing iSEE-style linked dashboards to the Python bioinformatics ecosystem.

If you use AnnData / Scanpy / MuData / Zarr, you know the struggle of wiring up UMAP plots, violin plots, QC panels, and genome browsers by hand. R has Shiny and iSEE.

👉 PySEE fills that gap in Python: a lightweight, notebook-first toolkit for interactive exploration + reproducible code export.

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✨ Features

✅ MVP (v0.1) - COMPLETED

• AnnData support out of the box with comprehensive validation
• Four linked panels:
  • UMAP/t-SNE/PCA embedding (interactive scatter plots)
  • Gene expression violin/box/strip plots with grouping
  • Gene expression heatmaps with hierarchical clustering
  • Quality control metrics with filtering thresholds
• Linked selection: brushing propagates across all panels
• Reproducible code export: selections → Python snippet
• Notebook-first UX (Jupyter/VS Code, no server setup needed)
• Interactive visualizations with Plotly backend
• Data validation and preprocessing utilities
• CLI interface for command-line usage

🚀 v0.2 - IN DEVELOPMENT

• ✅ Heatmap Panel: Gene expression matrices with clustering
• ✅ QC Metrics Panel: Data quality assessment and filtering
• 🔄 Dot Plot Panel: Marker gene visualization (planned)
• 🔄 Advanced Selection Tools: Lasso, polygon selection (planned)
• 🧬 Genome browser panels (IGV / JBrowse)
• 🧩 Spatial viewer (Vitessce) and imaging viewer (napari)
• ☁️ Cloud-scale rendering (Datashader, Zarr-backed data)
• 🎛️ Plugin system for custom panels
• 🌍 Deployment as shareable web apps (FastAPI/Dash backend)

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🚀 Why PySEE?

• Python-native: integrates directly with AnnData, Scanpy, scvi-tools, PyTorch
• Linked & interactive: selections propagate across panels
• Reproducible: every UI action can export a Python snippet
• Complementary: works alongside projects like OLAF (LLM-based bioinformatics) and OLSA (AI benchmarks) as the visual exploration layer

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📊 Quickstart

Installation

# Clone the repository
git clone https://github.com/Linnnnberg/PySEE.git
cd PySEE

# Create virtual environment
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install dependencies
pip install -r requirements.txt

System Requirements

Local Development:

• Minimum: 8 GB RAM (small datasets only)
• Recommended: 16 GB RAM (small + medium datasets)
• Optimal: 32 GB RAM (all datasets including large)

Cloud/Server (Recommended for Large Datasets):

• Google Colab: Free tier (12 GB RAM) - medium datasets
• Google Colab Pro: 25 GB RAM - large datasets
• AWS/GCP: 32+ GB RAM - very large datasets

Dataset Size Guidelines

Dataset Size	Cells	Memory	Local (16GB)	Cloud/Server
Small	3K	350 MB	✅ Perfect	✅ Perfect
Medium	68K	8.5 GB	⚠️ Caution	✅ Perfect
Large	100K+	15+ GB	❌ Not recommended	✅ Recommended

Check Your System

Run the system requirements checker:

python check_system_requirements.py

Cloud Deployment

For large datasets, use cloud instead of complex local memory strategies:

# Google Colab example
!pip install pysee scanpy
import scanpy as sc
from pysee import PySEE

adata = sc.datasets.pbmc68k_reduced()  # 68K cells, works great in cloud
app = PySEE(adata)
# ... add panels and analyze

Install PySEE in development mode

pip install -e .

### Basic Usage

```python
import scanpy as sc
from pysee import PySEE, UMAPPanel, ViolinPanel, HeatmapPanel, QCPanel

# Load and preprocess data
adata = sc.datasets.pbmc3k()
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata)

# Create PySEE dashboard
app = PySEE(adata, title="My Analysis")

# Add UMAP panel
app.add_panel(
    "umap",
    UMAPPanel(
        panel_id="umap",
        embedding="X_umap",
        color="leiden",
        title="UMAP Plot"
    )
)

# Add violin panel
app.add_panel(
    "violin",
    ViolinPanel(
        panel_id="violin",
        gene="CD3D",  # T-cell marker
        group_by="leiden",
        title="Gene Expression"
    )
)

# Add heatmap panel
app.add_panel(
    "heatmap",
    HeatmapPanel(
        panel_id="heatmap",
        title="Gene Expression Heatmap"
    )
)

# Add QC panel
app.add_panel(
    "qc",
    QCPanel(
        panel_id="qc",
        title="Quality Control Metrics"
    )
)

# Link panels: selections propagate across all panels
app.link(source="umap", target="violin")
app.link(source="umap", target="heatmap")

# Render panels
umap_fig = app.render_panel("umap")
violin_fig = app.render_panel("violin")
heatmap_fig = app.render_panel("heatmap")
qc_fig = app.render_panel("qc")

# Display in Jupyter notebook
umap_fig.show()
violin_fig.show()
heatmap_fig.show()
qc_fig.show()

# Export reproducible code
print(app.export_code())

Command Line Usage

# Run with sample data
python example.py

# Use CLI with your own data
pysee your_data.h5ad --umap-color leiden --violin-gene CD3D --violin-group leiden

# Export code instead of running dashboard
pysee your_data.h5ad --export-code > my_analysis.py

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📚 Documentation

Core Components

• PySEE: Main dashboard class that manages panels and interactions
• AnnDataWrapper: Data handling and validation for AnnData objects
• BasePanel: Abstract base class for all visualization panels
• UMAPPanel: Interactive scatter plots for dimensionality reduction
• ViolinPanel: Gene expression distribution plots with grouping

Panel Types

UMAP Panel

UMAPPanel(
    panel_id="umap",
    embedding="X_umap",  # or "X_pca", "X_tsne", etc.
    color="leiden",      # column in adata.obs for coloring
    title="UMAP Plot"
)

Violin Panel

ViolinPanel(
    panel_id="violin",
    gene="CD3D",         # gene name to visualize
    group_by="leiden",   # column in adata.obs for grouping
    title="Gene Expression"
)

Linking Panels

# Link UMAP selections to violin plot
app.link(source="umap", target="violin")

# Multiple links
app.link("umap", "heatmap")
app.link("umap", "qc_plot")

Code Export

# Export current dashboard state as Python code
code = app.export_code()
print(code)

# Save to file
with open("my_analysis.py", "w") as f:
    f.write(code)

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🧪 Examples

Example 1: Basic Analysis

# See example.py for a complete working example
python example.py

Example 2: Custom Configuration

# Create panels with custom settings
umap_panel = UMAPPanel(
    panel_id="custom_umap",
    embedding="X_pca",
    color="total_counts",
    title="PCA Plot"
)
umap_panel.set_point_size(5)
umap_panel.set_opacity(0.8)

violin_panel = ViolinPanel(
    panel_id="custom_violin",
    gene="MS4A1",  # B-cell marker
    group_by="leiden",
    title="B-cell Marker"
)
violin_panel.set_plot_type("box")
violin_panel.set_show_points(True)

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🛠️ Development

Project Structure

pysee/
├── core/           # Core dashboard and data handling
├── panels/         # Visualization panels
├── cli/            # Command-line interface
├── utils/          # Utility functions
└── __init__.py     # Package initialization

Running Tests

# Run basic functionality test
python test_pysee.py

# Run example with real data
python example.py

CI/CD Pipeline

PySEE uses GitHub Actions for automated testing and quality assurance:

• Fast CI: ~3 minutes with optimized dependencies
• Multi-Python Support: Tests on Python 3.9, 3.10, 3.11, 3.12
• Quality Checks: flake8, black, mypy, pytest
• Automated Testing: All commits and PRs are automatically tested
• Build Verification: Package builds and installs correctly

Contributing

PySEE follows a feature branch workflow with protected main branch and automated CI/CD.

Quick Start:

1. Fork the repository
2. Create a feature branch: git checkout -b feature/your-feature
3. Make your changes and test locally
4. Submit a pull request to develop branch
5. Address review feedback
6. Wait for approval and merge

Detailed Workflow: See GIT_WORKFLOW.md for complete development guidelines.

Version Strategy: See VERSION_STRATEGY.md for release and versioning guidelines.

Requirements:

• All PRs must pass CI checks before merging
• Code must be reviewed by at least one maintainer
• Follow conventional commit message format
• Include tests for new features

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📋 Roadmap

v0.2 (Next Release)

• Heatmap panel for gene expression matrices
• QC metrics panel for data quality assessment
• Dot plot panel for marker gene visualization
• Enhanced selection tools (lasso, polygon selection)
• Jupyter widget integration

v0.3 (Future)

• Genome browser integration (IGV.js)
• Spatial transcriptomics viewer (Vitessce)
• Plugin system for custom panels
• Web deployment capabilities
• Cloud-scale data support

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📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

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🙏 Acknowledgments

• Inspired by iSEE for R
• Built on Scanpy and AnnData
• Visualization powered by Plotly

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📞 Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Documentation: GitHub Wiki