vectorscope 1.2.3

Interactive vector embedding visualization and transformation system

VectorScope

Interactive web-based system for exploring, transforming, and visualizing vector embeddings.

Overview

VectorScope is a visualization tool designed for exploring high-dimensional vector embeddings. It provides an interactive interface for:

• Loading and managing multiple embedding datasets
• Applying transformations (scaling, rotation, PCA-based affine)
• Creating projections to 2D/3D space (PCA, t-SNE, UMAP)
• Selecting and tracking specific points across views
• Building visual transformation pipelines via a graph editor

Features

• Multiple Data Sources: Load data from CSV, NumPy files (.npy, .npz), or built-in sklearn datasets
• Column Configuration: For tabular data, choose which columns are features vs labels
• Visual Transformation Graph: Build data pipelines by connecting layers, transformations, and views
• Interactive Projections: Configure PCA components, t-SNE perplexity, UMAP parameters, and more
• Linked Viewports: Synchronized selection across multiple views
• Session Persistence: Save and reload entire workspaces

Roadmap

✅ Completed Features

• Core Infrastructure

  • FastAPI backend with REST API
  • React + TypeScript frontend with Zustand state management
  • Vite dev server with API proxy
  • Session save/load functionality

• Data Loading

  • CSV file upload with column configuration
  • NumPy file support (.npy, .npz)
  • Built-in sklearn datasets (iris, digits, wine, etc.)
  • Synthetic data generation (clustered Gaussian)

• Projections

  • PCA with configurable component selection
  • t-SNE with perplexity, learning rate, iterations parameters
  • UMAP with n_neighbors, min_dist, spread parameters
  • Direct axes view (raw dimension values)
  • Histogram view (per-dimension distribution)
  • Box plot view (per-dimension by class)
  • Corner plot (all axis pairs + diagonal histograms)

• Transformations

  • Scaling transformation with per-axis sliders (linked/unlinked modes)
  • Rotation transformation with selectable rotation plane (any dimension pair)
  • PCA-based affine transformation (with explained variance display)

• Visualization

  • Multiple synchronized viewports with Plotly (2D and 3D scatter)
  • Linked selection across views
  • View sets (save/load viewport configurations)
  • Graph editor for transformation pipelines
  • View editor with header bar layout (layer/view selection, add view)
  • Configurable axis ranges (X, Y, Z for 3D views)

• Annotations & Selections

  • Interactive box selection (drag to select points)
  • Additive selection (Shift + box select to add more points)
  • Point toggling (Shift + click to add/remove individual points)
  • Click-to-clear (click empty area to clear selection)
  • Named selections (save selections for reuse)
  • Selection management (apply, delete saved selections)
  • Virtual points / Barycenters (create centroids from selections)
  • Named barycenters with custom labels
  • Auto-generate selections from class labels
  • Auto-generate barycenters from class labels

🔄 In Progress

• Custom axis projections (define axes from point pairs)
• Instance tracking panel

📋 Planned Features

• Transformation Coefficient Visualization

  • Visualize how output axes relate to input axes
  • Stacked bar chart showing normalized coefficients per output dimension
  • Color-coded by input dimension contribution
  • Helps interpret PCA components and affine transforms

• Phase 5: Polish

  • Keyboard shortcuts
  • Improved error handling & loading states

• Phase 6: Onboarding & UX

  • Interactive tutorial (React Joyride or Shepherd.js)
  • Step-by-step guided tour for first-time users
  • Contextual help tooltips
  • In-app help panel

• Future Ideas

  • Export visualizations as images
  • Collaborative sessions
  • Plugin system for custom transformations

Quick Start

Option 1: Install from PyPI

Install the backend package:

pip install vectorscope

Then run the server:

uvicorn backend.main:app --port 8000

Note: The PyPI package includes the backend API. For the full interactive UI, use the development installation below.

Option 2: Development Installation

Prerequisites

• Pixi package manager (handles Python environment)
• Node.js 18+ (for frontend)

Installation

# Clone the repository
git clone https://github.com/cranmer/vectorscope.git
cd vectorscope

# Install Python dependencies
pixi install

# Install frontend dependencies
cd frontend && npm install && cd ..

Running

Start the backend and frontend:

# Start both backend and frontend
pixi run dev

# Or start them separately:
# Terminal 1: Backend (port 8000)
pixi run backend

# Terminal 2: Frontend (port 5173)
cd frontend && npm run dev

Open http://localhost:5173 in your browser.

Architecture

┌─────────────────────────────────────────────────────────────┐
│                     Frontend (React)                         │
├─────────────┬─────────────┬─────────────┬──────────────────┤
│  Viewports  │ Graph Editor│   Config    │  State (Zustand) │
│  (Plotly)   │ (ReactFlow) │   Panels    │                  │
└──────┬──────┴──────┬──────┴──────┬──────┴────────┬─────────┘
       │             │             │               │
       └─────────────┴──────┬──────┴───────────────┘
                            │ REST API (Vite Proxy)
                            ▼
       ┌────────────────────────────────────────────┐
       │           Backend (FastAPI)                 │
       ├─────────────┬─────────────┬────────────────┤
       │ Data Store  │ Transform   │ Projection     │
       │ (Layers)    │ Engine      │ Engine         │
       └─────────────┴─────────────┴────────────────┘

Core Concepts

• Layer: A collection of points with n-dimensional vectors. Source layers contain original data; derived layers are created by transformations.
• Point: A single data point with a vector, optional label, and metadata.
• Transformation: An operation that maps one layer to another (scaling, rotation, affine).
• Projection: A dimension reduction from n-D to 2D/3D for visualization (PCA, t-SNE).

Project Structure

vectorscope/
├── backend/               # FastAPI Python backend
│   ├── main.py           # Application entry point
│   ├── models/           # Pydantic data models
│   │   ├── layer.py      # Layer, Point, PointData
│   │   ├── transformation.py
│   │   └── projection.py
│   ├── services/         # Business logic
│   │   ├── data_store.py       # In-memory layer storage
│   │   ├── transform_engine.py # Transformation logic
│   │   └── projection_engine.py # PCA, t-SNE computation
│   ├── routers/          # API endpoints
│   │   ├── layers.py
│   │   ├── transformations.py
│   │   ├── projections.py
│   │   └── scenarios.py
│   └── fixtures.py       # Test data loaders
├── frontend/             # React TypeScript frontend
│   ├── src/
│   │   ├── App.tsx       # Main application component
│   │   ├── components/
│   │   │   ├── Viewport.tsx      # Plotly scatter plot
│   │   │   ├── GraphEditor.tsx   # ReactFlow DAG editor
│   │   │   ├── ConfigPanel.tsx   # Node configuration UI
│   │   │   └── ViewportGrid.tsx  # Multi-viewport layout
│   │   ├── stores/
│   │   │   └── appStore.ts       # Zustand state management
│   │   ├── api/
│   │   │   └── client.ts         # REST API client
│   │   └── types/
│   │       └── index.ts          # TypeScript interfaces
│   ├── vite.config.ts    # Vite configuration with API proxy
│   └── package.json
├── scenarios/            # Saved scenario files
├── docs/                 # Documentation (Sphinx)
└── pixi.toml            # Pixi environment configuration

API Reference

Layers

Endpoint	Method	Description
/layers	GET	List all layers
/layers/{id}	GET	Get layer by ID
/layers/{id}	PATCH	Update layer (name, columns)
/layers/{id}/points	GET	Get points in a layer
/layers/upload	POST	Upload data file (CSV, NPY, NPZ)
/layers/synthetic	POST	Generate synthetic dataset
/layers/sklearn/{name}	POST	Load sklearn dataset

Projections

Endpoint	Method	Description
/projections	GET	List all projections
/projections	POST	Create projection (PCA, t-SNE)
/projections/{id}	PATCH	Update projection parameters
/projections/{id}/coordinates	GET	Get 2D coordinates

Transformations

Endpoint	Method	Description
/transformations	GET	List all transformations
/transformations	POST	Create transformation
/transformations/{id}	PATCH	Update transformation parameters

Scenarios

Endpoint	Method	Description
/scenarios	GET	List available scenarios
/scenarios/save	POST	Save current state
/scenarios/load/{name}	POST	Load saved scenario
/scenarios/upload	POST	Upload scenario files

Extending VectorScope

Adding a New Transformation Type

1. Define the transformation type in backend/models/transformation.py:

   class TransformationType(str, Enum):
       SCALING = "scaling"
       ROTATION = "rotation"
       PCA = "pca"
       # Add your new type:
       MY_TRANSFORM = "my_transform"
   

2. Implement the transformation in backend/services/transform_engine.py:

   def _apply_my_transform(self, vectors: np.ndarray, params: dict) -> np.ndarray:
       # Your transformation logic
       return transformed_vectors
   

3. Add to the apply method:

   def apply_transformation(self, transformation, vectors):
       if transformation.type == TransformationType.my_transform:
           return self._apply_my_transform(vectors, transformation.parameters)
   

4. Update the frontend in ConfigPanel.tsx to show UI controls for your transformation.

Adding a New Projection Type

1. Define the projection type in backend/models/projection.py:

   class ProjectionType(str, Enum):
       pca = "pca"
       tsne = "tsne"
       # Add your new type:
       my_projection = "my_projection"
   

2. Implement the projection in backend/services/projection_engine.py:

   def _compute_my_projection(self, vectors: np.ndarray, params: dict) -> np.ndarray:
       # Your projection logic (should return 2D or 3D coordinates)
       return coordinates
   

3. Add to compute method:

   def _compute_projection(self, projection):
       if projection.type == ProjectionType.my_projection:
           coords = self._compute_my_projection(vectors, projection.parameters)
   

4. Update the frontend to show your projection type in dropdowns and add any parameter controls.

Tech Stack

• Backend: Python 3.11+, FastAPI, NumPy, scikit-learn, Pydantic
• Frontend: React 18, TypeScript, Plotly.js, ReactFlow, Zustand
• Build Tools: Vite, Pixi (Python environment management)

Development

Running Tests

# Backend tests
pixi run test-backend

# Frontend tests
cd frontend && npm test

Code Style

• Python: Follow PEP 8, use type hints
• TypeScript: Use strict mode, prefer interfaces over types

License

MIT License - see LICENSE for details.

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Run tests
5. Submit a pull request

Credits

Conceptualized by: Kyle Cranmer

Implemented by: Claude Code (Anthropic's AI coding assistant)

Acknowledgments

• Plotly.js for interactive visualizations
• ReactFlow for the graph editor
• scikit-learn for dimensionality reduction algorithms