tmap (Python 3.9+ & Apple Silicon Compatible)

This is a fork of tmap that is compatible with Python 3.9-3.12 and Apple Silicon (arm64).

tmap is a very fast visualization library for large, high-dimensional data sets. The graph layouts are based on the OGDF library.

Installation

Option 1: Install from GitHub (Recommended)

pip install git+https://github.com/afloresep/silicon-tmap-compatible.git

Option 2: Install from pre-built wheels

Check the Releases page for pre-built wheels for your platform.

Option 3: Build from source

For Apple Silicon Macs or if you need to build from source:

# Clone the repository
git clone https://github.com/afloresep/silicon-tmap-compatible.git
cd silicon-tmap-compatible

# Create conda environment with build dependencies
conda create -n tmap python=3.12 -y
conda activate tmap
conda install -c conda-forge cmake ninja llvm-openmp numpy scipy matplotlib annoy pybind11 -y

# Build OGDF
cd ogdf-conda/src
mkdir -p build installed
cd build
cmake .. \
  -DCMAKE_INSTALL_PREFIX="$PWD/../installed" \
  -DCMAKE_BUILD_TYPE=Release \
  -DCMAKE_OSX_ARCHITECTURES=arm64  # Only for Apple Silicon
cmake --build . --parallel
cmake --install .
cd ../../..

# Install tmap
export LIBOGDF_INSTALL_PATH="$PWD/ogdf-conda/src/installed"
pip install . --no-build-isolation

Visualization

We recommend using faerun to plot the data laid out by tmap:

pip install faerun

Quick Example

import tmap as tm
import numpy as np

# Generate random data
data = np.random.rand(1000, 100)

# Create MinHash fingerprints
mh = tm.Minhash(128)
fps = [tm.VectorFloat(row) for row in data]
lf = tm.LSHForest(128)
lf.batch_add(mh.batch_from_weight_array(fps))
lf.index()

# Layout
cfg = tm.LayoutConfiguration()
cfg.k = 20
x, y, s, t, _ = tm.layout_from_lsh_forest(lf, cfg)

# Plot with faerun or matplotlib
import matplotlib.pyplot as plt
plt.scatter(x, y, s=1)
plt.show()

Tutorial and Documentation

See the original documentation at http://tmap.gdb.tools

Examples

Compatibility

Changes from Original

• Fixed compatibility with Python 3.9-3.12
• Fixed Apple Silicon (arm64) builds
• Updated deprecated distutils imports
• Added proper pyproject.toml build configuration

License

BSD 3-Clause License - see LICENSE.md

Credits

Original tmap by Daniel Probst and the Reymond Group.