py-sigxtalk 0.1.0

Python rewrite of SigXTalk: Dissecting crosstalk induced by cell-cell communication

py-sigxtalk

Python rewrite of SigXTalk: Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.

Installation

# Install from source
cd py-sigxtalk
pip install -e ".[dev]"

Quick Start

import pysigxtalk as psx

# Load databases
rtf_db, tftg_db = psx.load_databases(species="human")

# Prepare inputs
inputs = psx.prepare_input(exp_mat, target_genes, lr_pairs, rtf_db, tftg_db)

# Run HGNN
pathways = psx.run_hgnn(inputs, epochs=10, device="cpu")

# Calculate PRS
prs_results = psx.compute_prs(inputs.exp_clu, pathways, n_estimators=10)

# Visualize
psx.plot_counts_histogram(prs_results)
psx.plot_counts_bar(prs_results, topk=20)
psx.plot_fid_spe(prs_results, key_tg="CD68")

Benchmark

Python vs R (single core, PBMC3k dataset):

Step	Python	R (ranger)
HGNN	31s	31s
PRS	33s	219s
Total	80s	266s
Speedup	3.33x	-
Correlation	0.9912	-

PRS Weight Correlation:

Timing Comparison:

Visualization Gallery

Crosstalk Counts:

Histogram	Bar Chart

Crosstalk Analysis:

Fid/Spe	Alluvial	Ridgeline

Network Diagrams:

Chord	CCI Chord	CCI Circle

Heatmaps:

Signal Contribution	Rec-TG Heatmap	Circular Bar

Examples

example/
├── quickstart.ipynb              # Full analysis workflow
├── benchmark.ipynb               # Python vs R comparison
├── data/                         # Input data & results
│   ├── pbmc3k_final.h5ad         # PBMC3k dataset
│   ├── prs_results.csv           # PRS results
│   ├── prs_results_python.csv    # Python PRS results
│   └── prs_results_r.csv         # R PRS results
├── figures/                      # Generated figures
│   ├── 01-11_*.png               # 11 visualization figures
│   └── benchmark_*.png           # Benchmark plots
└── scripts/                      # Utility scripts
    ├── run_benchmark.py          # Benchmark runner
    ├── tutorial.py               # Tutorial script
    └── compare_R_vs_Python.py    # R vs Python comparison

Citation

Hou, J. et al. Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data. Nature Communications (2025).