COMMOTR: Cell-Cell Communication via Collective Optimal Transport

Infer cell-cell communication in spatial transcriptomics data using collective optimal transport (COT). COMMOTR provides a complete workflow for analyzing ligand-receptor interactions with spatial constraints.

Details

COMMOTR implements the COMMOT algorithm from Cang et al. (Nature Methods, 2023) in R with high-performance C++ backends for optimal transport computations.

Core Analysis Functions:

• spatial_communication: Infer cell-cell communication

• communication_direction: Compute communication directions

• cluster_communication: Cluster-level analysis

Data Functions:

• ligand_receptor_database: Load LR databases

• filter_lr_database: Filter LR pairs by expression

Visualization Functions:

• plot_cell_communication: Cell-level plots with vector fields

• plot_cluster_communication: Cluster-level network plots

• plot_communication_dotplot: Dotplot visualization

References

Cang, Z., Zhao, Y., Almet, A.A. et al. Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature Methods 20, 218-228 (2023). doi:10.1038/s41592-022-01728-4

See also

• GitHub: https://github.com/Zaoqu-Liu/COMMOTR

• Original COMMOT: https://github.com/zcang/COMMOT

Author

Zaoqu Liu liuzaoqu@163.com