diff --git a/README.md b/README.md index 5c923eb..de81e5b 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [badge-tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml/badge.svg [badge-docs]: https://img.shields.io/readthedocs/cellmapper -k-NN-based mapping of cells across representations to tranfer labels, embeddings and expression values. Works for millions of cells, on CPU and GPU, across molecular modalities, between spatial and non-spatial data, for arbitrary query and reference datasets. +k-NN-based mapping of cells across representations to tranfer labels, embeddings and expression values. Works for millions of cells, on CPU and GPU, across molecular modalities, between spatial and non-spatial data, for arbitrary query and reference datasets. Using `faiss` to compute k-NN graphs, CellMapper takes about 30 seconds to transfer cell type labels from 1.5M cells to 1.5M cells on a single RTX 4090 with 60 GB CPU memory. ## Getting started @@ -40,7 +40,6 @@ See the [changelog][]. ## Contact -For questions and help requests, you can reach out in the [scverse discourse][]. If you found a bug, please use the [issue tracker][]. ## Citation @@ -48,7 +47,6 @@ If you found a bug, please use the [issue tracker][]. Please cite this GitHub repo if you find CellMapper useful for your research. [uv]: https://github.com/astral-sh/uv -[scverse discourse]: https://discourse.scverse.org/ [issue tracker]: https://github.com/quadbio/cellmapper/issues [tests]: https://github.com/quadbio/cellmapper/actions/workflows/test.yaml [documentation]: https://cellmapper.readthedocs.io diff --git a/src/cellmapper/cellmapper.py b/src/cellmapper/cellmapper.py index 75a747b..702dbe7 100644 --- a/src/cellmapper/cellmapper.py +++ b/src/cellmapper/cellmapper.py @@ -235,14 +235,14 @@ def compute_mappping_matrix( Parameters ---------- - n_neighbors - Number of nearest neighbors. - use_rep - Data representation based on which to find nearest neighbors. - use_rapids - Whether to use cuML and cuPy for GPU-accelerated nearest neighbor search. - batch_size - Batch size for processing rows during Jaccard computation. + method + Method to use for computing the mapping matrix. Options include: + - "jaccard": Jaccard similarity. Inspired by GLUE: Cao et al., Nature Biotechnology, 2022: https://www.nature.com/articles/s41587-022-01284-4 + - "gaussian": Gaussian kernel with adaptive bandwith. Loosely inspired by MAGIC: Van Dijk et al., Cell, 2018: https://www.sciencedirect.com/science/article/pii/S0092867418307244?via%3Dihub + - "scarches": scArches kernel. Inspired by scArches: Lotfollahi et al., Nature Biotechnology, 2021: https://www.nature.com/articles/s41587-021-01001-7 + - "inverse_distance": Inverse distance kernel. + - "random": Random kernel, useful for testing. + - "hnoca": HNOCA kernel. Inspired by HNOCA-tools: He et al., Nature 2024: https://www.nature.com/articles/s41586-024-08172-8 Returns -------