diff --git a/docs/source/Tutorials/SpaTrack.rst b/docs/source/Tutorials/SpaTrack.rst index 085692ab..8a25b6c1 100644 --- a/docs/source/Tutorials/SpaTrack.rst +++ b/docs/source/Tutorials/SpaTrack.rst @@ -24,6 +24,17 @@ Highlighted features 5. could be extensively applied on both ST data and scRNA-seq data. 6. requires lower computing memory and loads than RNA-velocity methods, making it a fast and effective option for TI study. +Preparation +--------------------- + +Torch is the necessary dependency and needs to be installed first. + + CPU: pip install torch==2.4.1+cpu --extra-index-url https://download.pytorch.org/whl + + GPU(CUDA11): pip install torch==2.4.1+cu118 --extra-index-url https://download.pytorch.org/whl/ + + GPU(CUDA12): pip install torch==2.4.1+cu124 --extra-index-url https://download.pytorch.org/whl/ + Turorials --------------------- diff --git a/stereo/core/st_pipeline.py b/stereo/core/st_pipeline.py index b12820fc..dd886d4d 100644 --- a/stereo/core/st_pipeline.py +++ b/stereo/core/st_pipeline.py @@ -987,7 +987,7 @@ def umap( @logit def neighbors(self, pca_res_key: str = 'pca', - method: Literal['umap', 'gauss'] = 'umap', + method: Literal['umap', 'gauss', 'rapids'] = 'umap', metric: str = 'euclidean', n_pcs: int = None, n_neighbors: int = 10, @@ -998,7 +998,8 @@ def neighbors(self, Compute a spatial neighborhood graph over all cells. :param pca_res_key: the key of PCA analysis to get corresponding result from `self.result`. - :param method: use `umap` or `gauss` to compute connectivities. + :param method: use `umap` or `gauss` to compute connectivities, + set to `rapids` means to run on GPU using the `umap` method. :param metric: a known metric's name or a callable that returns a distance, include: * euclidean