spateo.tdr.morphometrics.morphofield.gaussian_process¶
Functions¶
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Calculating and predicting the vector field during development by the Gaussian Process method. |
Module Contents¶
- spateo.tdr.morphometrics.morphofield.gaussian_process._con_K(x: numpy.ndarray, y: numpy.ndarray, beta: float = 0.1, method: str = 'cdist', return_d: bool = False) Tuple[numpy.ndarray, numpy.ndarray] | numpy.ndarray [source]¶
- spateo.tdr.morphometrics.morphofield.gaussian_process._con_K_geodist(x: numpy.ndarray, kernel_dict: dict, beta: float = 0.1, return_d: bool = False) Tuple[numpy.ndarray, numpy.ndarray] | numpy.ndarray [source]¶
- spateo.tdr.morphometrics.morphofield.gaussian_process._gp_velocity(X: numpy.ndarray, vf_dict: dict) numpy.ndarray [source]¶
- spateo.tdr.morphometrics.morphofield.gaussian_process.morphofield_gp(adata: anndata.AnnData, spatial_key: str = 'align_spatial', vf_key: str = 'VecFld_morpho', NX: numpy.ndarray | None = None, grid_num: List[int] | None = None, inplace: bool = True) anndata.AnnData | None [source]¶
Calculating and predicting the vector field during development by the Gaussian Process method.
- Parameters:
- adata
AnnData object that contains the cell coordinates of the two states after alignment.
- spatial_key
The key from the
.obsm
that corresponds to the spatial coordinates of each cell.- vf_key
The key in
.uns
that corresponds to the reconstructed vector field.- key_added
The key that will be used for the vector field key in
.uns
.- NX
The spatial coordinates of new data point. If NX is None, generate new points based on grid_num.
- grid_num
The number of grids in each dimension for generating the grid velocity. Default is
[50, 50, 50]
.- inplace
Whether to copy adata or modify it inplace.
- Returns:
An
AnnData
object is updated/copied with thekey_added
dictionary in the.uns
attribute.The
key_added
dictionary which contains:X: Cell coordinates of the current state. V: Developmental direction of the X. grid: Grid coordinates of current state. grid_V: Prediction of developmental direction of the grid. method: The method of learning vector field. Here method == ‘gaussian_process’.