pyrovelocity._velocity_module#

class pyrovelocity._velocity_module.VelocityModule(num_cells, num_genes, model_type='auto', guide_type='velocity_auto', likelihood='Poisson', shared_time=True, t_scale_on=False, plate_size=2, latent_factor='none', latent_factor_operation='selection', latent_factor_size=10, inducing_point_size=0, include_prior=False, use_gpu=0, num_aux_cells=0, only_cell_times=True, decoder_on=False, add_offset=True, correct_library_size=True, cell_specific_kinetics=None, kinetics_num=None, **initial_values)[source]#

Bases: PyroBaseModuleClass

VelocityModule is an scvi-tools pyro module that combines the VelocityModelAuto and pyro AutoGuideList classes.

Parameters:

  • num_cells (int) – Number of cells.

  • num_genes (int) – Number of genes.

  • model_type (str, optional) – Model type. Default is “auto”.

  • guide_type (str, optional) – Guide type. Default is “velocity_auto”.

  • likelihood (str, optional) – Likelihood type. Default is “Poisson”.

  • shared_time (bool, optional) – If True, a shared time parameter will be used. Default is True.

  • t_scale_on (bool, optional) – If True, scale time parameter. Default is False.

  • plate_size (int, optional) – Size of the plate set. Default is 2.

  • latent_factor (str, optional) – Latent factor. Default is “none”.

  • latent_factor_operation (str, optional) – Latent factor operation mode. Default is “selection”.

  • latent_factor_size (int, optional) – Size of the latent factor. Default is 10.

  • inducing_point_size (int, optional) – Inducing point size. Default is 0.

  • include_prior (bool, optional) – If True, include prior in the model. Default is False.

  • use_gpu (int, optional) – GPU device index. Default is 0.

  • num_aux_cells (int, optional) – Number of auxiliary cells. Default is 0.

  • only_cell_times (bool, optional) – If True, only model cell times. Default is True.

  • decoder_on (bool, optional) – If True, use the decoder. Default is False.

  • add_offset (bool, optional) – If True, add offset to the model. Default is True.

  • correct_library_size (Union[bool, str], optional) – Library size correction method. Default is True.

  • cell_specific_kinetics (Optional[str], optional) – Cell-specific kinetics method. Default is None.

  • kinetics_num (Optional[int], optional) – Number of kinetics. Default is None.

  • **initial_values – Initial values for the model parameters.

Examples

>>> from scvi.module.base import PyroBaseModuleClass
>>> from pyrovelocity._velocity_module import VelocityModule
>>> num_cells = 10
>>> num_genes = 20
>>> velocity_module1 = VelocityModule(
...     num_cells, num_genes, model_type="auto",
...     guide_type="auto_t0_constraint", add_offset=False
... )
-----------
auto
auto_t0_constraint
>>> type(velocity_module1.model)
<class 'pyrovelocity._velocity_model.VelocityModelAuto'>
>>> type(velocity_module1.guide)
<class 'pyro.infer.autoguide.guides.AutoGuideList'>
>>> velocity_module2 = VelocityModule(
...     num_cells, num_genes, model_type="auto",
...     guide_type="auto", add_offset=True
... )
-----------
auto
auto
>>> type(velocity_module2.model)
<class 'pyrovelocity._velocity_model.VelocityModelAuto'>
>>> type(velocity_module2.guide)
<class 'pyro.infer.autoguide.guides.AutoGuideList'>
__init__(num_cells, num_genes, model_type='auto', guide_type='velocity_auto', likelihood='Poisson', shared_time=True, t_scale_on=False, plate_size=2, latent_factor='none', latent_factor_operation='selection', latent_factor_size=10, inducing_point_size=0, include_prior=False, use_gpu=0, num_aux_cells=0, only_cell_times=True, decoder_on=False, add_offset=True, correct_library_size=True, cell_specific_kinetics=None, kinetics_num=None, **initial_values)[source]#
property guide: pyro.infer.autoguide.guides.AutoGuideList#
property model: VelocityModelAuto#